From eelke.spaak at donders.ru.nl  Wed May  1 09:40:01 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 1 May 2013 09:40:01 +0200
Subject: [FieldTrip] beggining Help
In-Reply-To: <f1d7aa427e33f400.517f0918@upo.es>
References: <f1d7aa427e33f400.517f0918@upo.es>
Message-ID: <CABPNLUosNHWq+LkeH-xUtWp4+t4aXkMyMqr=pO_HoepNpTBigg@mail.gmail.com>

Dear Gabriel,

Since you indicate that you are "completely new to fieldtrip and
almost new to EEG analysis", I would recommend you get started by
going through some of our tutorials:
http://fieldtrip.fcdonders.nl/tutorial These will help get you
acquainted with FieldTrip's work style, as well as teach you some
basics of EEG analysis. Understanding of the basics is vital if you
want to (sensibly) do connectivity analysis later on.

There are also some tutorials on connectivity, which you will find on
the same page.

As for getting your data into FieldTrip, all FT data is encapsulated
in a Matlab structure. Once your data is in Matlab, you can make a FT
structure out of it by creating a structure that resembles the output
of ft_preprocessing. Refer to the documentation for ft_datatype_raw
for details on this
(http://fieldtrip.fcdonders.nl/reference/ft_datatype_raw or "edit
ft_datatype_raw" in matlab).

Best, and good luck,
Eelke

On 29 April 2013 23:58, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear fieldtrip experts,
>
>
> I'm completely new to fieldtrip and almost new to the EEG analysis, I have
> resting-state EEG registers for my subjects in txt format, that I can load
> into matlab into something like: #timeSamples x #sensors. And I know the
> name and order of  all sensors
>
> I want to calculate the imaginary coherence, the PPC, the PLI and WPLI from
> my data, but I couldn't find how to do so in the manual. Can anyone help me
> with the steps to achieve that goal?
> I want to get those indices between all pairs of sensors, and chosen pairs
> (sensors manually selected according to my hypothesis), I hope it be
> posssible.
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jose.herrero66 at gmail.com  Wed May  1 12:08:19 2013
From: jose.herrero66 at gmail.com (Jose Herrero)
Date: Wed, 1 May 2013 06:08:19 -0400
Subject: [FieldTrip] ft_mvaranalysis with unequal length trials
Message-ID: <CA+zL3byUZEhYX3-T-Q5XQRGd1fSHEJCJu6KWT-B8Zz8bHXeNQg@mail.gmail.com>

Hi,

using ft_mvaranalysis with unequal length trials, i encountering the
following error (see below). This error does not occur after commenting out
line 241 where the data gets preprocessed. Is this ok?

mdata       = ft_mvaranalysis(cfg, trials)
the input is raw data with 25 channels and 237 trials
removing 234 trials in which no data was selected
the call to "ft_redefinetrial" took 0 seconds
preprocessing
preprocessing trial 3 from 3

the call to "ft_preprocessing" took 0 seconds
??? Index exceeds matrix dimensions.

Error in ==> ft_mvaranalysis at 293
  maxtim = max(maxtim, data.time{k}(end));


-- 
Jose L Herrero, PhD
Department of Psychiatry
Columbia University College of Physicians and Surgeons
Cognitive Neuroscience and Schizophrenia Program
Nathan S. Kline Institute for Psychiatric Research
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From robince at gmail.com  Wed May  1 18:41:37 2013
From: robince at gmail.com (Robin)
Date: Wed, 1 May 2013 17:41:37 +0100
Subject: [FieldTrip] MNE tutorial
Message-ID: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From joerg.neuberg at tu-ilmenau.de  Wed May  1 20:42:25 2013
From: joerg.neuberg at tu-ilmenau.de (=?utf-8?Q?J=C3=B6rg_Neuberg?=)
Date: Wed, 1 May 2013 20:42:25 +0200
Subject: [FieldTrip] Error: requested samples occur twice in the data
Message-ID: <27F2D05FEDC14EF9839BD48C5B218D24@JoergPC>

Hi FieldTrippers,

we are students using fieldtrip for a project at our university. Now, we have some trouble. We want to search for muscle artifacts and we receive an error message.
We started our signal processing with “ft_definetrial” to define the trials and “ft_preprocessing” to become our data. Then we cut out the stimulus artifact and interpolated the gaps. The data is saved as mat-file.

Now, we are looking for muscle artifacts with the following code:

---------- begin code --------
% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel = 'MEG*';
cfg.artfctdef.zvalue.cutoff      = 0.5;
cfg.artfctdef.zvalue.trlpadding  = 0;   
cfg.artfctdef.zvalue.fltpadding  = 0;
cfg.artfctdef.zvalue.artpadding  = 0.1;

cfg.artfctdef.muscle.bpfilter    = 'yes';
cfg.artfctdef.muscle.bpfreq      = [110 140];
cfg.artfctdef.muscle.bpfiltord   = 2;
cfg.artfctdef.muscle.bpfilttype  = 'but';
cfg.artfctdef.muscle.hilbert     = 'yes';
cfg.artfctdef.muscle.boxcar      = 0.2;

% make the process interactive
cfg.artfctdef.zvalue.interactive = 'yes';

[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);
---------- end code --------

Unfortunately there is an error and we haven’t an idea where is the problem. Maybe the overlap of the trials is a reason for this. But we can’t change this for our data because we need this trial length. Example: trial 1 from 100 to 120, trial 2 from 115 to 135.

---------- begin error --------
searching for artifacts in 306 channel
searching trials.Error using ft_fetch_data (line 123)
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 260)
      dat{trlop} = ft_fetch_data(data,        'header', hdr,
      'begsample', trl(trlop,1)-fltpadding, 'endsample',
      trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary',
      strcmp(cfg.continuous,'no
Error in muscle_artifacts (line 53)
[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);”
---------- end error --------

Do you have any idea to help us? We would be grateful for any help.

Greetings,
Joerg
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From robince at gmail.com  Thu May  2 14:04:03 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 13:04:03 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
Message-ID: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>

Running the full Freesurfer reconstruction pipeline (without the hybrid
skull stripping and Talaraich alignment on the fieldtrip side) appears to
have been successful.

However, when I try to continue with the tutorial I find that my volume and
source grid don't line up (even before any issues converting to sensor
space):

Figure: http://imgur.com/uo9uPUc (code below)

Does anyone have any idea what could be wrong?

What coordinate system is the sub-oct-6-src.fif file in (created by MNE
suite)?
If it is in talairach coordinates, how do I load the Talairach aligned
image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)

Do I need to manually include the transform from transform/talairach.xfm?
To include that can I use it directly as mri.transform in fieldtrip or do I
need to multiply it by the existing mri.transform which is there when
loading the raw anatomy scan (.img)? Come to think of it what does that
transform represent?

Sorry if these are not fieldtrip questions but I am trying to follow the
fieldtrip MNE tutorial so I was hoping someone might know.

Thanks

Robin

% load freesurfer image
mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
% load MNE grid% computed with mne_setup_source_space --ico -6
bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code
'-oct-6-src.fif']), 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
% Volume conduction model
cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
seg = ft_volumesegment(cfg, mri_fs_tal);
cfg = [];cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
% Check volume conduction
figure; hold on
ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight

On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From brungio at gmail.com  Thu May  2 14:26:10 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:26:10 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEs8D9eEdweRBGDhjGtXK_299sguhE9nqYYXG5ftRZi1pA@mail.gmail.com>

Hi Robin,

I had a similar problem during the field trip course. In my case I found
out that one set of coordinates was in mm and then other in m, so I just
had to multiply one set of coordinates.

Another thing you should be aware of is that you can segment your
anatomical using procedures other than the default ones. For example, Spm12
has new, better procedures. Importing an already prepared segmentation in
ft requires some hacking, but if you are interested I can tell you how as
soon as I get a decent internet connection.

Finally, remember that the single shell model is not that great. You should
prepare a better volume conduction model.

    Bruno
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:28:16 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:28:16 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>

Ah, I just saw that your problem might be with the origin of the anatomical
space. Have you tried to see what happens if you set its origin to the
anterior commissure before giving it in input to field trip?
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:42:08 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:42:08 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
	<CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
Message-ID: <CAGgLGEs+cJ_8Bxi=gEt=QhFv31oaRD2DfxHoosadVsiP8vU86Q@mail.gmail.com>

Sorry, my replies were not meant for the list.
On May 2, 2013 8:28 AM, "Bruno L. Giordano" <brungio at gmail.com> wrote:

> Ah, I just saw that your problem might be with the origin of the
> anatomical space. Have you tried to see what happens if you set its origin
> to the anterior commissure before giving it in input to field trip?
> On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:
>
>>  Running the full Freesurfer reconstruction pipeline (without the hybrid
>> skull stripping and Talaraich alignment on the fieldtrip side) appears to
>> have been successful.
>>
>> However, when I try to continue with the tutorial I find that my volume
>> and source grid don't line up (even before any issues converting to sensor
>> space):
>>
>> Figure: http://imgur.com/uo9uPUc (code below)
>>
>> Does anyone have any idea what could be wrong?
>>
>> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
>> suite)?
>> If it is in talairach coordinates, how do I load the Talairach aligned
>> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>>
>> Do I need to manually include the transform from transform/talairach.xfm?
>> To include that can I use it directly as mri.transform in fieldtrip or do I
>> need to multiply it by the existing mri.transform which is there when
>> loading the raw anatomy scan (.img)? Come to think of it what does that
>> transform represent?
>>
>> Sorry if these are not fieldtrip questions but I am trying to follow the
>> fieldtrip MNE tutorial so I was hoping someone might know.
>>
>> Thanks
>>
>> Robin
>>
>> % load freesurfer image
>> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
>> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
>> % load MNE grid% computed with mne_setup_source_space --ico -6
>> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
>> sourcespace = ft_convert_units(bnd, 'cm');
>> % Volume conduction model
>> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
>> seg = ft_volumesegment(cfg, mri_fs_tal);
>> cfg = [];cfg.method = 'singleshell';
>> vol = ft_prepare_headmodel(cfg, seg);
>> % Check volume conduction
>> figure; hold on
>> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
>> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>>
>> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>>
>> I am trying to run through the MNE tutorial here:
>>
>> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>>
>> Unfortunately after the volumetric processing in freesurfer my
>> intermediate result looks wrong.
>>
>> I have followed the steps (including interactive alignment to
>> Talairach) according to the tutorial. I wondered if anyone has any
>> idea what could be wrong, or could point to some more possible
>> diagnostic commands to run?
>>
>> The original Subject01.mgz file seems to have been saved correctly.
>> But if I load the orig.mgz created with:
>> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
>> and plot it with ft_sourceplot it has the same offset and upside down
>> position as the final incorrectly segments freesurfer image. Could
>> this indicate a problem?
>>
>> Thanks for any help,
>>
>> Cheers
>>
>> Robin
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
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From robince at gmail.com  Thu May  2 15:46:22 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 14:46:22 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CALsWBNOLx+KZ93GFdEi+wtdXujYwth1GniK8o3H-cJvd2KGsTA@mail.gmail.com>

By running from MNE suite:
mne_setup_mri --subject BON02 --mri T1

to create a COR.fif image from the Freesurfer output (including Talaraich
transformation) at least that COR.fir and the oct-6-src.fif mesh seem to
line up.

But now I am not sure which coordinate system they are in? (cordsys is
'neuromag' in fieldtrip) nor how to obtain the necessary inverse transform
from this space to the raw anatomy voxel space (so I can build the
transform from oct-6-src mesh to sensor space; I already have the transform
to take the original raw anatomy .img to the sensor coordinate system).

Thanks,

Robin

On Thu, May 2, 2013 at 1:04 PM, Robin <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
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From jan.schoffelen at donders.ru.nl  Thu May  2 15:57:00 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 15:57:00 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
Message-ID: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
> 
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
> 
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
> 
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
> 
> The cohspctrm looks like this:
> val(:,:,1,1) =
> 
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
> 
> I get the following warning during ft_connectivityanalysis
> 
> Warning: Divide by zero.
>> In ft_connectivity_corr at 103
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>> In ft_connectivity_corr at 104
>  In ft_connectivityanalysis at 524
> 
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
> 
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From lmelloni at gmail.com  Thu May  2 18:56:19 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 12:56:19 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
Message-ID: <-7204743264059944684@unknownmsgid>

Hi jan-mathijs

Unfortunately I get the same result whether or not I remove the mean.
Best,
-- Lucía

On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

Hi!
I am trying to calculate coherence using ft_connectivityanalysis, but
I am getting only ones and infinity as output in cohspctrm with all of
my data sets.

I first run ft_freqanalysis with
cfg.method = 'mtmfft';
cfg.taper = 'dpss';
cfg.output = 'fourier';
cfg.foilim = [1 45];
cfg.tapsmofrq = 1;
cfg.keeptrials = 'yes';
cfg.keeptapers = 'yes';
freq = ft_freqanalysis(cfg, data);

Whether I do or I do not specify cfg.channel and cfg.channelcmb here
does not seem to make a difference for my problem later on. The
spectra look absolutely fine.

I then run ft_connectivityanalysis with
cfg.method    = 'coh';
cfg.removemean= 'yes';
cfg.trials    = 'all';
cfg.feedback  = 'yes';
cfg.complex   = 'abs';
coh           = ft_connectivityanalysis(cfg, freq);

The cohspctrm looks like this:
val(:,:,1,1) =

    1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
Inf   Inf   Inf (etc.)

I get the following warning during ft_connectivityanalysis

Warning: Divide by zero.

In ft_connectivity_corr at 103

 In ft_connectivityanalysis at 524
Warning: Divide by zero.

In ft_connectivity_corr at 104

 In ft_connectivityanalysis at 524

The same happens if I try to calculate PLV through ft_connectivityanalysis.
This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
Windows 7 (64bit).

Any advice?
Thanks!
Lucia
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


Jan-Mathijs Schoffelen, MD PhD

Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From jan.schoffelen at donders.ru.nl  Thu May  2 21:12:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 21:12:22 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <-7204743264059944684@unknownmsgid>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
Message-ID: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>

Hi Lucia,

The warnings indicate that you are dividing by zero. Are you sure that your cfg is correct?

Please try

cfg = [];
cfg.method = 'coh';
coh = ft_connectivityanalysis(cfg, freq);

This should work.

Best,
Jan-Mathijs

On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:

> Hi jan-mathijs
> 
> Unfortunately I get the same result whether or not I remove the mean. 
> Best,
> -- Lucía
> 
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> 
>> Hi Lucia,
>> 
>> Could you remove cfg.removemean = 'yes' and try again?
>> 
>> Best,
>> 
>> Jan-Mathijs
>> 
>> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>> 
>>> Hi!
>>> I am trying to calculate coherence using ft_connectivityanalysis, but
>>> I am getting only ones and infinity as output in cohspctrm with all of
>>> my data sets.
>>> 
>>> I first run ft_freqanalysis with
>>> cfg.method = 'mtmfft';
>>> cfg.taper = 'dpss';
>>> cfg.output = 'fourier';
>>> cfg.foilim = [1 45];
>>> cfg.tapsmofrq = 1;
>>> cfg.keeptrials = 'yes';
>>> cfg.keeptapers = 'yes';
>>> freq = ft_freqanalysis(cfg, data);
>>> 
>>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>>> does not seem to make a difference for my problem later on. The
>>> spectra look absolutely fine.
>>> 
>>> I then run ft_connectivityanalysis with
>>> cfg.method    = 'coh';
>>> cfg.removemean= 'yes';
>>> cfg.trials    = 'all';
>>> cfg.feedback  = 'yes';
>>> cfg.complex   = 'abs';
>>> coh           = ft_connectivityanalysis(cfg, freq);
>>> 
>>> The cohspctrm looks like this:
>>> val(:,:,1,1) =
>>> 
>>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>> Inf   Inf   Inf (etc.)
>>> 
>>> I get the following warning during ft_connectivityanalysis
>>> 
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 103
>>>  In ft_connectivityanalysis at 524
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 104
>>>  In ft_connectivityanalysis at 524
>>> 
>>> The same happens if I try to calculate PLV through ft_connectivityanalysis.
>>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>>> Windows 7 (64bit).
>>> 
>>> Any advice?
>>> Thanks!
>>> Lucia
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> Jan-Mathijs Schoffelen, MD PhD 
>> 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> 
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>> 
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>> 
>> http://www.hettaligebrein.nl
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From evaladez at psych.udel.edu  Thu May  2 23:07:51 2013
From: evaladez at psych.udel.edu (Emilio Valadez)
Date: Thu, 2 May 2013 17:07:51 -0400
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
Message-ID: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>

Dear FieldTrippers,

I am trying to compute phase-amplitude coupling (PAC) between the phase of theta activity at one channel and the amplitude of gamma activity at another channel over a specific time window within trials. I have read that PAC is captured with a phase-locking value (PLV), which leads me to think that this might be computed with ft_connectivityanalysis. If this is true, what would the configuration structure and input data need to look like? Or, is there an alternative way to compute PAC using FieldTrip? Thank you in advance!

All the best,
Emilio
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From lmelloni at gmail.com  Fri May  3 00:56:30 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 18:56:30 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
Message-ID: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>

Hi Jan-Mathijs,
still the same result with the code that you suggested.

selection fourierspctrm along dimension 2
averaging crsspctrm over rpt
removing dimension rpt from crsspctrm
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 87
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 89
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 106
  In ft_connectivityanalysis at 524
the call to "ft_connectivityanalysis" took 0 seconds


Lucia

-- 
Lucia.


On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Lucia,
>
> The warnings indicate that you are dividing by zero. Are you sure that
> your cfg is correct?
>
> Please try
>
> cfg = [];
> cfg.method = 'coh';
> coh = ft_connectivityanalysis(cfg, freq);
>
> This should work.
>
> Best,
> Jan-Mathijs
>
> On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
> Hi jan-mathijs
>
> Unfortunately I get the same result whether or not I remove the mean.
> Best,
> -- Lucía
>
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
> Hi Lucia,
>
> Could you remove cfg.removemean = 'yes' and try again?
>
> Best,
>
> Jan-Mathijs
>
> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>
> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
>
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
>
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
>
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
>
> The cohspctrm looks like this:
> val(:,:,1,1) =
>
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
>
> I get the following warning during ft_connectivityanalysis
>
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 103
>
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 104
>
>  In ft_connectivityanalysis at 524
>
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
>
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jm.horschig at donders.ru.nl  Fri May  3 08:32:30 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 03 May 2013 08:32:30 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
Message-ID: <518359FE.4070207@donders.ru.nl>

Dear Lucia,

could you try whether the error persists with a recent version? If it 
does, could you go test whether this code gives the same error:

/
% ************* code starts here /
/%dummy data
cfg             = [];
cfg.ntrials     = 500;
cfg.triallength = 1;
cfg.fsample     = 200;
cfg.nsignal     = 3;
cfg.method      = 'ar';
cfg.params(:,:,1) = [ 0.8 0   0;
                       0   0.9 0.5;
                       0.4 0   0.5];
cfg.params(:,:,2) = [-0.5    0  0;
                         0 -0.8  0;
                         0    0 -0.2];
cfg.noisecov      = [0.3 0 0;
                        0 1 0;
                        0 0 0.2];

data            = ft_connectivitysimulation(cfg);


% freqanalysis
cfgf           = [];
cfgf.method    = 'mtmfft';
cfgf.output    = 'fourier';
cfgf.tapsmofrq = 2;
freq           = ft_freqanalysis(cfgf, data);

% connectivityanalysis
cfgc           = [];
cfgc.method    = 'coh';
c1             = ft_connectivityanalysis(cfgc, freq);

c1.cohspctrm//
% ************* code ends here
/
The code snippet above is part of our test suite for making sure that 
everything works fine. If it does work for you, but does not with your 
own data instead of simulated data, the error must be somewhere in your 
data, e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that 
it will all work fine if you use an updated version of FieldTrip.

Best,
Jörn


On 5/3/2013 12:56 AM, Lucia Melloni wrote:
> Hi Jan-Mathijs,
> still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
> Lucia
>
> -- 
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen 
> <jan.schoffelen at donders.ru.nl <mailto:jan.schoffelen at donders.ru.nl>> 
> wrote:
>
>     Hi Lucia,
>
>     The warnings indicate that you are dividing by zero. Are you sure
>     that your cfg is correct?
>
>     Please try
>
>     cfg = [];
>     cfg.method = 'coh';
>     coh = ft_connectivityanalysis(cfg, freq);
>
>     This should work.
>
>     Best,
>     Jan-Mathijs
>
>     On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
>>     Hi jan-mathijs
>>
>>     Unfortunately I get the same result whether or not I remove the
>>     mean.
>>     Best,
>>     -- Lucía
>>
>>     On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen
>>     <jan.schoffelen at donders.ru.nl
>>     <mailto:jan.schoffelen at donders.ru.nl>> wrote:
>>
>>>     Hi Lucia,
>>>
>>>     Could you remove cfg.removemean = 'yes' and try again?
>>>
>>>     Best,
>>>
>>>     Jan-Mathijs
>>>
>>>     On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>>
>>>>     Hi!
>>>>     I am trying to calculate coherence using
>>>>     ft_connectivityanalysis, but
>>>>     I am getting only ones and infinity as output in cohspctrm with
>>>>     all of
>>>>     my data sets.
>>>>
>>>>     I first run ft_freqanalysis with
>>>>     cfg.method = 'mtmfft';
>>>>     cfg.taper = 'dpss';
>>>>     cfg.output = 'fourier';
>>>>     cfg.foilim = [1 45];
>>>>     cfg.tapsmofrq = 1;
>>>>     cfg.keeptrials = 'yes';
>>>>     cfg.keeptapers = 'yes';
>>>>     freq = ft_freqanalysis(cfg, data);
>>>>
>>>>     Whether I do or I do not specify cfg.channel and cfg.channelcmb
>>>>     here
>>>>     does not seem to make a difference for my problem later on. The
>>>>     spectra look absolutely fine.
>>>>
>>>>     I then run ft_connectivityanalysis with
>>>>     cfg.method    = 'coh';
>>>>     cfg.removemean= 'yes';
>>>>     cfg.trials    = 'all';
>>>>     cfg.feedback  = 'yes';
>>>>     cfg.complex   = 'abs';
>>>>     coh           = ft_connectivityanalysis(cfg, freq);
>>>>
>>>>     The cohspctrm looks like this:
>>>>     val(:,:,1,1) =
>>>>
>>>>         1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>>>     Inf   Inf   Inf (etc.)
>>>>
>>>>     I get the following warning during ft_connectivityanalysis
>>>>
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 103
>>>>      In ft_connectivityanalysis at 524
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 104
>>>>      In ft_connectivityanalysis at 524
>>>>
>>>>     The same happens if I try to calculate PLV through
>>>>     ft_connectivityanalysis.
>>>>     This is with Fieldtrip version 20130422 and 20130427, Matlab
>>>>     R2009a,
>>>>     Windows 7 (64bit).
>>>>
>>>>     Any advice?
>>>>     Thanks!
>>>>     Lucia
>>>>     _______________________________________________
>>>>     fieldtrip mailing list
>>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>     Jan-Mathijs Schoffelen, MD PhD
>>>
>>>     Donders Institute for Brain, Cognition and Behaviour,
>>>     Centre for Cognitive Neuroimaging,
>>>     Radboud University Nijmegen, The Netherlands
>>>
>>>     Max Planck Institute for Psycholinguistics,
>>>     Nijmegen, The Netherlands
>>>
>>>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>>>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>>>
>>>     http://www.hettaligebrein.nl <http://www.hettaligebrein.nl/>
>>>
>>>     _______________________________________________
>>>     fieldtrip mailing list
>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>     Jan-Mathijs Schoffelen, MD PhD
>
>     Donders Institute for Brain, Cognition and Behaviour,
>     Centre for Cognitive Neuroimaging,
>     Radboud University Nijmegen, The Netherlands
>
>     Max Planck Institute for Psycholinguistics,
>     Nijmegen, The Netherlands
>
>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>
>     http://www.hettaligebrein.nl
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From gregor.volberg at psychologie.uni-regensburg.de  Fri May  3 09:35:40 2013
From: gregor.volberg at psychologie.uni-regensburg.de (Gregor Volberg)
Date: Fri, 03 May 2013 09:35:40 +0200
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
In-Reply-To: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
References: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
Message-ID: <518368CC.9030102@psychologie.uni-regensburg.de>

Dear Emilio,

I might not be fully up to date with the functionality of 
ft_connectivityanalysis, but as much as I know there is some 
preprocessing necessary to get a phase-to-amplitude coupling. A common 
strategy is to compute a Hilbert transform on the upper frequency band. 
This can be used to get the 'analytic amplitude', which is essentially a 
waveform that connects the amplitude peaks of the higher frequency. If 
the gamma amplitude is driven by the theta phase, then the analytic 
waveform  should be phase-locked with the theta cycle. The latter part 
of the analysis could be performed with the option 'plv' in 
ft_connectivityanalysis.
For the processing steps you might want to have a look at an example 
script  at http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh.

Best regards,
Gregor



Am 02.05.2013 23:07, schrieb Emilio Valadez:
> Dear FieldTrippers,
>
> I am trying to compute phase-amplitude coupling (PAC) between the phase
> of theta activity at one channel and the amplitude of gamma activity at
> another channel over a specific time window within trials. I have read
> that PAC is captured with a phase-locking value (PLV), which leads me to
> think that this might be computed with ft_connectivityanalysis. If this
> is true, what would the configuration structure and input data need to
> look like? Or, is there an alternative way to compute PAC using
> FieldTrip? Thank you in advance!
>
> All the best,
>
> Emilio
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>

-- 
Dr. rer. nat. Gregor Volberg
Institut für Psychologie
Universität Regensburg
Universitätsstraße 31
D-93053 Regensburg, Germany
Tel: +49 941 943 3862
Fax: +49 941 943 3233


From lmelloni at gmail.com  Fri May  3 14:48:01 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Fri, 3 May 2013 08:48:01 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <518359FE.4070207@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
	<518359FE.4070207@donders.ru.nl>
Message-ID: <CA+_59hd_kx38K4817yAKBnQdd6wSQsb6yTyb-0wQgU_v-8VdPw@mail.gmail.com>

Hi Jörn,
I downloaded version 20130502 and ran both my code and the test code that
you had emailed. I get 1 and inf with both.
The freq input seems to be ok, so ist must be an issue with
ft_connectivityanalysis.
Lucia

-- 
Lucia.


On Fri, May 3, 2013 at 2:32 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Lucia,
>
> could you try whether the error persists with a recent version? If it
> does, could you go test whether this code gives the same error:
>
> *
> % ************* code starts here *
> *%dummy data
> cfg             = [];
> cfg.ntrials     = 500;
> cfg.triallength = 1;
> cfg.fsample     = 200;
> cfg.nsignal     = 3;
> cfg.method      = 'ar';
> cfg.params(:,:,1) = [ 0.8 0   0;
>                       0   0.9 0.5;
>                       0.4 0   0.5];
> cfg.params(:,:,2) = [-0.5    0  0;
>                         0 -0.8  0;
>                         0    0 -0.2];
> cfg.noisecov      = [0.3 0 0;
>                        0 1 0;
>                        0 0 0.2];
>
> data            = ft_connectivitysimulation(cfg);
>
>
> % freqanalysis
> cfgf           = [];
> cfgf.method    = 'mtmfft';
> cfgf.output    = 'fourier';
> cfgf.tapsmofrq = 2;
> freq           = ft_freqanalysis(cfgf, data);
>
> % connectivityanalysis
> cfgc           = [];
> cfgc.method    = 'coh';
> c1             = ft_connectivityanalysis(cfgc, freq);
>
> c1.cohspctrm**
> % ************* code ends here
> *
> The code snippet above is part of our test suite for making sure that
> everything works fine. If it does work for you, but does not with your own
> data instead of simulated data, the error must be somewhere in your data,
> e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that it will
> all work fine if you use an updated version of FieldTrip.
>
> Best,
> Jörn
>
>
>
> On 5/3/2013 12:56 AM, Lucia Melloni wrote:
>
>  Hi Jan-Mathijs,
>  still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
>  Lucia
>
> --
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Lucia,
>>
>>  The warnings indicate that you are dividing by zero. Are you sure that
>> your cfg is correct?
>>
>>  Please try
>>
>>  cfg = [];
>> cfg.method = 'coh';
>> coh = ft_connectivityanalysis(cfg, freq);
>>
>>  This should work.
>>
>>  Best,
>> Jan-Mathijs
>>
>>  On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>>
>>  Hi jan-mathijs
>>
>>  Unfortunately I get the same result whether or not I remove the mean.
>> Best,
>> -- Lucía
>>
>> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
>> jan.schoffelen at donders.ru.nl> wrote:
>>
>>  Hi Lucia,
>>
>>  Could you remove cfg.removemean = 'yes' and try again?
>>
>>  Best,
>>
>>  Jan-Mathijs
>>
>>  On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>
>>  Hi!
>> I am trying to calculate coherence using ft_connectivityanalysis, but
>> I am getting only ones and infinity as output in cohspctrm with all of
>> my data sets.
>>
>> I first run ft_freqanalysis with
>> cfg.method = 'mtmfft';
>> cfg.taper = 'dpss';
>> cfg.output = 'fourier';
>> cfg.foilim = [1 45];
>> cfg.tapsmofrq = 1;
>> cfg.keeptrials = 'yes';
>> cfg.keeptapers = 'yes';
>> freq = ft_freqanalysis(cfg, data);
>>
>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>> does not seem to make a difference for my problem later on. The
>> spectra look absolutely fine.
>>
>> I then run ft_connectivityanalysis with
>> cfg.method    = 'coh';
>> cfg.removemean= 'yes';
>> cfg.trials    = 'all';
>> cfg.feedback  = 'yes';
>> cfg.complex   = 'abs';
>> coh           = ft_connectivityanalysis(cfg, freq);
>>
>> The cohspctrm looks like this:
>> val(:,:,1,1) =
>>
>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>> Inf   Inf   Inf (etc.)
>>
>> I get the following warning during ft_connectivityanalysis
>>
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 103
>>
>>  In ft_connectivityanalysis at 524
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 104
>>
>>  In ft_connectivityanalysis at 524
>>
>> The same happens if I try to calculate PLV through
>> ft_connectivityanalysis.
>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>> Windows 7 (64bit).
>>
>> Any advice?
>> Thanks!
>> Lucia
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>   _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From vale.niccolai at gmail.com  Fri May  3 15:09:58 2013
From: vale.niccolai at gmail.com (Valentina Niccolai)
Date: Fri, 3 May 2013 15:09:58 +0200
Subject: [FieldTrip] neuromag122_neighb
Message-ID: <CAF0jnAnVQrzd+jJPEwGO6FKKADNhdGinsQAAzfc0mrPcp0+LkQ@mail.gmail.com>

Hallo!

I would like to use the template neuromag122_neighb.mat to repair channels,
but it seems to me that this template contains labels form the neuromag306
system.  Is it right? And can I find the template somewhere?


Best,

Valentina
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From Markus.Butz at uni-duesseldorf.de  Fri May  3 16:06:24 2013
From: Markus.Butz at uni-duesseldorf.de (Markus Butz)
Date: Fri, 03 May 2013 15:06:24 +0100
Subject: [FieldTrip] Problems reading in DICOM
Message-ID: <75e09cb13160d.5183d270@uni-duesseldorf.de>




Thanks for your replies and help Robert, Jörn, and Eelke!
Finally it worked out, but the problem was rather on my side, as there where several series of different MRTs scans in one folder of which some did not work, some worked out strange as they had just some files (16-26), and some worked fine. Unfortunately I tried most intensively on the subject who came with no correct series at all. :-(  
To be fair, all the files appeared exactlty the same, but ft_read_mri is luckily mentioning which series it works on and how many files it include, which finally made me wonder. ;-) 
 
Thanks again and have a good weekend 
Markus 
  
ps: Sorry for the belated thanks! 
 
 

 
Am 13.03.13, schrieb Robert Oostenveld <r.oostenveld at donders.ru.nl>: 


> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Hi  
> 
> 
> DICOM files come with different extensions. I guess it depends on the scanner (Siemens/Philips/...). But the file format should be the same as it is a standard format, so the extension should not matter. The fileio/ft_filetype.m function detects both dcm and ima files as dicom.
> 
> 
> 
> if the files have no extension, the autodetection fails and you should explicitly specify the format as
>    mri = ft_read_mri('single_file_of_DICOM_series', 'format', 'dicom');
> I now realize that to be a hidden option. I'll get that fixed in the function documentation.
> 
> 
> 
> 
> 
> 
> I recommend that you specify a filename from somewhere in the middle of the stack of files. There are often a few localizer scans in the same directory, and these (due to the sorting of the file names) tend to end up at the beginning or end of the (alphabetical) directory listing. 
> 
> 
> cheers
> Robert
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 13 Mar 2013, at 14:22, Jörn M. Horschig wrote:
> 
> 
> 
> > 
> > 
> > Hi Markus,
> > 
> > I kept on avoiding these errors by using MRIcron's dcm2nii functionality: http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html
> > But pay attention to the coordinate system when importing it into FieldTrip afterwards, it can be quite a hassle...
> > 
> > Maybe Robert or JM know whether reading in .dcm files is possible, but I have to admit that I never tried ;) 
> > 
> > Best,
> > Jörn
> > 
> > On 3/13/2013 12:11 PM, Markus Butz wrote:
> > 
> > 
> > > 
> > > 
> > > 
> > > Dear list, 
> > > 
> > > 
> > > I am experiencing problems reading in external MRI in DICOM format from a CD (doing it the first time though). 
> > > I wanted to do it the new and easy way as described here:
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom
> > > 
> > > 
> > > % read the DICOM files 
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > 
> > > 
> > > However, I have no single slices with extension *.ima but one dataset with the extension *.dcm and the other dataset with no extension for the single slice files. I am also not sure where to copy the DICOMDIR file.
> > > 
> > > 
> > > When I try to open a single file of the *.dcm series I get:
> > > 
> > > 
> > > mri = ft_read_mri('508652C3.dcm');
> > > 
> > > 
> > > ??? Undefined function or variable "hdr".
> > > 
> > > 
> > > Error in ==> ft_read_mri at 216
> > >   hdr     = hdr(keep); 
> > > 
> > > 
> > > Trying to read in a single file of the no extension series I get:
> > > 
> > > 
> > > mri = ft_read_mri('73850486');
> > > 
> > > 
> > > ??? Error using ==> dicominfo at 41
> > > The specified file is not in DICOM format
> > > 
> > > 
> > > The Image Processing toolbox V 7.2 is installed and this is fieldtrip-20111101.
> > > 
> > > 
> > > Any help appreciated!
> > > 
> > > 
> > > Markus
> > > 
> > > 
> > > 
> > > 
> > >  
> > > 
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > 
> > 
> > 
> > 
> > -- 
> > Jörn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour 
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen 
> > Neuronal Oscillations Group
> > FieldTrip Development Team
> > 
> > P.O. Box 9101
> > NL-6500 HB Nijmegen
> > The Netherlands
> > 
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel:    +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> > 
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> > 
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 

 
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From jimparkinson at me.com  Fri May  3 22:57:26 2013
From: jimparkinson at me.com (Jim Parkinson)
Date: Fri, 03 May 2013 21:57:26 +0100
Subject: [FieldTrip] 2x2x3 Repeated Measures ANOVA in FT
Message-ID: <CACd4eMnmVjveKaT2xUf-H--Ld7PBNnkZhBQRN1JeaZ5OznppiQ@mail.gmail.com>

Hi All

Sorry for the very simplistic question here but I am finding it difficult
to construct an answer - if indeed there is one - from previous posts.

I have a study which is a 2x2x3 repeated measures design, event-related
using 64 channel EEG.  The design is  a culmination of a number of previous
studies, so in that sense is justified, and eyeballing the
data suggests that the effects are pulling in the directions we have
hypothesised.  I would really like to attempt to pull interaction effects,
main effects and then specified (a priori and justified)  contrasts from my
EEG data.  So, is it even possible using cluster permutation methods to
report 3-way, 2-way and main effect stats from such a design, and if so,
what is the best/most justifiable method? Secondly, considering the amount
of *possible*n simple contrasts available in a 2x2x3 design - even if I
don;t run them all because it is not meaningful to do so - what is the best
method to correct for multiple comparisons in the simpel contrasts I do end
up running?

Thans for any help in this confusing matter!

best,
 Jim
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From chadwick.boulay at gmail.com  Mon May  6 07:36:18 2013
From: chadwick.boulay at gmail.com (Chadwick Boulay)
Date: Mon, 06 May 2013 14:36:18 +0900
Subject: [FieldTrip] Please help me get component dipole fitting results
 using custom anatomy into normalized template for EEGLAB clustering.
Message-ID: <51874152.9090903@gmail.com>

Dear Fieldtrip users,

Using the subject's MRI and recorded EEG electrode locations, I've 
managed to segment the MRI, create the volume conduction model, align 
the electrodes, create a sourcemodel using a grid warped from the MNI 
template, create the leadfield, and perform ft_dipolefitting on IC 
weights (imported from EEGLAB). The geometry, electrode positions, and 
mri all line up (coordsys='ctf', unit='cm') and the calculated dipole 
positions are what I would expect.

[Aside: All of my topoplots have the electrodes positioned correctly 
relative to each other but the nose and ears are 90 degrees from where I 
would expect them. Do the topoplot functions not know how to deal with 
ctf coordsys?]

How can I normalize these dipole locations into the template brain so 
that I may perform component clustering in EEGLAB?
I have some ideas but I don't know how to implement them.

1) Calculate the transformation matrix to normalize the original MRI to 
the template MRI, then apply that transformation to the dipole positions 
and momentums. I'm guessing I need to use mri_norm = 
ft_volumenormalize(cfg, mri); but then I don't know how to use 
mri_norm.transform and mri_norm.initial. Further, the output of 
ft_dipolefitting doesn't seem to be suitable for ft_transform_geometry.

2) Since the sourcemodel grid is warped from the template brain, I can 
find the sourcemodel grid index closest to the dipole location then set 
the new dipole location to be the location of the template grid at the 
same index. I don't know how to do this for the momentum but I probably 
don't need the momentum for clustering.

3) Start over from the beginning, normalizing the MRI and the electrode 
locations as soon as possible then performing all subsequent 
calculations using the normalized geometry.

I searched the documentation and the list archives but I could not find 
an answer. I am surprised because I expected dipole normalisation to be 
a common requirement. Maybe I am missing something simple.
Thank you in advance for any help.
-Chad

-- 
Chadwick Boulay
JSPS Postdoctoral Fellow
Keio University
Yokohama Japan
boulay at brain.bio.keio.ac.jp




From mushfa.yousuf at googlemail.com  Mon May  6 14:47:44 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Mon, 6 May 2013 14:47:44 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
Message-ID: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>

Hello;

Yes you were right. I have defined the wrong sensors i.e 'grad' instead of
'elec' while calculating the Leadfield.

Actually I am trying to calculate Combined source reconstruction from both
EEG and MEG sensors.

Do you have any idea, how to define both elec and grad definition  while
calculating first forward then inverse solution.

Because in a fieldtrip either you can defined elec or grad at one time.


Regards;


Mushfa Yousuf

Neurozentrum,
Universitätsklinikum Schleswig-Holstein,
Campus Kiel (UKSH), Deutschland


On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:

> Hi Mushfa,
>
> My guess is that the channels that have you used to compute .csdspctrm are
> not the same as the channels in cfg.elec.    If you set cfg.channel =
> freqPost.label, does that solve it?
>
> Cheers,
> Johanna
>
>
> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>
>> Hello Fieldtrippers,
>>
>> I am doing source reconstruction using EEG channels on a fieldtrip.
>>
>> I have computed Forward solution i.e head model using  'Openmeeg' and
>> lead field successfully.
>>
>> For the inverse solution using 'dics' method, I wrote the following
>> syntax
>>
>>
>>
>>
>>
>>  cfg              = [];
>>  cfg.method       = 'dics';
>>  cfg.frequency    = 130;
>>  cfg.elec         = dataFIC12.hdr.elec;
>>  cfg.grid         = grid;
>>  cfg.vol          = vol;
>>
>>  sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>> and I have received the following error:
>>
>>
>> ??? Error using ==> mtimes
>> Inner matrix dimensions must agree.
>>
>> Error in ==> beamformer_dics at 314
>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>         leadfield
>>
>> Error in ==> ft_sourceanalysis at 595
>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>       squeeze(Cf(i,:,:)), optarg{:});
>>
>> Error in ==> newCode at 214
>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>>
>>
>> Any help would be appreciated.
>>
>>
>> Regards;
>>
>>
>> Mushfa Yousuf
>>
>> Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From chaowang0704 at gmail.com  Tue May  7 13:35:20 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 14:35:20 +0300
Subject: [FieldTrip] Some Questions on the resample design
Message-ID: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>

I
 have been using field-trip. Recently, I tried to use it for statistic
test by non-parametric method, e.g. bootstrap and permutation. As usual,
the two method involve resample original data with or without replacement.
I carefully inspected the code in the function *resampledesign* but I was
quite confused by the method in the bootstrap section:

254resample = zeros(cfg.numrandomization, Nrepl);
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From chaowang0704 at gmail.com  Tue May  7 14:08:57 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 15:08:57 +0300
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
Message-ID: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>

I'm sorry to make a mistake just now. The previous message sent didn't
fullfill my meaning.

I carefully inspected the code in the function *resampledesign* but I was
quite confused by the codes in the bootstrap section (For paired design,
the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
and design(2,N+1:2*N)=2 and N is for example the subject number; and
cfg.uvar=2):
91     Nvar  = size(design,1);   % number of factors or regressors
92     Nrepl = size(design,2);   % number of replications
...
...
248   units = design(cfg.uvar,:);
249   for k = 1:length(unique(units))
250     sel = find(units==k);
251     indx(:,k) = sel;
252     Nrep(k)   = length(sel);
253   end
254   resample = zeros(cfg.numrandomization, Nrepl);
...
...
274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
275   for i=1:cfg.numrandomization*10
276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
277   end

278   tmp = unique(tmp, 'rows');
279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
size(tmp,1), cfg.numrandomization*10);
...
...
292   for i=1:cfg.numrandomization
293      for k=1:size(indx,1)
294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
295      end
296   end

My question was on the code in 276 line. These code was to generate a
number of rand numbers (about cfg.numrandomization lines) in the range of 1
to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
If the function '*sort*' is used, then every row of matrix tmp is the same,
which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line to
the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
result is by no means what we want, I think. What we do want is several
rows numbers with same range but with distinct orders. Only in this way,
can we guarantee that each resample is not the same.



On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:

> I
> have been using field-trip. Recently, I tried to use it for statistic test
> by non-parametric method, e.g. bootstrap and permutation. As usual, the two
> method involve resample original data with or without replacement. I
> carefully inspected the code in the function *resampledesign* but I was
> quite confused by the method in the bootstrap section:
>
> 254resample = zeros(cfg.numrandomization, Nrepl);
>
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From zriouil.imane at gmail.com  Tue May  7 14:48:24 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 7 May 2013 14:48:24 +0200
Subject: [FieldTrip] convert .plx to .nex ?
Message-ID: <CABu=cReD7OPEna8o=40exmxV=QQvcWNxmbyj9w=mWzaJRPD2dg@mail.gmail.com>

Hi

i have a problem to read data with extension .plx and i want to convert
this to .nex. it's possible or no?

please respond me
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From johanna.zumer at donders.ru.nl  Tue May  7 14:53:40 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Tue, 7 May 2013 14:53:40 +0200
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
	<CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
Message-ID: <CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA@mail.gmail.com>

Dear Chao,

I'm not familiar with this piece of code, but I had a quick look.  Line
276, with the 'sort' command, is testing for the number of unique 'rows'
(line 278).  It then uses this information to modify the value of
cfg.numrandomization (line 283 which you have not displayed), which is
reduced if not enough unique information to do the requested number of
randomizations.   Then (I think) the actual randomization should be
occuring in subsequent lines of code (292-296).    Note also that this part
of code is only reached if max(design(cfg.uvar,:)) < 20.

Does that help?    Maybe someone else with more experience in this section
of code can comment as well?

Or if you still find that it indeed is not randomizing, you can file a bug
here (http://bugzilla.fcdonders.nl/), ideally with a small test script.

Cheers,
Johanna




2013/5/7 Chao Wang <chaowang0704 at gmail.com>

> I'm sorry to make a mistake just now. The previous message sent didn't
> fullfill my meaning.
>
> I carefully inspected the code in the function *resampledesign* but I was
> quite confused by the codes in the bootstrap section (For paired design,
> the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
> and design(2,N+1:2*N)=2 and N is for example the subject number; and
> cfg.uvar=2):
> 91     Nvar  = size(design,1);   % number of factors or regressors
> 92     Nrepl = size(design,2);   % number of replications
> ...
> ...
> 248   units = design(cfg.uvar,:);
> 249   for k = 1:length(unique(units))
> 250     sel = find(units==k);
> 251     indx(:,k) = sel;
> 252     Nrep(k)   = length(sel);
> 253   end
> 254   resample = zeros(cfg.numrandomization, Nrepl);
> ...
> ...
> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');
> 279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
> size(tmp,1), cfg.numrandomization*10);
> ...
> ...
> 292   for i=1:cfg.numrandomization
> 293      for k=1:size(indx,1)
> 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> 295      end
> 296   end
>
> My question was on the code in 276 line. These code was to generate a
> number of rand numbers (about cfg.numrandomization lines) in the range of 1
> to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
> If the function '*sort*' is used, then every row of matrix tmp is the
> same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line
> to the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
> result is by no means what we want, I think. What we do want is several
> rows numbers with same range but with distinct orders. Only in this way,
> can we guarantee that each resample is not the same.
>
>
>
> On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:
>
>> I
>> have been using field-trip. Recently, I tried to use it for statistic
>> test by non-parametric method, e.g. bootstrap and permutation. As usual,
>> the two method involve resample original data with or without replacement.
>> I carefully inspected the code in the function *resampledesign* but I
>> was quite confused by the method in the bootstrap section:
>>
>> 254resample = zeros(cfg.numrandomization, Nrepl);
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From antony.passaro at gmail.com  Wed May  8 23:17:21 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Wed, 8 May 2013 17:17:21 -0400
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
Message-ID: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>

 Hi Fieldtrippers,

I am trying to perform a group-level comparison of 2 conditions across 10
subjects based on the DTF connectivity. For the time being, we are looking
at the DTF for a subset of frequencies (alpha) and choosing the avgoverfreq
option which gives us a 4096 x 1 matrix since we are looking at 64 x 64
channels. Using ft_freqstatistics, I noticed that it will throw an error
explaining that there is not yet an implementation for data with channelcmb
for a cluster analysis so I took it upon myself to identify channel pairs
which should be considered neighbors and build a new neighbor structure
prior to running ft_freqstatistics. To do that, I took the basic neighbor
structure for 64 channels and then created a new neighbor structure of 4096
channel pairs based on the code below:

for i=1:4096
    label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
end

labelcmb = dtf.labelcmb;

chans=64;

%Identify the channel pairs which are neighbors with the target channel
NBtarget = {};
for ch=1:chans^2
    NBtarget(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,1},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat(x,['_' labelcmb{ch,2}]),{neighbours(
1,target).neighblabel},'UniformOutput',0);
    NBtarget(ch).neighblabel = tempnb{:};
end

%Identify the channel pairs which are neighbors with the reference channel
NBref = {};
for ch=1:chans^2
    NBref(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,2},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat([labelcmb{ch,1}
'_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
    NBref(ch).neighblabel = tempnb{:};
end


%Append both sets of neighbors (ref and target)
NBboth= {};
for ch=1:chans^2
    NBboth(ch).label = label{ch};
    NBboth(ch).neighblabel = [NBref(ch).neighblabel;
NBtarget(ch).neighblabel];
end


This seems to work and the clustering method proceeds without error. My
question is the following: is this the proper way to utilize the clustering
method using ft_freqstatistics on connectivity data or am I missing
something?

Thanks,
-Tony
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From chaowang0704 at gmail.com  Thu May  9 10:51:37 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Thu, 9 May 2013 11:51:37 +0300
Subject: [FieldTrip] Some Questions on the resample design (Johanna
	Zumer)
Message-ID: <CAGvTfVmzpDNoJ7FKbeeKHCzBPunx0J1+=b5yJKqxfs6qN9hHRw@mail.gmail.com>

Dear

Johanna,

Thank you! I understand your meaning and that's right
that
this part of code is only reached if

max(design(cfg.uvar,:)) < 20, but what I do not understand is that for what
reason,
the '20' is set to test the
max(design(cfg.uvar,:)). And besides, by using 'sort', each row of tmp will
be the same, in ascending order, which will lead the 278 line using
'unique' to have tmp only one row. That is size(tmp,1)=1; this will
lead to cfg.numrandomization=1
in 284 line.

> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');

Best regards!

Chao

Message: 4

> Date: Tue, 7 May 2013 14:53:40 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Some Questions on the resample design
> Message-ID:
>         <
> CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Chao,
>
> I'm not familiar with this piece of code, but I had a quick look.  Line
> 276, with the 'sort' command, is testing for the number of unique 'rows'
> (line 278).  It then uses this information to modify the value of
> cfg.numrandomization (line 283 which you have not displayed), which is
> reduced if not enough unique information to do the requested number of
> randomizations.   Then (I think) the actual randomization should be
> occuring in subsequent lines of code (292-296).    Note also that
> 
> this part
> of code is only reached if
> 
> max(design(cfg.uvar,:)) < 20.
>
> Does that help?    Maybe someone else with more experience in this section
> of code can comment as well?
>
> Or if you still find that it indeed is not randomizing, you can file a bug
> here (http://bugzilla.fcdonders.nl/), ideally with a small test script.
>
> Cheers,
> 
> Johanna
>
>
>
>
> 2013/5/7 Chao Wang <chaowang0704 at gmail.com>
>
> > I'm sorry to make a mistake just now. The previous message sent didn't
> > fullfill my meaning.
> >
> > I carefully inspected the code in the function *resampledesign* but I was
> > quite confused by the codes in the bootstrap section (For paired design,
> > the design matrix should be like this, design(1,:)=[1:N 1:N],
> design(2,1:N)=1
> > and design(2,N+1:2*N)=2 and N is for example the subject number; and
> > cfg.uvar=2):
> > 91     Nvar  = size(design,1);   % number of factors or regressors
> > 92     Nrepl = size(design,2);   % number of replications
> > ...
> > ...
> > 248   units = design(cfg.uvar,:);
> > 249   for k = 1:length(unique(units))
> > 250     sel = find(units==k);
> > 251     indx(:,k) = sel;
> > 252     Nrep(k)   = length(sel);
> > 253   end
> > 254   resample = zeros(cfg.numrandomization, Nrepl);
> > ...
> > ...
> > 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> > 275   for i=1:cfg.numrandomization*10
> > 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> > 277   end
> >
> > 278   tmp = unique(tmp, 'rows');
> > 279   fprintf('found %d unique rows in bootstrap matrix of %d
> bootstraps',
> > size(tmp,1), cfg.numrandomization*10);
> > ...
> > ...
> > 292   for i=1:cfg.numrandomization
> > 293      for k=1:size(indx,1)
> > 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> > 295      end
> > 296   end
> >
> > My question was on the code in 276 line. These code was to generate a
> > number of rand numbers (about cfg.numrandomization lines) in the range
> of 1
> > to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> > design and Nrep is the number of repetition (Nrep(:)=2 for paired
> design).
> > If the function '*sort*' is used, then every row of matrix tmp is the
> > same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278
> line
> > to the result: temp=1:Nrepl/Nrep(1) (because of the function unique).
> This
> > result is by no means what we want, I think. What we do want is several
> > rows numbers with same range but with distinct orders. Only in this way,
> > can we guarantee that each resample is not the same.
>
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From marianapbranco1 at gmail.com  Fri May 10 10:08:41 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Fri, 10 May 2013 10:08:41 +0200
Subject: [FieldTrip] Real-time processing
References: <9B1A8EA6-CCDE-4CED-83FD-C5D2F21607F5@student.tudelft.nl>
Message-ID: <31275A3B-B8D6-4C46-8B30-5EF745AD13BA@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From mengtongxiao at gmail.com  Fri May 10 11:39:29 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Fri, 10 May 2013 17:39:29 +0800
Subject: [FieldTrip] cooradinate
Message-ID: <CADiddyVv3S8CvCQY-RPFo4GTj1Su68U5WWdjmy2L9MwsCi1Emg@mail.gmail.com>

Dear all，

I got some ROIs from MNE. But  in MNE it use brain template that is *MNI152 .
*
I want use fieldtrip compute the spatial filter for ROIs.
For this reason ,I want got the position in sourcemodel from template in
fieldtrip.
I see the fieldtrip seem to use *MNI305  ,*isn,t it?
If fieldtrip use *MNI305 ,*  this problem is making me question whether a
transformation  is really necessary ?
The both "MNI" space cooradation * x ,y,z axis *represent right,anterior,
superior.(+x=right,+y=anterior,+z=superior)?(MNI cooradation from
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
I find infieldtrip (http://fieldtrip.fcdonders.nl/tutorial/connectivity)
sourcemodel is that *x ,y,z axis *represent anterior, right,superior?
If a transformation  is really necessary ,how should I do?

Then I am puzzed what do *x ,y,z axis *represent in stanard_1020.elc

Thanks for your help,
best,
xiao
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From mengtongxiao at gmail.com  Mon May 13 03:30:06 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Mon, 13 May 2013 09:30:06 +0800
Subject: [FieldTrip] grid-template
Message-ID: <CADiddyVrmgpO+fX+SoyY7cWHBXfc=4Tch9js+fcTV4V9QRfj_w@mail.gmail.com>

Dear all,

I want to konw what is  the MNI-template  that  constructed 3D-grids in the
fieldtrip (Template sourcemodels ) ?
is it MNI305 ,clin27 ,MNI125 or something else?

thanks,
xiao
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From jm.horschig at donders.ru.nl  Mon May 13 11:13:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 11:13:14 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
Message-ID: <5190AEAA.3020301@donders.ru.nl>

Dear Mushfa,

I think you have to compute two leadfield matrices, one for EEG (elec) 
and one for MEG (grad), and then concatenate these (and make sure that 
the order of sensors won't get mixed up anywhere, because  
sourceanalysis just expects the leadfield matrix to be ordered like your 
data. If that's not the case, you either encounter the previous error 
you described or (if the number of channels matches, but order is mixed 
up) it will just return wrong source estimated activity.

Best,
Jörn

On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
> Hello;
>
> Yes you were right. I have defined the wrong sensors i.e 'grad' 
> instead of 'elec' while calculating the Leadfield.
>
> Actually I am trying to calculate Combined source reconstruction from 
> both EEG and MEG sensors.
>
> Do you have any idea, how to define both elec and grad definition  
> while calculating first forward then inverse solution.
>
> Because in a fieldtrip either you can defined elec or grad at one time.
>
>
> Regards;
>
>
> Mushfa Yousuf
>
> Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer 
> <johanna.zumer at gmail.com <mailto:johanna.zumer at gmail.com>> wrote:
>
>     Hi Mushfa,
>
>     My guess is that the channels that have you used to compute
>     .csdspctrm are not the same as the channels in cfg.elec.    If you
>     set cfg.channel = freqPost.label, does that solve it?
>
>     Cheers,
>     Johanna
>
>
>     2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com
>     <mailto:mushfa.yousuf at googlemail.com>>
>
>         Hello Fieldtrippers,
>
>         I am doing source reconstruction using EEG channels on a
>         fieldtrip.
>
>         I have computed Forward solution i.e head model using
>          'Openmeeg' and lead field successfully.
>
>         For the inverse solution using 'dics' method, I wrote the
>         following syntax
>
>
>
>
>
>          cfg              = [];
>          cfg.method       = 'dics';
>          cfg.frequency    = 130;
>          cfg.elec         = dataFIC12.hdr.elec;
>          cfg.grid         = grid;
>          cfg.vol          = vol;
>
>          sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>         and I have received the following error:
>
>
>         ??? Error using ==> mtimes
>         Inner matrix dimensions must agree.
>
>         Error in ==> beamformer_dics at 314
>                 filt = pinv(lf' * invCf * lf) * lf' * invCf;          %
>                 Gross eqn. 3, use PINV/SVD to cover rank deficient
>                 leadfield
>
>         Error in ==> ft_sourceanalysis at 595
>               dip(i) = beamformer_dics(grid, sens, vol, [],
>         squeeze(Cf(i,:,:)), optarg{:});
>
>         Error in ==> newCode at 214
>         sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>
>
>         Any help would be appreciated.
>
>
>         Regards;
>
>
>         Mushfa Yousuf
>
>         Neurozentrum,
>         Universitätsklinikum Schleswig-Holstein,
>         Campus Kiel (UKSH), Deutschland
>
>
>         _______________________________________________
>         fieldtrip mailing list
>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From naran.kutt at gmail.com  Mon May 13 11:48:17 2013
From: naran.kutt at gmail.com (Narayanan Kutty)
Date: Mon, 13 May 2013 05:48:17 -0400
Subject: [FieldTrip] Mutual Information
Message-ID: <CAGgtWvU9tSr=6XGAt__T=mQUWQx-7h34oLjS_kgMekRkJYzdVQ@mail.gmail.com>

Hello All,

Are there any functions within fieldtrip to calculate mutual information
between channels at the sensor level. I remember that eeglab used to have a
plugin for that. Couldn't find anything in fieldtrip.

Thank you,
Naran.
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From jm.horschig at donders.ru.nl  Mon May 13 14:14:44 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 14:14:44 +0200
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
	<CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
Message-ID: <5190D934.5020407@donders.ru.nl>

Dear Tony,

I had a quick look at your code, and I think it is fine. However, I 
would define neighbours purely based on the target sensor, not on the 
reference, e.g. when computing cortico-muscular coherence on channel 
level, you  are interested in spatial clusters near the cortex and not 
in cluster on the arm where the reference sensor is.
Also check out this:

data = ft_checkdata(data, 'cmbrepresentation', 'full');

This will turn chancmb (Nx1) into chan X chan (RxS, where R*S = N).

Best,
Jörn

On 5/8/2013 11:17 PM, Antony Passaro wrote:
> Hi Fieldtrippers,
> I am trying to perform a group-level comparison of 2 conditions across 
> 10 subjects based on the DTF connectivity. For the time being, we are 
> looking at the DTF for a subset of frequencies (alpha) and choosing 
> the avgoverfreq option which gives us a 4096 x 1 matrix since we are 
> looking at 64 x 64 channels. Using ft_freqstatistics, I noticed that 
> it will throw an error explaining that there is not yet an 
> implementation for data with channelcmb for a cluster analysis so I 
> took it upon myself to identify channel pairs which should be 
> considered neighbors and build a new neighbor structure prior to 
> running ft_freqstatistics. To do that, I took the basic neighbor 
> structure for 64 channels and then created a new neighbor structure of 
> 4096 channel pairs based on the code below:
> for i=1:4096
> label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
> end
> labelcmb = dtf.labelcmb;
>
> chans=64;
> %Identify the channel pairs which are neighbors with the target channel
> NBtarget = {};
> for ch=1:chans^2
> NBtarget(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,1},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat(x,['_' 
> labelcmb{ch,2}]),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBtarget(ch).neighblabel = tempnb{:};
> end
>
> %Identify the channel pairs which are neighbors with the reference channel
> NBref = {};
> for ch=1:chans^2
> NBref(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,2},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat([labelcmb{ch,1} 
> '_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBref(ch).neighblabel = tempnb{:};
> end
>
>
> %Append both sets of neighbors (ref and target)
> NBboth= {};
> for ch=1:chans^2
> NBboth(ch).label = label{ch};
> NBboth(ch).neighblabel = [NBref(ch).neighblabel; 
> NBtarget(ch).neighblabel];
> end
> This seems to work and the clustering method proceeds without error. 
> My question is the following: is this the proper way to utilize the 
> clustering method using ft_freqstatistics on connectivity data or am I 
> missing something?
> Thanks,
> -Tony
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From sanbelluzo at gmail.com  Mon May 13 21:13:08 2013
From: sanbelluzo at gmail.com (Santiago Belluzo)
Date: Mon, 13 May 2013 16:13:08 -0300
Subject: [FieldTrip] Emotiv + FieldTrip + Matlab
In-Reply-To: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
References: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
Message-ID: <CAKkp94yg=a2VrUUSN2dxGBLTQD4E_6JOJ=VSXKrNLBVjBv8h3w@mail.gmail.com>

Hi, i´m trying to use emotiv2ft in a windows machine and Matlab return this
message

"Waiting for the device to become ready - press [Escape] to quit
EDK: User added, will now start acquisition.
Streaming 16 out of 22 channels
Could not connect to buffer server at localhost:1972."


In http://fieldtrip.fcdonders.nl/development/realtime/emotiv?s[]=emotiv said
that  "If port 1972 cannot be accessed on a Windows machine it may help to
first initialize the port from matlab, e.g., via ft_realtime_fileproxy".
But i´m not sure how to do it....
 Someone can help me?.

Santiago.


2013/3/4 Santiago Belluzo <sanbelluzo at gmail.com>

> *Hi, I'm new to FieldTrip and I'm interested in using it to capture **realtime data from the Emotiv headset using the function emotiv2ft.I`ve tried some examples like signalviewer andpowerviewer with random signal from signalproxy to check that the FieldTripBuffer works fine. Then i`ve tried to use emotiv2ft and have problems.  *
>
> *I'm not sure about how to call to this interface from within **Matlab.*
>
> *I`ve read some messages from the mailinglist with similar problem but in there is not clear for me how they solve it. *
>
> *I´ll be waiting for any help!.*
>
> *Thanks.*
>
> --
> Santiago
>



-- 
Santiago Belluzo
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From chenxiaogang1986 at 163.com  Tue May 14 03:37:29 2013
From: chenxiaogang1986 at 163.com (Xiaogang Chen)
Date: Tue, 14 May 2013 09:37:29 +0800 (CST)
Subject: [FieldTrip] ft_topoplotCC of vector
Message-ID: <5ef5e6c2.25f7.13ea0af63fd.Coremail.chenxiaogang1986@163.com>

Hi all,

 

I am trying to plot some results that are not the output from a ft function, using a ft_topoplotCC function. However, I don’t know how to use it. Would you send me some simple examples? Thanks very much.

 

Best,

 

Xiaogang Chen 
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From yoel.sher at mail.huji.ac.il  Tue May 14 18:09:37 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Tue, 14 May 2013 19:09:37 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
Message-ID: <519261C1.3020002@mail.huji.ac.il>

Dear FieldTrippers,

I would like to know if there is an option to extract the Topographic 
map (Such as the scalp in ft_topoplotER) to a matrix. I've searched 
around the functions in fieldtrip and couldn't find any..

Many Thanks,
Yoel


From eelke.spaak at donders.ru.nl  Tue May 14 19:25:40 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 14 May 2013 19:25:40 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <519261C1.3020002@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
Message-ID: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>

Dear Yoel,

I'm not sure if I understand what you mean exactly, but do you simply
want the values plotted by ft_topoplotER in case of plotting the
results of ft_timelockanalysis? In that case, you can look at the
tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
rather trivial, so I think you must mean something else.

Best,
Eelke

On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear FieldTrippers,
>
> I would like to know if there is an option to extract the Topographic map
> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
> functions in fieldtrip and couldn't find any..
>
> Many Thanks,
> Yoel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From yoel.sher at mail.huji.ac.il  Wed May 15 12:08:20 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:08:20 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
Message-ID: <51935E94.7090605@mail.huji.ac.il>

Dear Eelke,

First, thanks for you fast replay. Second, let me clarify my question. 
I'm looking for other result than the average ERP/ERF. I'm looking for a 
matrix that output the EEG value per each location (not just the 
electrodes) on the scalp. Of course that every location other than the 
electrode is an interpolated value. The plot of ft_topoplotER shows that 
matrix (but does not output, as far as I know).

Regards,
Yoel

On 05/14/2013 08:25 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> I'm not sure if I understand what you mean exactly, but do you simply
> want the values plotted by ft_topoplotER in case of plotting the
> results of ft_timelockanalysis? In that case, you can look at the
> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
> rather trivial, so I think you must mean something else.
>
> Best,
> Eelke
>
> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear FieldTrippers,
>>
>> I would like to know if there is an option to extract the Topographic map
>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
>> functions in fieldtrip and couldn't find any..
>>
>> Many Thanks,
>> Yoel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From eelke.spaak at donders.ru.nl  Wed May 15 12:22:21 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 15 May 2013 12:22:21 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <51935E94.7090605@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
Message-ID: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>

Dear Yoel,

Ah, I understand now; you want the interpolated matrix. This is not
possible with standard FieldTrip code.

However, it should not be very difficult to get this. I would
recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
Then, when the code breaks at that point, you can type in the command
window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
you have the x and y coordinates and the data (z) in variables in your
base workspace.

Getting this matrix programmatically in a script should also be
possible, but that would require custom hacks of ft_plot_topo (e.g.
you could put this assignin call in your local copy of the function,
or add Xi,Yi,Zi as output arguments, etc.)

Good luck,
best,

Eelke

On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear Eelke,
>
> First, thanks for you fast replay. Second, let me clarify my question. I'm
> looking for other result than the average ERP/ERF. I'm looking for a matrix
> that output the EEG value per each location (not just the electrodes) on the
> scalp. Of course that every location other than the electrode is an
> interpolated value. The plot of ft_topoplotER shows that matrix (but does
> not output, as far as I know).
>
> Regards,
> Yoel
>
>
> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>
>> Dear Yoel,
>>
>> I'm not sure if I understand what you mean exactly, but do you simply
>> want the values plotted by ft_topoplotER in case of plotting the
>> results of ft_timelockanalysis? In that case, you can look at the
>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>> rather trivial, so I think you must mean something else.
>>
>> Best,
>> Eelke
>>
>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>
>>> Dear FieldTrippers,
>>>
>>> I would like to know if there is an option to extract the Topographic map
>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>> the
>>> functions in fieldtrip and couldn't find any..
>>>
>>> Many Thanks,
>>> Yoel
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>


From yoel.sher at mail.huji.ac.il  Wed May 15 12:47:06 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:47:06 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
	<CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
Message-ID: <519367AA.60204@mail.huji.ac.il>

Dear Eelke,

Many thanks, I'll try it out.

Best,
- Yoel

On 05/15/2013 01:22 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> Ah, I understand now; you want the interpolated matrix. This is not
> possible with standard FieldTrip code.
>
> However, it should not be very difficult to get this. I would
> recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
> Then, when the code breaks at that point, you can type in the command
> window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
> you have the x and y coordinates and the data (z) in variables in your
> base workspace.
>
> Getting this matrix programmatically in a script should also be
> possible, but that would require custom hacks of ft_plot_topo (e.g.
> you could put this assignin call in your local copy of the function,
> or add Xi,Yi,Zi as output arguments, etc.)
>
> Good luck,
> best,
>
> Eelke
>
> On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear Eelke,
>>
>> First, thanks for you fast replay. Second, let me clarify my question. I'm
>> looking for other result than the average ERP/ERF. I'm looking for a matrix
>> that output the EEG value per each location (not just the electrodes) on the
>> scalp. Of course that every location other than the electrode is an
>> interpolated value. The plot of ft_topoplotER shows that matrix (but does
>> not output, as far as I know).
>>
>> Regards,
>> Yoel
>>
>>
>> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>> Dear Yoel,
>>>
>>> I'm not sure if I understand what you mean exactly, but do you simply
>>> want the values plotted by ft_topoplotER in case of plotting the
>>> results of ft_timelockanalysis? In that case, you can look at the
>>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>>> rather trivial, so I think you must mean something else.
>>>
>>> Best,
>>> Eelke
>>>
>>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>> Dear FieldTrippers,
>>>>
>>>> I would like to know if there is an option to extract the Topographic map
>>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>>> the
>>>> functions in fieldtrip and couldn't find any..
>>>>
>>>> Many Thanks,
>>>> Yoel
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From ggonesc at upo.es  Wed May 15 19:37:11 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 15 May 2013 19:37:11 +0200
Subject: [FieldTrip] PLV and ImC computation
Message-ID: <8d77945c28ba0f58.5193e3e7@upo.es>

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From mbj0310 at gmail.com  Thu May 16 08:28:13 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 15:28:13 +0900
Subject: [FieldTrip] About preprocessing and define trial
Message-ID: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>


Dear all,

Hello, my name is BJ Min from Korea.

I am just a beginner in the Fieldtrip.
Anyway, with the help of tutorials, I could make grand average ERP of my data finally. 

However, my question is about the order of preprocessing. According to the tutorials, and examples, it looks the ft_definetrial step is the first, then ft_preprocessing step is followed.  But, is there any method to flip these two steps? What I want to do is preprocessing (filtering, notch filtering) first then to use ft_definetrial sequentially.

Best regards


BeomJun Min, M.D.

Ph. D. student, Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST) 
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
500-712, Republic of Korea (South) 
Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr

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From eelke.spaak at donders.ru.nl  Thu May 16 08:52:02 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 08:52:02 +0200
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
Message-ID: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>

Dear BeomJun,

What you describe is definitely possible. If you specify:

cfg = [];
cfg.dataset = 'dataset';
data = ft_preprocessing(cfg);

you will get one very big 'trial' in the data structure, representing
just all your data. In the step above, you can also specify filter
options.

After this step, you can segment your data into trials by using
ft_redefinetrial (rather than ft_definetrial). However, you still need
a trl matrix containing the trial definition. The easiest way to
obtain this is to still call ft_definetrial as you used to do:

cfg = [];
cfg.dataset = 'dataset';
cfg.trialdef.....
% all the trial definition options go here
cfgout = ft_definetrial(cfg);

and then just save the output trl matrix:

trl = cfgout.trl;

now you can call ft_redefinetrial:

cfg = [];
cfg.trl = trl;
data = ft_redefinetrial(cfg, data);

and your data will be segmented.

Hope this helps,
Best,

Eelke


On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I am just a beginner in the Fieldtrip.
> Anyway, with the help of tutorials, I could make grand average ERP of my
> data finally.
>
> However, my question is about the order of preprocessing. According to the
> tutorials, and examples, it looks the ft_definetrial step is the first, then
> ft_preprocessing step is followed.  But, is there any method to flip these
> two steps? What I want to do is preprocessing (filtering, notch filtering)
> first then to use ft_definetrial sequentially.
>
> Best regards
>
>
> BeomJun Min, M.D.
>
> Ph. D. student, Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From mbj0310 at gmail.com  Thu May 16 10:06:51 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 17:06:51 +0900
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
	<CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
Message-ID: <CA+v9jvJ0bo1UFp+_qSezeO8B4LpyQ+RDiSr=2pKLWK6-8pRf4w@mail.gmail.com>

Dear Eelke Spaak

Thank you very much.
It works perfect!

Best regards.


2013/5/16 Eelke Spaak <eelke.spaak at donders.ru.nl>

> Dear BeomJun,
>
> What you describe is definitely possible. If you specify:
>
> cfg = [];
> cfg.dataset = 'dataset';
> data = ft_preprocessing(cfg);
>
> you will get one very big 'trial' in the data structure, representing
> just all your data. In the step above, you can also specify filter
> options.
>
> After this step, you can segment your data into trials by using
> ft_redefinetrial (rather than ft_definetrial). However, you still need
> a trl matrix containing the trial definition. The easiest way to
> obtain this is to still call ft_definetrial as you used to do:
>
> cfg = [];
> cfg.dataset = 'dataset';
> cfg.trialdef.....
> % all the trial definition options go here
> cfgout = ft_definetrial(cfg);
>
> and then just save the output trl matrix:
>
> trl = cfgout.trl;
>
> now you can call ft_redefinetrial:
>
> cfg = [];
> cfg.trl = trl;
> data = ft_redefinetrial(cfg, data);
>
> and your data will be segmented.
>
> Hope this helps,
> Best,
>
> Eelke
>
>
> On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
> >
> > Dear all,
> >
> > Hello, my name is BJ Min from Korea.
> >
> > I am just a beginner in the Fieldtrip.
> > Anyway, with the help of tutorials, I could make grand average ERP of my
> > data finally.
> >
> > However, my question is about the order of preprocessing. According to
> the
> > tutorials, and examples, it looks the ft_definetrial step is the first,
> then
> > ft_preprocessing step is followed.  But, is there any method to flip
> these
> > two steps? What I want to do is preprocessing (filtering, notch
> filtering)
> > first then to use ft_definetrial sequentially.
> >
> > Best regards
> >
> >
> > BeomJun Min, M.D.
> >
> > Ph. D. student, Department of Medical System Engineering (DMSE)
> > Gwangju Institute of Science and Technology (GIST)
> > 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> > 500-712, Republic of Korea (South)
> > Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> > E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From eelke.spaak at donders.ru.nl  Thu May 16 10:07:47 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 10:07:47 +0200
Subject: [FieldTrip] Second-level one-sample t test with clustering
Message-ID: <CABPNLUqSFsDCGBZCMQa2ZzQ5TDxLjH2ynmCy5jYzkQMNGJddTA@mail.gmail.com>

Dear fellow FieldTrippers,

At the moment, I want to do second-level source statistics on my data
(but the question is the same for sensor statistics). I have computed
two-sample t-scores for each subject, between the trials in conditions
A and B.

Now, the appropriate per-voxel test to do across subjects would be a
one-sample t-test. This is rather easy to do, but I would like to use
cluster permutations to correct for multiple comparisons. My idea is
to generate fake data of all zeroes, the same size as my t-score
descriptive data per subject, and then do a paired-samples t test
between the real data and these zeroes (using ft_statfun_depsamplesT).
The voxel-level t statistic of data vs 0 should be the same as a
one-sample test of course. However, I am not sure the permutations of
the data would give me a valid distribution of the cluster statistic.

The test for the real data would be (comparing column 1 to column 2):
dataA 0
dataB 0
dataC 0
dataD 0

whereas a permutation might look like so:
0 dataA
dataB 0
dataC 0
0 dataD

Intuitively, I think this makes sense, as the t score of 0 vs data
will be the negative of t(data vs 0), I should get an appropriate
randomization distribution. But I'm not completely sure of this.

So, my question: does anyone see a problem with my approach? Or is
this a valid way of cluster-correcting a one-sample T test? If not,
what would be the right way to proceed?

Many thanks,
best,
Eelke


From e.maris at psych.ru.nl  Thu May 16 16:31:15 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 16:31:15 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
Message-ID: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>

Hi Eelke,

This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.

Eric


http://www.nphyscog.com/contact
----- fieldtrip-request at science.ru.nl schreef:
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
> 
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


From eelke.spaak at donders.ru.nl  Thu May 16 16:43:32 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 16:43:32 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>

Hi Eric,

Thanks, that's what I expected. However, that approach does not take
into account the different between-trial variances in the different
subjects. What would you recommend to take those into account?

Best,
Eelke

On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> Hi Eelke,
>
> This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.
>
> Eric
>
>
> http://www.nphyscog.com/contact
> ----- fieldtrip-request at science.ru.nl schreef:
>> Send fieldtrip mailing list submissions to
>> fieldtrip at science.ru.nl
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> or, via email, send a message with subject or body 'help' to
>> fieldtrip-request at science.ru.nl
>>
>> You can reach the person managing the list at
>> fieldtrip-owner at science.ru.nl
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of fieldtrip digest..."
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From e.maris at psych.ru.nl  Thu May 16 17:28:36 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 17:28:36 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
Message-ID: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>

Hi Eelke,

It all depends on the null hypothesis that you want to test. It's better
to discuss this with you in person or at some meeting with other
colleagues (for non-Donders Discussion List readers, Eelke and I work at
the same institute), because at the end it is a matter of deciding on what
is an interesting null hypothesis (both for you and the reviewers of your
paper).

I remember a discussion with a colleague about the same issue (using
first-level t-statistics at the second level), and he was quite unhappy
when I questioned this approach (by asking whether this is really the null
hypothesis he was interested in). At the end, it turned out that he also
had tried the standard approach (using only condition means) but this did
not result in a significant p-value.

Best,

Eric


> -----Original Message-----
> From: eelke.spaak at gmail.com [mailto:eelke.spaak at gmail.com] On Behalf Of
> Eelke Spaak
> Sent: donderdag 16 mei 2013 16:44
> To: Eric Maris; FieldTrip discussion list
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
> 
> Hi Eric,
> 
> Thanks, that's what I expected. However, that approach does not take
> into account the different between-trial variances in the different
> subjects. What would you recommend to take those into account?
> 
> Best,
> Eelke
> 
> On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> > Hi Eelke,
> >
> > This not valid. At the second level, you must use the condition means
> (per subject) as the observations about which you have a hypothesis and
> which therefore have to be permuted.
> >
> > Eric
> >
> >
> > http://www.nphyscog.com/contact
> > ----- fieldtrip-request at science.ru.nl schreef:
> >> Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> or, via email, send a message with subject or body 'help' to
> >> fieldtrip-request at science.ru.nl
> >>
> >> You can reach the person managing the list at
> >> fieldtrip-owner at science.ru.nl
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of fieldtrip digest..."
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From tim.curran at Colorado.EDU  Fri May 17 14:36:54 2013
From: tim.curran at Colorado.EDU (Tim Curran)
Date: Fri, 17 May 2013 06:36:54 -0600
Subject: [FieldTrip] Postdoctoral Position, Curran Lab,
	University of Colorado Boulder
In-Reply-To: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
	<022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
Message-ID: <AEF2F5AF-5A3C-4FA3-B17D-1429D57A46FC@colorado.edu>

Postdoctoral Position
Curran Lab, University of Colorado Boulder
Postdoctoral research position available in the lab of Tim Curran at the Department of Psychology & Neuroscience, University of Colorado Boulder to work on NIH-funded ERP studies of memory and perceptual expertise.  Desirable qualifications include research experience related to memory, perceptual expertise, ERP/EEG, and/or related domains.  Anticipated start date is summer or fall of 2013.  The University of Colorado is an Equal Opportunity/Affirmative Action employer. For further information contact, tim.curran at colorado.edu<mailto:tim.curran at colorado.edu>.  Applicants must submit a CV, a statement of research experience/interests, and a cover letter including email addresses for at least three referees to contact for recommendation letters if needed. Applications will be accepted electronically at https://www.jobsatcu.com/postings/63602
http://psych.colorado.edu/~tcurran/




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From ggonesc at upo.es  Fri May 17 17:45:40 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Fri, 17 May 2013 17:45:40 +0200
Subject: [FieldTrip] problem in connectivityanalysis
Message-ID: <9f89709b303dae2.51966cc4@upo.es>

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From jessetinker at gmail.com  Fri May 17 21:36:12 2013
From: jessetinker at gmail.com (Jesse Tinker)
Date: Fri, 17 May 2013 12:36:12 -0700
Subject: [FieldTrip] Segmentation Memory Issue
Message-ID: <CACKMsgNPvYLv33cxDr0fM-SJ3QR_8y1aY+93fBmGqMOT+Lo58Q@mail.gmail.com>

Hello Fieldtrippers!

This is my first post ever and I just want to say thank you to everyone for
promoting such a vibrant and supportive intellectual community.

I have an issue which seems so simple but I am somewhat stymied by: using
fieldtrip to accomplish the coregistration. The main points of my code are:

mri = ft_read_mri( );

mri = ft_volumerealign(cfg, mri);           % Mark fiducials

mrireslice = ft_volumereslice(cfg,mri);  %To apply the resultant
transformation matrix

segmentedmri  = ft_volumesegment(cfg, mrireslice);



First, if I skip the reslice step, everything works fine. However, if I do
the reslice and then try to segment, spm_preproc tries to create a 1.8 Tb
array. Although it bravely tries, my 24 Gb of RAM inevitably fails. The
analogous array for the unsliced mri is 2Mb.

I found this confusing as the quantity of information in the resliced image
is the exact same. I traced through all the coding and the computation that
fails is based on the transformation matrix of the MRI which, of course,
changes with the reslicing. I am happy to provide details of that but won't
at the moment.

My question, has anyone else encountered this or developed a workaround?

Very much appreciated,

Jesse
British Columbia Mental Health and Research Institute
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From mengtongxiao at gmail.com  Sat May 18 16:06:20 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sat, 18 May 2013 22:06:20 +0800
Subject: [FieldTrip] a .mat file about meg data do preprocessing
Message-ID: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>

Dear all,
I have a .mat file about meg data(102*98800，channel*time,channel is
'MEG0111','MEG0121'.....'M*1' );
Then I use eeglab read it,got .set file;I want use ft_timelockanalysis then
*cfg = [];
cfg.dataset     = 'megalpha.set';
cfg.grad=grad;
data_org        = ft_preprocessing(cfg)*
>grad =
     chanori: [102x3 double]
     chanpos: [102x3 double]
    chantype: {102x1 cell}
    chanunit: {102x1 cell}
     coilori: [510x3 double]
     coilpos: [510x3 double]
       label: {102x1 cell}
         tra: [102x510 double]
        unit: 'cm'
Warning: creating default channel names
> In fileio\private\read_eeglabheader at 53
  In ft_read_header at 572
  In ft_preprocessing at 343
processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005'
'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012'
'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019'
'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026'
'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033'
'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040'
'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047'
'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054'
'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061'
'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068'
'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075'
'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082'
'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089'
'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096'
'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
reading and preprocessing
reading and preprocessing trial 1 from 1
data_org =
           hdr: [1x1 struct]
         label: {102x1 cell}
          time: {[1x98800 double]}
         trial: {[102x98800 double]}
       fsample: 1037
    sampleinfo: [1 98800]
           cfg: [1x1 struct]

*cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'M*1';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);*
timelock =
       avg: [0x98800 double]
       var: [0x98800 double]
      time: [1x98800 double]
       dof: [0x98800 double]
     label: {0x1 cell}
    dimord: 'chan_time'
       cov: []
       cfg: [1x1 struct]

there is no error displyed in command window but the timlock is empty,why?

thanks for you help,
best,
xiao
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From eeguser at hotmail.com  Sat May 18 18:21:48 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 19:21:48 +0300
Subject: [FieldTrip] computing threshold for PLV
Message-ID: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>

Dear FT Experts,



I have calculated PLV for a set of EEG data from 5 different patients. 
Now I want to convert the PLV matrix of each patient into a binary 
matrix. For this I need a threshold PLV value below which I can assume 
the phase locking is zero.

My question is, how do I compute this threshold. I know hard 
thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), 
but I guess it is not a very good option.



Can somebody suggest a better and robust (statistical) way of determining the threshold ?  		 	   		  
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From sherrykhan78 at gmail.com  Sat May 18 18:37:28 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 12:37:28 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>

You can randomly shift in time the epochs, to compute null-distribution,
and then threshold at some  p-value say p < 0.01, you can even correct
for multiple comparison in space and time using  this principle.



On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com>wrote:

> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Sat May 18 19:25:50 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 18 May 2013 19:25:50 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
Message-ID: <4EDB7A1D-4484-454B-A9CE-5AE826E2AE98@donders.ru.nl>

Dear all,

Note that shuffling the epochs with respect to one another (where for one of the channels in the pair the epoch order stays fixed) usually yields a too liberal null-distribution. The reason is that the shuffling also destroys all structure in the data that is due to electromagnetic field spread. So, even if an observed pattern of PLV is caused by a single underlying neural generator, shuffling the epochs most likely makes this pattern 'significant'. However, it still does not reflect physiological interaction between sources.

Best,
Jan-Mathijs


On May 18, 2013, at 6:37 PM, Sheraz Khan wrote:

> You can randomly shift in time the epochs, to compute null-distribution, and then threshold at some  p-value say p < 0.01, you can even correct for multiple comparison in space and time using  this principle.
> 
> 
> 
> On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com> wrote:
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From smoratti at psi.ucm.es  Sat May 18 20:11:11 2013
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Sat, 18 May 2013 20:11:11 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,

Stephan



________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From eeguser at hotmail.com  Sat May 18 21:42:05 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 22:42:05 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
Message-ID: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>




Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es
Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,
You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
Hope that helps,
Stephan



________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain
and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? _______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  
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From sherrykhan78 at gmail.com  Sun May 19 01:55:07 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 19:55:07 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
Message-ID: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>

Most of the previois discussion targeted toward event related plv for
continous data may be look at Hipp 2012 Nature Neuroscience orthogonal
correlation paper
On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:

>  Dear FT Experts
>
> Thank you for your inputs. I should add here that I have continuous EEG
> data (so effectively single trial). The way I am computing PLV is by
> dividing my data into windows of 2 seconds each and computing PLV for each
> window and then I finally average the PLV values of all the windows.
>
> So when we talk of shuffling trials, in my case should i consider each of
> 2 second window as a trial ? Sorry if this sounds stupid as I am new to
> this kind of analysis.
>
> ------------------------------
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
>
> Dear Sheraz,
>
> You might consult the following article: Lachaux, J. P. et al. 1999.
> Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208.
> In principle you have to create surrogate data that represent the null
> hypothesis that there is no phase locking between your electrodes, sources,
> etc. Then you create hundreds or thousands of surrogate data sets and
> calculate each time you PLV. That way you create a distribution of your PLV
> values under the Null hypothesis. Then you check in what percentile your
> observed PLV lies (e. g. if its beyond the 95% percentile you would reject
> the Null hypothesis).
>
> Hope that helps,
>
> Stephan
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
>
> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________ fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mengtongxiao at gmail.com  Sun May 19 09:32:37 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sun, 19 May 2013 15:32:37 +0800
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ@mail.gmail.com>

Dear all，
when I use ft_timelockanalysis like follow,there are some mistake.

cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'all';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);
the input is raw data with 102 channels and 1 trials
averaging trials
averaging trial 1 of 1

the call to "ft_timelockanalysis" took 5 seconds
??? Error using ==> mxSerialize
Error during serialization of (null)

Error in ==> ft_postamble_provenance at 76
  cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
  cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
  'UniformOutput', false), 'UniformOutput', false);

Error in ==> ft_postamble at 55
  evalin('caller', ['ft_postamble_' cmd]);
Error in ==> ft_timelockanalysis at 401
ft_postamble provenance timelock

Thank you so much for your help!!
xiao
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From eeguser at hotmail.com  Sun May 19 09:54:21 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sun, 19 May 2013 10:54:21 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>,
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>,
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <BLU176-W121107702786A05888CC94B9AE0@phx.gbl>

So, does it mean that PLV method does not make much sense for continuous data ? To be more specific, I am trying to investigate synchrony from epileptic EEG recordings.

Date: Sat, 18 May 2013 19:55:07 -0400
From: sherrykhan78 at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper

On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:







Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.

So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es

Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,
Stephan




________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/


Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain

and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982



El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.

My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From politzerahless at gmail.com  Sun May 19 14:27:37 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 19 May 2013 07:27:37 -0500
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CAJT2k_8-ndM9giikDhgz4qem475i-bf76MkE=_BSX1MOAuy+nQ@mail.gmail.com>

Hello Xiao,

I don't know if this is what is causing the error, but I did notice that
your dataset apparently only has one trial. Usually ft_timelockanalysis()
would take a dataset consisting of multiple trials and average them; you
may need to run ft_preprocessing() to divide your dataset into trials.

Best,
Steve



>
> Message: 1
> Date: Sun, 19 May 2013 15:32:37 +0800
> From: ?? <mengtongxiao at gmail.com>
> To: fieldtrip <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] help about ft_timelockanalysis
> Message-ID:
>         <
CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ at mail.gmail.com>
> Content-Type: text/plain; charset="gb2312"
>
> Dear all?
> when I use ft_timelockanalysis like follow,there are some mistake.
>
> cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'all';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);
> the input is raw data with 102 channels and 1 trials
> averaging trials
> averaging trial 1 of 1
>
> the call to "ft_timelockanalysis" took 5 seconds
> ??? Error using ==> mxSerialize
> Error during serialization of (null)
>
> Error in ==> ft_postamble_provenance at 76
>   cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
>   cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
>   'UniformOutput', false), 'UniformOutput', false);
>
> Error in ==> ft_postamble at 55
>   evalin('caller', ['ft_postamble_' cmd]);
> Error in ==> ft_timelockanalysis at 401
> ft_postamble provenance timelock
>
> Thank you so much for your help!!
> xiao
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From stephanie.ries at berkeley.edu  Mon May 20 06:32:49 2013
From: stephanie.ries at berkeley.edu (Stephanie Kathleen Ries-cornou)
Date: Sun, 19 May 2013 21:32:49 -0700
Subject: [FieldTrip] dipole modeling using field trip
Message-ID: <CAHckMuRtCLu8LGLxXX57ktWhx3DbNK2m5P4Oy9R5047GPuChFA@mail.gmail.com>

Hi,

I would like to know if it possible to reject horizontal eye movements from
scalp EEG signal using equivalent dipole modeling in Fieldtrip. I have
tried doing this using ICA but it was not possible to identify a component
reflecting saccades for all subjects. Has anyone ever done this? If yes,
any suggestion would be great!

I am trying to learn about source reconstruction using two dipoles thinking
this might be a good start and have started going through the tutorial. I
got the following error messages:

>> data = ft_dipolesimulation(cfg);
using headmodel specified in the configuration
using gradiometers specified in the configuration
computing simulated data
Error using  .*
Matrix dimensions must agree.

Error in ft_dipolesimulation (line 203)
    simulated.trial{trial}  = simulated.trial{trial} + lf(:,i:3:end) * ...

This was fixed when I removed the "..." but then I got this message:

Error using ft_fetch_vol (line 76)
no headmodel specified

Error in prepare_headmodel (line 51)
vol = ft_fetch_vol(cfg, data);

Error in ft_dipolesimulation (line 106)
[vol, sens, cfg] = prepare_headmodel(cfg, []);

The "vol" parameter is defined, so I do not know where the error is coming
from.

Best,

Stephanie


Stephanie Ries, PhD
Knight Lab - Helen Wills Neuroscience Institute
University of California at Berkeley
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From ggonesc at upo.es  Mon May 20 09:28:55 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Mon, 20 May 2013 09:28:55 +0200
Subject: [FieldTrip] problem with PLV and ImC computing
Message-ID: <1115d37d2b1643b.5199ecd7@upo.es>

I'm re-sending this, becasue searching at the fieldtrip archives, I've notice that my message was scrubbed...


Dear Fieltrip experts,

I  have my continuous data imported to fieldtrip with matlab, I'm looking  for performing connectivity analysis between pairs of sensors, I have  succed as:
data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels and 2000 samples
data.label {59x1};
data.time {1xNepochs};

then, calculate only the FFT of all sensors as:
cfg=[];
cfg.output='fourier';
cfg.method='mtmfft';
cfg.taper='hanning';
cfg.foilim=[8.5 9.5];
cfg.tapsmofrq=0;
cfg.trials='all';
cfg.keeptrials='yes';
cfg.channel='all';
fourier=ft_freqanalysis(cfg, data)
as output I get:
dimord = 'rpttap_chan_freq'
freq= [1x9]
fourierspctrm=[7x59x9 double]

Then compute the imaginary part of coherency as:
cfg=[];
cfg.method ='cohe';
cfg.complex='imag';
cfg.channelcbm={'all' 'all'};
coher = ft_connectivityanalysis (cfg, fourier)
as output get: 
dimord='chan_chan_freq';
cohspctrm=[59x59x9 double];
dof=7;

I have two main questions:

A)  As you see, this makes an average over the epochs of each channel, and  not over the samples (which in this case are the 9 frequencies of the  FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for each epoch (repetition) on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt, Is this possible?



B)  Another question I have is: for the Imaginary part of Coherence is not  necessary to compute the cross-spectrum with 'powandcsd', only the FFT,  but for the PLV, PPC or WPLI is that way too?



Many thanks in advanced,
Gabriel.
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From jan.schoffelen at donders.ru.nl  Tue May 21 08:24:48 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 21 May 2013 08:24:48 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <EF65D844-0661-44BA-8369-78933B7102A8@donders.ru.nl>

Hi all,

PLV is in principle a perfectly valid method to investigate synchrony, also in continuous data. Jörg (Hipp)'s paper introduces a connectivity metric that is insensitive to the effects of electromagnetic field spread, but it is a measure whose relationship to synchrony is hard to interpret; it quantifies amplitude envelope correlations after explicit removal of the instantaneous mixing, and does not quantify the consistency of phase relationships, as does PLV. If you are after interpreting the connectivity in terms of synchrony, you could look into using the imaginary part of coherency, or the weighted phase lag index, although neither of these methods are easy in their interpretation, either.

Best,
Jan-Mathijs

On May 19, 2013, at 1:55 AM, Sheraz Khan wrote:

> Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper
> 
> On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:
> Dear FT Experts
> 
> Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
> 
> So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.
> 
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
> 
> Dear Sheraz,
> 
> You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
> 
> Hope that helps,
> 
> Stephan
> 
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
> 
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From jm.horschig at donders.ru.nl  Tue May 21 08:31:22 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:31:22 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <9f89709b303dae2.51966cc4@upo.es>
References: <9f89709b303dae2.51966cc4@upo.es>
Message-ID: <519B14BA.9030908@donders.ru.nl>

Dear Gabriel,

> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?

No. You should think of coherence more as a measure for the consistency 
of the phase relation between channels across trials, so coherence is 
just not defined per trial,neither would it make sense to compute 
coherence for a single trial.

> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
I see some terminology issues here. Let me try to explain in a simple 
(aka least-mathematical I can think of) way:

For all these connectivity measures, we need the phase information from 
the Fourier transform (FFT) to compute the cross-spectral density matrix 
(CSD). The CSD can be regarded as the equivalent in the frequency domain 
to the covariance matrix in the time domain, thus it is a measures how a 
certain channels activity is co-modulated with another channels activity 
(for a particular frequency) - makes pretty much sense to make use of 
this when computing connectivity, right? :)
As you might know, a Fourier transform returns complex numbers, where 
the imaginary part of this number contains phase information. When 
calling ft_freqanalysis, you can decide if it shall only return the 
(squared) real part of the frequency spectrum (cfg.output='pow'), or 
instead the full CSD (cfg.output = 'powandcsd'). Alternatively, you can 
also let ft_freqanalysis return the raw Fourier coefficients 
(cfg.output='fourier'). From the Fourier coefficients, however, you can 
easily obtain the CSD or the power spectrum basically by multiplication 
the Fourier matrix with itself (transposed). All of these measures 
quantify the phase relation between channels across trials, and as phase 
information is coded in the imaginary part of the fourier output, thus 
for connectivityanalysis you need the CSD which can be obtained either 
by 'powandcsd' or by 'fourier'.

I hope that somehow clarifies your questions.

Best,
Jörn

On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> Dear Fieltrip experts,
>
> I have my continuous data imported to fieldtrip with matlab, I'm 
> looking for performing connectivity analysis between pairs of sensors, 
> I have succed as:
> data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels 
> and 2000 samples
> data.label {59x1};
> data.time {1xNepochs};
>
> then, calculate only the FFT of all sensors as:
> cfg=[];
> cfg.output='fourier';
> cfg.method='mtmfft';
> cfg.taper='hanning';
> cfg.foilim=[8.5 9.5];
> cfg.tapsmofrq=0;
> cfg.trials='all';
> cfg.keeptrials='yes';
> cfg.channel='all';
> fourier=ft_freqanalysis(cfg, data)
> as output I get:
> dimord = 'rpttap_chan_freq'
> freq= [1x9]
> fourierspctrm=[7x59x9 double]
>
> Then compute the imaginary part of coherency as:
> cfg=[];
> cfg.method ='cohe';
> cfg.complex='imag';
> cfg.channelcbm={'all' 'all'};
> coher = ft_connectivityanalysis (cfg, fourier)
> as output get:
> dimord='chan_chan_freq';
> cohspctrm=[59x59x9 double];
> dof=7;
>
> I have two main questions:
>
> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?
>
>
>
> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
>
>
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From jm.horschig at donders.ru.nl  Tue May 21 08:39:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:39:14 +0200
Subject: [FieldTrip] a .mat file about meg data do preprocessing
In-Reply-To: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
References: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
Message-ID: <519B1692.3080101@donders.ru.nl>

Dear Xiao,

Somehow your channel names seem to not be recognized by FieldTrip, and 
then it reverts to default channel names (chan001, chan002, ...). You 
will see that data_org.label will have those channel labels. 
Subsequently, you define in the cfg for timelockanalysis channel names 
that are not in your data (your channels are called chanXXX, not MEGXXXX 
now), and FieldTrip thus does not perform the operation on any channel.
I don't know much about EEGLAB and how it is integrated with FieldTrip - 
there should be an eeglab2fieldtrip function though in 
fieldtrip/external/eeglab. Maybe you can try this, or maybe someone else 
here knows why your channel labels do not get copied over to FieldTrip 
correctly.

Good luck :)
Best,
Jörn

On 5/18/2013 4:06 PM, ?? wrote:
> Dear all,
> I have a .mat file about meg data(102*98800,channel*time,channel is 
> 'MEG0111','MEG0121'.....'M*1' );
> Then I use eeglab read it,got .set file;I want use ft_timelockanalysis 
> then
> /cfg = [];
> cfg.dataset     = 'megalpha.set';
> cfg.grad=grad;
> data_org        = ft_preprocessing(cfg)/
> >grad =
>      chanori: [102x3 double]
>      chanpos: [102x3 double]
>     chantype: {102x1 cell}
>     chanunit: {102x1 cell}
>      coilori: [510x3 double]
>      coilpos: [510x3 double]
>        label: {102x1 cell}
>          tra: [102x510 double]
>         unit: 'cm'
> Warning: creating default channel names
> > In fileio\private\read_eeglabheader at 53
>   In ft_read_header at 572
>   In ft_preprocessing at 343
> processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005' 
> 'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012' 
> 'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019' 
> 'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026' 
> 'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033' 
> 'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040' 
> 'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047' 
> 'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054' 
> 'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061' 
> 'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068' 
> 'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075' 
> 'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082' 
> 'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089' 
> 'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096' 
> 'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
> reading and preprocessing
> reading and preprocessing trial 1 from 1
> data_org =
>            hdr: [1x1 struct]
>          label: {102x1 cell}
>           time: {[1x98800 double]}
>          trial: {[102x98800 double]}
>        fsample: 1037
>     sampleinfo: [1 98800]
>            cfg: [1x1 struct]
> /cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'M*1';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);/
> timelock =
>        avg: [0x98800 double]
>        var: [0x98800 double]
>       time: [1x98800 double]
>        dof: [0x98800 double]
>      label: {0x1 cell}
>     dimord: 'chan_time'
>        cov: []
>        cfg: [1x1 struct]
> there is no error displyed in command window but the timlock is empty,why?
> thanks for you help,
> best,
> xiao
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From zriouil.imane at gmail.com  Tue May 21 10:18:58 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 21 May 2013 10:18:58 +0200
Subject: [FieldTrip] ft_read_event
Message-ID: <CABu=cRdhOYn=oSy0cHADOvqgWnCR3ui5cLwy9FUkpVz7KGKK_A@mail.gmail.com>

Hello,

i have a problems in ft_read_event. if you help me please


I try to follow all instructions on the tutorial: 'Preprocessing and
analysis of spike and local field potential data'

>> spike=ft_read_spike(filename)

spike =

        label: {'Elec_1_Neuron_1'  'Elec_2_Neuron_1'  'Elec_3_Neuron_1'}
    timestamp: {[1x20246 int32]  [1x9126 int32]  [1x74291 int32]}
     waveform: {[0x20246 double]  [0x9126 double]  [0x74291 double]}
         unit: {[1x20246 double]  [1x9126 double]  [1x74291 double]}
          hdr: [1x1 struct]
       dimord: '{chan}_lead_time_spike'

>> header=ft_read_header(filename)

header =

                nChans: 94
                    Fs: 781.2500
              nSamples: 862310
               nTrials: 1
           nSamplesPre: 0
                 label: {94x1 cell}
        FirstTimeStamp: 70433310
    TimeStampPerSample: 32
                  orig: [1x1 struct]
              chantype: {94x1 cell}
              chanunit: {94x1 cell}

>>cfg=[];
cfg.dataset=filename;
cfg.trialfun='trialfun_stimon_samples';
cfg=ft_definetrial(cfg)

evaluating trialfunction 'trialfun_stimon_samples'

??? Error using ==> fseek
Not enough input arguments.

Error in ==> read_nex_event at 49
status = fseek(fid,hdr.varheader(mrkvarnum).offset,'bof');

Error in ==> ft_read_event at 1528
    event = read_nex_event(filename);

Error in ==> trialfun_stimon_samples at 3
event = ft_read_event(cfg.dataset);

Error in ==> ft_definetrial at 157
    trl   = feval(cfg.trialfun, cfg);
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From ggonesc at upo.es  Tue May 21 17:52:21 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Tue, 21 May 2013 17:52:21 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <519B14BA.9030908@donders.ru.nl>
References: <9f89709b303dae2.51966cc4@upo.es> <519B14BA.9030908@donders.ru.nl>
Message-ID: <1348f6433edc26f9.519bb455@upo.es>

Thank you so much for your answer Jörn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from  -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
 [0.9323  0.3679  0.8629  1.6436  0.6404  1.8782  0.1139] 
val(:,:,1,2)
 [0.8509-0.1555i  0.2507-0.1066i  0.8173-0.0290i  1.4328-0.2427i  0.5457-0.0500i  1.6505-0.0161i  0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
 [1  1  1  1  1  1  1] 
val(:,:,1,2)
 [0.9694-0.2133i  0.7011-0.3564i  0.9951-0.0104i  0.9014-0.3481i  0.9781-0.0819i  0.9982-0.0046i  0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        Jörn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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From antony.passaro at gmail.com  Tue May 21 18:13:28 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Tue, 21 May 2013 12:13:28 -0400
Subject: [FieldTrip] Subject-level Statistics on mvar connectivity measures
Message-ID: <CAB8wAYS-F9FiW72edUz_s84dSuobXXA6nEwZYwWEhW5bL=ggkg@mail.gmail.com>

Hi everyone,

I have had some success processing the subject-level differences between
two conditions for phase-based measures such as coherence and plv but I was
wondering what the approach would be for the directed or mvar-based
measures such as dtf, granger, or pdc? Since there are no trials to shuffle
as you normally would for the phase-based connectivity measures, what would
be the optimal statistical approach? I thought about shuffling the trials
and recomputing the mvar over and over again for each condition as a
simulation but this doesn't seem practical as it would be too
computationally intensive.

Thank you,
-Tony
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From 13681530640 at 139.com  Wed May 22 04:20:45 2013
From: 13681530640 at 139.com (WangJing)
Date: Wed, 22 May 2013 10:20:45 +0800 (CST)
Subject: [FieldTrip] question About head model
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>




Hi


I am a freshman about field trip.


I am trying to build the forward model. but my mri data is different from the data in the tutorial. So I don't know how to bulid the head model. I use the date which is from the paper "Open Database of Epileptic EEG with MRI and Postoperational Assessment of Foci—a Real World Verification for the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans with morphologic substrate of the epilepsy (mostly cortical dysplasias, dysplastic tumors etc.). In some cases there is also a scan with the gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T scanner. The data is stored in the Digital Imaging and Communications in Medicine (DICOM) format. The name of the scan’s folder indicates its weighting.The scans have the following resolutions: T1: 512 × 512 pixels, pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels, pixel spacing 0.9375 mm,slice thickness 2.5 mm.


In the tutorial,the mri data stored in only one file, while the data which I used have many files, I don't know how to process. who can help me,Thanks1





Thanks very much!


Best Reagards


Jing Wang















--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-21 23:59:18
Subject：fieldtrip Digest, Vol 30, Issue 29

Send fieldtrip mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of fieldtrip digest..."


Today's Topics:

   1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)


----------------------------------------------------------------------

Message: 1
Date: Tue, 21 May 2013 17:52:21 +0200
From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] problem in connectivityanalysis
Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
Content-Type: text/plain; charset="iso-8859-1"

Thank you so much for your answer J?rn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139] 
val(:,:,1,2)
?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
?[1? 1? 1? 1? 1? 1? 1] 
val(:,:,1,2)
?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        J?rn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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------------------------------

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 30, Issue 29
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From johanna.zumer at donders.ru.nl  Wed May 22 09:30:17 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Wed, 22 May 2013 09:30:17 +0200
Subject: [FieldTrip] question About head model
In-Reply-To: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
	<2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
Message-ID: <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w@mail.gmail.com>

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci—a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan’s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 × 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-21 23:59:18
> Subject：fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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>
> End of fieldtrip Digest, Vol 30, Issue 29
> *****************************************
>
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From mushfa.yousuf at googlemail.com  Wed May 22 12:13:56 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Wed, 22 May 2013 12:13:56 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <5190AEAA.3020301@donders.ru.nl>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
Message-ID: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>

Hello Jörn;

I have calculated an indiviual leadfield for both EEG and MEG. The
structure of EEg and MEG shows the following variable

grid_meg =

        xgrid: [1x20 double]
        ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
        zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
          dim: [20 17 16]
          pos: [5440x3 double]
         unit: 'cm'
       inside: [1x3177 double]
      outside: [1x2263 double]
          cfg: [1x1 struct]
    leadfield: {1x5440 cell}


grid_eeg =

        xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
        ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
        zgrid: [2 3 4 5 6 7 8 9 10 11]
          dim: [16 13 10]
          pos: [2080x3 double]
         unit: 'cm'
       inside: [1x1331 double]
      outside: [1x749 double]
          cfg: [1x1 struct]
    leadfield: {1x2080 cell}


Can you please give me a rough idea that how to concatenate the variables
from both structure ?


Thank you

Regards ;

Mushfa Yousuf


On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Mushfa,
>
> I think you have to compute two leadfield matrices, one for EEG (elec) and
> one for MEG (grad), and then concatenate these (and make sure that the
> order of sensors won't get mixed up anywhere, because  sourceanalysis just
> expects the leadfield matrix to be ordered like your data. If that's not
> the case, you either encounter the previous error you described or (if the
> number of channels matches, but order is mixed up) it will just return
> wrong source estimated activity.
>
> Best,
> Jörn
>
>
> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>
> Hello;
>
>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
> of 'elec' while calculating the Leadfield.
>
>  Actually I am trying to calculate Combined source reconstruction from
> both EEG and MEG sensors.
>
>  Do you have any idea, how to define both elec and grad definition  while
> calculating first forward then inverse solution.
>
>  Because in a fieldtrip either you can defined elec or grad at one time.
>
>
>  Regards;
>
>
>  Mushfa Yousuf
>
>  Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>
>> Hi Mushfa,
>>
>>  My guess is that the channels that have you used to compute .csdspctrm
>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>> freqPost.label, does that solve it?
>>
>>  Cheers,
>> Johanna
>>
>>
>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>
>>>   Hello Fieldtrippers,
>>>
>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>
>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>> lead field successfully.
>>>
>>>  For the inverse solution using 'dics' method, I wrote the following
>>> syntax
>>>
>>>
>>>
>>>
>>>
>>>   cfg              = [];
>>>   cfg.method       = 'dics';
>>>  cfg.frequency    = 130;
>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>  cfg.grid         = grid;
>>>  cfg.vol          = vol;
>>>
>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>  and I have received the following error:
>>>
>>>
>>>  ??? Error using ==> mtimes
>>> Inner matrix dimensions must agree.
>>>
>>>  Error in ==> beamformer_dics at 314
>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>         leadfield
>>>
>>>  Error in ==> ft_sourceanalysis at 595
>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>
>>>  Error in ==> newCode at 214
>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>
>>>
>>>  Any help would be appreciated.
>>>
>>>
>>>  Regards;
>>>
>>>
>>>  Mushfa Yousuf
>>>
>>>  Neurozentrum,
>>> Universitätsklinikum Schleswig-Holstein,
>>> Campus Kiel (UKSH), Deutschland
>>>
>>>
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From ggonesc at upo.es  Wed May 22 19:36:08 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 22 May 2013 19:36:08 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <596f90904ed40d3b.519d1e28@upo.es>

Dear Fieldtrip experts,

I finally understood how fieltrip computes the plv, so, my last e-mail has no sense now. Given say this, I have one question:

I've followed the fieltrip implementation to compute the PLV, and found that it takes the CSD, and normalizes it for the amplitude of the replicates, this is to divide the csd by the absolute of the same csd, then makes an average of the normalized csd's, to finally take the absolute of the average-normalized-csd as the PLV.  I think it can be summarized to something like, PLV = |E( csd/abs(csd) )|

I do not see the similarity with the clasical formula that appears in the papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the cross-spectrum, and E|.| is the expected value; I cannot find the relationship between the implementation on fieltrip of the PLV and the formula on the papers.

Can anyone explain to me the relationship between the two approaches? or tell me the paper where it is explained?

Many thanks in advanced,
Gabriel

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From 13681530640 at 139.com  Thu May 23 03:38:08 2013
From: 13681530640 at 139.com (WangJing)
Date: Thu, 23 May 2013 09:38:08 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>


Dear Johanna,


 


    Thank you for your suggestion. 


    1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is t1_vibe_traGAD-5. which one is best?
    2.when I convert MRI from DICOM into CTF format,the vitamin E marker didn't be found. what can I do?


 


Best Regards,


Jing Wang














--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-22 15:33:13
Subject：fieldtrip Digest, Vol 30, Issue 31

Send fieldtrip mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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Today's Topics:

   1. Re: question About head model (Johanna Zumer)


----------------------------------------------------------------------

Message: 1
Date: Wed, 22 May 2013 09:30:17 +0200
From: Johanna Zumer <johanna.zumer at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] question About head model
Message-ID:
<CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci?a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan?s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> To?fieldtrip<fieldtrip at science.ru.nl>
> Date?2013-05-21 23:59:18
> Subject?fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 30, Issue 29
> *****************************************
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From eelke.spaak at donders.ru.nl  Thu May 23 10:09:17 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 23 May 2013 10:09:17 +0200
Subject: [FieldTrip] connectivity problem
In-Reply-To: <596f90904ed40d3b.519d1e28@upo.es>
References: <596f90904ed40d3b.519d1e28@upo.es>
Message-ID: <CABPNLUpec0sp=o5TWDKcU-PgQqGa_ROVSQ73uWWJbkwMHtEotA@mail.gmail.com>

Dear Gabriel,

If I am not mistaken, the classical formula in Lachaux et al. (1999)
Human Brain Mapping is PLV = 1/N * | sum(exp(i * theta(t,n))) | . This
is almost the same as the formula you mention, except, importantly,
that theta is the phase difference between two signals, so the angle
of the CSD, and *not* the imaginary part.

Note furthermore that 1 * exp(i*angle(z)) is equal to z/abs(z) for any
complex z, and you see that the implementation computes the classical
formula.

Hope this helps,
Best,
Eelke

On 22 May 2013 19:36, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear Fieldtrip experts,
>
> I finally understood how fieltrip computes the plv, so, my last e-mail has
> no sense now. Given say this, I have one question:
>
> I've followed the fieltrip implementation to compute the PLV, and found that
> it takes the CSD, and normalizes it for the amplitude of the replicates,
> this is to divide the csd by the absolute of the same csd, then makes an
> average of the normalized csd's, to finally take the absolute of the
> average-normalized-csd as the PLV.  I think it can be summarized to
> something like, PLV = |E( csd/abs(csd) )|
>
> I do not see the similarity with the clasical formula that appears in the
> papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the
> cross-spectrum, and E|.| is the expected value; I cannot find the
> relationship between the implementation on fieltrip of the PLV and the
> formula on the papers.
>
> Can anyone explain to me the relationship between the two approaches? or
> tell me the paper where it is explained?
>
> Many thanks in advanced,
> Gabriel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jeremiemattout at yahoo.fr  Thu May 23 10:19:09 2013
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Thu, 23 May 2013 09:19:09 +0100 (BST)
Subject: [FieldTrip] DCM for fMRI and EEG/MEG course - Seattle June 2013
Message-ID: <1369297149.1995.YahooMailNeo@web133005.mail.ir2.yahoo.com>

Dear Colleagues, We are pleased to announce DCM for fMRI and MEG/EEG, an intermediate-level, 3-day workshop designed for investigators having familiarity with the fundamental principles of fMRI or MEG/EEG data acquisition and analysis.. It will be held at the University of Washington in Seattle, WA from JUN 21-23, 2013, immediately following the OHBM 2013 meeting. This course will bring together investigators interested in using quantitative biophysical models to identify brain connectivity and dynamics using the tools of imaging neuroscience, including fMRI, EEG/MEG, and LFP. Presentations will include:
overviews of brain connectivity methods and models
descriptions of specifics of DCM for fMRI, EEG/MEG and LFP data
explanations of Bayesian analysis at both single-subject and group levels
explorations of DCM experimental design and other advanced issues
Each afternoon will include a laboratory session, in which participants will gather in small groups to work with the faculty through the stages of analyzing data from example experiments. Further details can be found at: http://www.neurometrika.org/DCM2013 Kind Regards, Tom Zeffiro, Jean Daunizeau & Jeremie Mattout
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From marianapbranco1 at gmail.com  Thu May 23 10:25:45 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 10:25:45 +0200
Subject: [FieldTrip] Online preprocessing
Message-ID: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From jm.horschig at donders.ru.nl  Thu May 23 11:37:59 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 11:37:59 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
Message-ID: <519DE377.1020805@donders.ru.nl>

Hi Mariana,

On 5/23/2013 10:25 AM, Mariana Branco wrote:
> Hello,
>
> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
> My questions are:
> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?

no, you should use ft_read_data directly. The way to go is to check the 
header of your buffer for new events using ft_read_event. Upon detection 
of a relevant trigger, you need to use the returned event sample to 
compute your beginning and endsample manually (this is what 
ft_definetrial, or more precisely, your trialfun, usually does).  Then 
you can use ft_read_data to read data from the buffer into memory. 
ft_read_data returns a datamatrix that can be used to create your 
data.trial field. Also, you need to manually create the rest of the 
data-structure.
> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
It is definitely possible, once you converted the matrix to a regular 
fieldtrip structure. However, since it is about speed in online 
processing, you can think about using low-level functions of FieldTrip 
directly. Note that for resampling, you can also set up the shared 
memory (eg. acq2ftx) such that is downsamples right from the start.

> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
Do not use Welch's method, use another function. I don't know about this 
particular example function, but I think you would greatly benefit from 
finding out where the error is yourself. Note that online streaming od 
data *is* complicated and requires *you* to have knowledge about this.
> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
It should be an example, yes. Usually, there should be, as explained 
above, some ft_read_event statement to read the trigger value(s). In 
that particular example, the trialfun is used rather than ft_read_data 
directly, but trialfun is basically a wrapper around ft_read_data. Also, 
in that example a bunch of trials is read in, not just one. The thing 
you need to do to adjust this is to filter out the event structure such 
that only in case of the trigger of interest some data processing is 
done (you can use ft_filter_event for this).

My best advise for you is to read all (most) example functions and 
adjust them so that they run in your lab. Then sketch a flow diagram how 
triggers/data will be sent and read, try to implement this yourself (by 
copy&pasting relevant parts out of the example functions). If you have 
specific questions, feel free to always ask, but as this stage (please 
excuse my bluntnessI think you do not really know what needs to be done. 
I could write a lot about this, but I think you will benefit more if you 
first try yourself (especially because I do not know how your lab is set 
up and how things needs to be adjusted). But, as just said, feel free to 
write again when you have other questions.

Good luck!
Best,
Jörn

>
> I am sorry for all the questions.

No problem, no  way to know everything :)

> Regards,
>
> Mariana Branco
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From marianapbranco1 at gmail.com  Thu May 23 11:57:27 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 11:57:27 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <519DE377.1020805@donders.ru.nl>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
Message-ID: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>

Hi Jörn,

Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.

Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. 
In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?

Thank you again for all the advices, I will definitely pose more question in the future.

Mariana Branco

On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:

> Hi Mariana,
> 
> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>> Hello,
>> 
>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>> My questions are:
>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
> 
> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
> 
>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
> 
> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
> 
> Good luck!
> Best,
> Jörn
> 
>> 
>> I am sorry for all the questions.
> 
> No problem, no  way to know everything :)
> 
>> Regards,
>> 
>> Mariana Branco
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
> 
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
> 
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
> 
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From jm.horschig at donders.ru.nl  Thu May 23 12:08:33 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 12:08:33 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
	<B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
Message-ID: <519DEAA1.5030402@donders.ru.nl>

Hi Mariana,

ft_preprocessing demeans by the whole time window, in your 0s to 5s. The 
baseline window you specify depends on the time axis itself, if it goes 
from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, 
then you need to define [-3 0]. Time is relative :)
Also, please check ft_timelockbaseline. But such a simple thing as 
subtracting a number from a matrix can also easily be done without 
relying on a fieldtrip function :)

Best,
Jörn

On 5/23/2013 11:57 AM, Mariana Branco wrote:
> Hi Jörn,
>
> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.
>
> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial.
> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?
>
> Thank you again for all the advices, I will definitely pose more question in the future.
>
> Mariana Branco
>
> On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
>
>> Hi Mariana,
>>
>> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>>> Hello,
>>>
>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>>> My questions are:
>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
>>
>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
>>
>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
>>
>> Good luck!
>> Best,
>> Jörn
>>
>>> I am sorry for all the questions.
>> No problem, no  way to know everything :)
>>
>>> Regards,
>>>
>>> Mariana Branco
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From andmib at gmail.com  Thu May 23 16:29:07 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Thu, 23 May 2013 10:29:07 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
Message-ID: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>

Hello all,

I am new to FieldTrip, so this is a very basic question I was hoping
someone might know an answer to.

I am using ft_read_data to read the first EPI volume after dummy scans are
thrown out. I want to write this volume to a .nii file to my disk. For some
reason, I am unable to figure out the correct structure that ft_volumewrite
wants. Using the output from ft_read_data ('dat') does not seem to work.
Does anybody have any suggestions?

[ For a longer explanation of exactly what I am aiming to do, in case you
have any suggestions: I have ROI that is defined in Talairach space. This
is the ROI I would like to pull my real-time data from for each subject in
my study. To do this, I plan to register a talairach template brain to
individual subject-space, and then apply that transformation to my ROI so
that it is in subject space. I was going to simply write out the subject's
EPI to an .nii file, and then run SPM's co-registration step which allows
for a 'child dataset' to be set (my ROI), with the source file being the
template, and the reference being the individual ROI].

Thanks
Andrew
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From ggonesc at upo.es  Thu May 23 16:46:53 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Thu, 23 May 2013 16:46:53 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <cade69b25ef8089f.519e47fd@upo.es>

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From johanna.zumer at donders.ru.nl  Fri May 24 10:21:24 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Fri, 24 May 2013 10:21:24 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
Message-ID: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>

Dear Andrew,

To read EPI (MRI) data, you should use ft_read_mri instead.   Then
hopefully the format will match what ft_volumewrite wants.

Cheers,
Johanna


2013/5/23 Andrew Brooks <andmib at gmail.com>

> Hello all,
>
> I am new to FieldTrip, so this is a very basic question I was hoping
> someone might know an answer to.
>
> I am using ft_read_data to read the first EPI volume after dummy scans are
> thrown out. I want to write this volume to a .nii file to my disk. For some
> reason, I am unable to figure out the correct structure that ft_volumewrite
> wants. Using the output from ft_read_data ('dat') does not seem to work.
> Does anybody have any suggestions?
>
> [ For a longer explanation of exactly what I am aiming to do, in case you
> have any suggestions: I have ROI that is defined in Talairach space. This
> is the ROI I would like to pull my real-time data from for each subject in
> my study. To do this, I plan to register a talairach template brain to
> individual subject-space, and then apply that transformation to my ROI so
> that it is in subject space. I was going to simply write out the subject's
> EPI to an .nii file, and then run SPM's co-registration step which allows
> for a 'child dataset' to be set (my ROI), with the source file being the
> template, and the reference being the individual ROI].
>
> Thanks
> Andrew
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From andmib at gmail.com  Fri May 24 15:15:09 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Fri, 24 May 2013 09:15:09 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
Message-ID: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>

Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
pull a single volume from the buffer using ft_read_data, and then write it
out to a nifti file using ft_volumewrite, but ft_read_data does not output
the volume in a structure that ft_volumewrite wants.


On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer
<johanna.zumer at donders.ru.nl>wrote:

> Dear Andrew,
>
> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
> hopefully the format will match what ft_volumewrite wants.
>
> Cheers,
> Johanna
>
>
> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>
>> Hello all,
>>
>> I am new to FieldTrip, so this is a very basic question I was hoping
>> someone might know an answer to.
>>
>> I am using ft_read_data to read the first EPI volume after dummy scans
>> are thrown out. I want to write this volume to a .nii file to my disk. For
>> some reason, I am unable to figure out the correct structure that
>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>> seem to work. Does anybody have any suggestions?
>>
>> [ For a longer explanation of exactly what I am aiming to do, in case you
>> have any suggestions: I have ROI that is defined in Talairach space. This
>> is the ROI I would like to pull my real-time data from for each subject in
>> my study. To do this, I plan to register a talairach template brain to
>> individual subject-space, and then apply that transformation to my ROI so
>> that it is in subject space. I was going to simply write out the subject's
>> EPI to an .nii file, and then run SPM's co-registration step which allows
>> for a 'child dataset' to be set (my ROI), with the source file being the
>> template, and the reference being the individual ROI].
>>
>> Thanks
>> Andrew
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From johanna.zumer at gmail.com  Fri May 24 16:29:00 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Fri, 24 May 2013 16:29:00 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
	<CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
Message-ID: <CAL4kA6eCbXBJAFL9q5COz_jqgqGqT2FN8wUP3n3kOqiyK7sh0w@mail.gmail.com>

I'm not familiar with the buffer, but if you can read in your data
successfully, then to convert it to the structure that ft_volumewrite
wants, you can get some information inside ft_datatype_volume for what are
required or optional fields.




2013/5/24 Andrew Brooks <andmib at gmail.com>

> Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
> pull a single volume from the buffer using ft_read_data, and then write it
> out to a nifti file using ft_volumewrite, but ft_read_data does not output
> the volume in a structure that ft_volumewrite wants.
>
>
> On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer <
> johanna.zumer at donders.ru.nl> wrote:
>
>> Dear Andrew,
>>
>> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
>> hopefully the format will match what ft_volumewrite wants.
>>
>> Cheers,
>> Johanna
>>
>>
>> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>>
>>>  Hello all,
>>>
>>> I am new to FieldTrip, so this is a very basic question I was hoping
>>> someone might know an answer to.
>>>
>>> I am using ft_read_data to read the first EPI volume after dummy scans
>>> are thrown out. I want to write this volume to a .nii file to my disk. For
>>> some reason, I am unable to figure out the correct structure that
>>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>>> seem to work. Does anybody have any suggestions?
>>>
>>> [ For a longer explanation of exactly what I am aiming to do, in case
>>> you have any suggestions: I have ROI that is defined in Talairach space.
>>> This is the ROI I would like to pull my real-time data from for each
>>> subject in my study. To do this, I plan to register a talairach template
>>> brain to individual subject-space, and then apply that transformation to my
>>> ROI so that it is in subject space. I was going to simply write out the
>>> subject's EPI to an .nii file, and then run SPM's co-registration step
>>> which allows for a 'child dataset' to be set (my ROI), with the source file
>>> being the template, and the reference being the individual ROI].
>>>
>>> Thanks
>>> Andrew
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From politzerahless at gmail.com  Sat May 25 15:11:18 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 25 May 2013 08:11:18 -0500
Subject: [FieldTrip] Sourcespace and volume conductor misaligned
Message-ID: <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=fFk0ouR0wzA@mail.gmail.com>

Hello all,

I am going through the workflow at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
the volume conduction model using ft_prepare_headmodel(), I noticed that
although the volume conduction model and sourcespace have the same
orientation and overall size/shape (after I converted the volume conduction
model to cm, which wasn't in the tutorial but my original model came out in
mm), they don't quite line up, as you can see in this figure:

http://i.imgur.com/mGEtLOa.png

I did interactively re-align the data to CTF (twice--in step 2 of
"Preprocessing of the anatomical MRI" and in step 4 of "Source model")
using fiducials, and to Talairach (step 5 of "Preprocessing of the
anatomical data"), so I'm not sure how it ended up this way. The code I've
used at each step is basically the same as that in the tutorial.

Is there any way to line up my volume conduction model and sourcespace now,
without going back and re-running most of the workflow?

Best,
Steve

-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From johanna.zumer at donders.ru.nl  Sat May 25 20:54:59 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Sat, 25 May 2013 20:54:59 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
In-Reply-To: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
	<2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
Message-ID: <CAL4kA6eTL_TwECF62W-OoWY=Y1mpBR6QoOLh+ug8AcXNbVxQ1A@mail.gmail.com>

Dear Jing,

1.  Every MRI scanner is different, so I'm not familiar with that naming
scheme, but it seems the 'GAD' at the end of the file name indicates that
was with the Gadolinium contrast agent, so I would suggest to not use that,
but instead use the first (plain) T1.

2. I'm not sure what to suggest.  I assume you can see the vitamin E marker
clearly when viewing the DICOM file?   Is the issue that some slices are
missing in the conversion, or that the contrast on the image is not the
same?  or right/left flipped?

Best,
Johanna


2013/5/23 WangJing <13681530640 at 139.com>

> Dear Johanna,
>
>     Thank you for your suggestion.
>     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> t1_vibe_traGAD-5. which one is best?
>     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> didn't be found. what can I do?
>
> Best Regards,
> Jing Wang
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-22 15:33:13
> Subject：fieldtrip Digest, Vol 30, Issue 31
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: question About head model (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 May 2013 09:30:17 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] question About head model
> Message-ID:
> <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> It is best to use the T1 MRI rather than the other scans.   To open a DICOM
> format file, you can try one of these options:
>
> % read the DICOM files
> mri = ft_read_mri('single_file_of_DICOM_series.IMA');
>  % or use a graphical file selection[f, p] = uigetfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> >('*');
> mri = ft_read_mri(fullfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> >(p,
> f));
>
>
> I copied the above from documentation on the FieldTrip wiki:
>
> http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
>
>
> Then you can save the 'mri' into a *.mat file for future use with FieldTrip.
>
> Best regards,
> Johanna
>
>
> 2013/5/22 WangJing <13681530640 at 139.com>
>
> > Hi
> > I am a freshman about field trip.
> > I am trying to build the forward model. but my mri data is different from
> > the data in the tutorial. So I don't know how to bulid the head model. I
> > use the date which is from the paper "Open Database of Epileptic EEG with
> > MRI and Postoperational Assessment of Foci?a Real World Verification for
> > the EEG Inverse Solutions",http://eeg.pl/epi
> . MRI recordings containing a
>
> > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> > with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> > dysplastic tumors etc.). In some cases there is also a scan with the
>
> > gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> > scanner. The data is stored in the Digital Imaging and Communications in
> > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
>
> > In the tutorial,the mri data stored in only one file, while the data which
>
> > I used have many files, I don't know how to process. who can help me,Thanks1
> >  Thanks very much!
> > Best Reagards
> > Jing Wang
> >
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-21 23:59:18
> > Subject?fieldtrip Digest, Vol 30, Issue 29
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 21 May 2013 17:52:21 +0200
> > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you so much for your answer J?rn,
> >
> >
>
> > Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
> >
> >
>
> > Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
> >
> >
> >
>
> > I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> > data.dimord = 'rpt_rpt_chan_chan_freq'
> > ans size(data.crsspctrm) = [1 7 59 59];
> >
>
> > So, both are apparently the same, but the data inside this matrices is different,
> >
> >
>
> > for example, when calculating the ImC the first 7 columns for the first two rows are:
> > val(:,:,1,1)
> > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > val(:,:,1,2)
> >
>
> > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> >
> > while when calculating the PLV are:
> > val(:,:,1,1)
> > ?[1? 1? 1? 1? 1? 1? 1]
> > val(:,:,1,2)
> >
>
> > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> >
> >
> >
>
> > I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
> >
> >
>
> > If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
> >
> >
> >
> >
> >
>
> > On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
> >
> >
> > Many thanks in advanced,
> > Gabriel.
> >
> >
> >
> >
> > ----- Mensaje original -----
> > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >
> >
> >
> >
> >
> > > Dear Gabriel,
> >        >
> >
>
> >        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
> >                         >
> >
>
> > >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
> >        >
> >
>
> >        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
> >        >
> >
>
> > >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
> >
>
> > >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
> >        >
> > >        I hope that somehow clarifies your questions.
> >        >
> > >        Best,
> > >        J?rn
> >        >
> > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> >           > Dear Fieltrip experts,
> >          >
> >
>
> > >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
> >
>
> > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> > >          data.label {59x1};
> > >          data.time {1xNepochs};
> >          >
> > >          then, calculate only the FFT of all sensors as:
> > >          cfg=[];
> > >          cfg.output='fourier';
> > >          cfg.method='mtmfft';
> > >          cfg.taper='hanning';
> > >          cfg.foilim=[8.5 9.5];
> > >          cfg.tapsmofrq=0;
> > >          cfg.trials='all';
> > >          cfg.keeptrials='yes';
> > >          cfg.channel='all';
> > >          fourier=ft_freqanalysis(cfg, data)
> > >          as output I get:
> > >          dimord = 'rpttap_chan_freq'
> > >          freq= [1x9]
> > >          fourierspctrm=[7x59x9 double]
> >          >
> > >          Then compute the imaginary part of coherency as:
> >            > cfg=[];
> >              > cfg.method ='cohe';
> >              > cfg.complex='imag';
> >                > cfg.channelcbm={'all'               'all'};
> >              > coher = ft_connectivityanalysis (cfg, fourier)
> >          > as output get:
> >            > dimord='chan_chan_freq';
> >              > cohspctrm=[59x59x9 double];
> >              > dof=7;
> >            >
> >          > I have two main questions:
> >          >
> >
>
> >          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
> >                  >
> >                  >
> >                  >
> >
>
> >                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
> >                  >
> >                  >
> >                  >
> >                  >
> > >                  Many thanks in advanced,
> >                  > Gabriel.
> >                  >
> >                       >
> >               >
> >
>
> >        > _______________________________________________ > fieldtrip mailing list >
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >      >
> >
>
> >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > http://www.ru.nl/donders
>
> >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
>
> > <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> >
> >
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> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 30, Issue 29
> > *****************************************
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
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>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 30, Issue 31
> *****************************************
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From 13681530640 at 139.com  Sun May 26 11:26:07 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
Subject: [FieldTrip] Question about Memory requirement Of Head model
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
Message-ID: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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From julian.keil at gmail.com  Sun May 26 12:23:34 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Sun, 26 May 2013 12:23:34 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
Message-ID: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>

Dear Jing Wang,

this might be due to you using a 32bit System.
As far as I know, 32bit Windows can only use ~3 GB of Memory. At least that's what I experienced using Win XP, maybe it's different for the server.
However, I'd advise you to switch to a 64bit System and try again.

Best,

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 26.05.2013 um 11:26 schrieb WangJing:

> Hello Everyone,
>      I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.
> for example 1:
> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]
> cfg = [];
> ft_sourceplot(cfg,mri);
>  
> the result is:
> ??? Out of memory. Type HELP MEMORY for your options.
> Error in ==> ft_sourceplot at 368
>   ana  = (ana-dmin)./(dmax-dmin);
>  
> example 2:
> clear all
> mri = ft_read_mri('IM-0001-0001.dcm');
> cfg = [];
> cfg.method = 'interactive';
> cfg.coordsys = 'ctf';
> mri_realigned = ft_volumerealign(cfg,mri);
> clear mri
> cfg=[];
> mrirs = ft_volumereslice(cfg,mri_realigned);
>  
> when run to the last code, I face the same problem.
>  
> Thank you!
> Best Regards!
> Jing Wang
>  
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From 13681530640 at 139.com  Sun May 26 17:01:10 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 23:01:10 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 37
References: <mailman.9.1369562405.16243.fieldtrip@science.ru.nl>
Message-ID: <2b1851a22104e22-00005.Richmail.00025896525295133618@139.com>


Hello Everyone,


    I have resolved the problem when I ran it in computer with 64 bit OS,  thanks.


Best Regards,


Jing Wang





 













--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-26 18:00:05
Subject：fieldtrip Digest, Vol 30, Issue 37

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Today's Topics:

   1. Question about Memory requirement Of Head model (WangJing)


----------------------------------------------------------------------

Message: 1
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
From: WangJing <13681530640 at 139.com>
To: fieldtrip <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Question about Memory requirement Of Head model
Message-ID:
<2b1851a17ca79ab-00017.Richmail.00027836529255037638 at 139.com>
Content-Type: text/plain; charset="utf-8"


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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------------------------------

_______________________________________________
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fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 30, Issue 37
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From jm.horschig at donders.ru.nl  Mon May 27 11:54:00 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 27 May 2013 11:54:00 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
	<95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
Message-ID: <51A32D38.3060908@donders.ru.nl>

Hi all,

Julian is right, that's a limit of the 32bit system (the OS does not 
matter, just the number of bits). FieldTrip itself does not have any 
requirements other than Matlab does, however the size of your data 
matters. If you want to put data with more than 3gigs into memory, it's 
just not possible with a 32bit OS or Matlab (note that even if you have 
a 64bit OS but 32bit Matlab then the 3GB limit hold). So the only way 
for you to go is to clear variables from memory or reduce the size of 
the data you want to read it (or, go to 64bit). Maybe closing background 
tasks or other programs that are running will help as well.

Best,
Jörn

On 5/26/2013 12:23 PM, Julian Keil wrote:
> Dear Jing Wang,
>
> this might be due to you using a 32bit System.
> As far as I know, 32bit Windows can only use ~3 GB of Memory. At least 
> that's what I experienced using Win XP, maybe it's different for the 
> server.
> However, I'd advise you to switch to a 64bit System and try again.
>
> Best,
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 26.05.2013 um 11:26 schrieb WangJing:
>
>> Hello Everyone,
>>      I want to know what's the requiement of fieldtrip to hardware 
>> and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is 
>> windows sever 2003, and the matlab is 2011a(32bit).I often encounter 
>> the problem of out of Memery.
>> for example 1:
>> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 
>> 512 144]
>> cfg = [];
>> ft_sourceplot(cfg,mri);
>> the result is:
>> ??? Out of memory. Type HELP MEMORY for your options.
>> Error in ==> ft_sourceplot at 368
>>   ana  = (ana-dmin)./(dmax-dmin);
>> example 2:
>> clear all
>> mri = ft_read_mri('IM-0001-0001.dcm');
>> cfg = [];
>> cfg.method = 'interactive';
>> cfg.coordsys = 'ctf';
>> mri_realigned = ft_volumerealign(cfg,mri);
>> clear mri
>> cfg=[];
>> mrirs = ft_volumereslice(cfg,mri_realigned);
>> when run to the last code, I face the same problem.
>> Thank you!
>> Best Regards!
>> Jing Wang
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From member at linkedin.com  Mon May 27 14:14:43 2013
From: member at linkedin.com (Stavros Dimitriadis)
Date: Mon, 27 May 2013 12:14:43 +0000 (UTC)
Subject: [FieldTrip] Invitation to connect on LinkedIn
Message-ID: <1730678420.35398857.1369656883124.JavaMail.app@ela4-app0128.prod>

LinkedIn
------------




    Stavros Dimitriadis requested to add you as a connection on LinkedIn:
  

------------------------------------------

Diego,

I'd like to add you to my professional network on LinkedIn.

- Stavros

Accept invitation from Stavros Dimitriadis
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From johanna.zumer at gmail.com  Mon May 27 15:12:27 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Mon, 27 May 2013 15:12:27 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
	<CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
Message-ID: <CAL4kA6cbk1c8bBztUG6JD_5k1W6Ds8CY3zRqer4uVxy-Edtpsg@mail.gmail.com>

Hi Mushfa,

The values inside grid_*.leadfield are the ones that need to be
concatenated, per grid position.   So the first thing to do is figure out
which rows in grid_eeg.pos match up with which rows in grid_meg.pos, and
then only for those that match, concatenate so that the *.leadfield is of
size [(number of eeg channels + number of meg channels)  X 3].

It might be easier to first ensure that the grid used to create these
leadfields have the same 'inside' positions (inside the volume conductor).

Best,
Johanna



2013/5/22 Mushfa Yousuf <mushfa.yousuf at googlemail.com>

> Hello Jörn;
>
> I have calculated an indiviual leadfield for both EEG and MEG. The
> structure of EEg and MEG shows the following variable
>
> grid_meg =
>
>         xgrid: [1x20 double]
>         ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
>         zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
>           dim: [20 17 16]
>           pos: [5440x3 double]
>          unit: 'cm'
>        inside: [1x3177 double]
>       outside: [1x2263 double]
>           cfg: [1x1 struct]
>     leadfield: {1x5440 cell}
>
>
> grid_eeg =
>
>         xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
>         ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
>         zgrid: [2 3 4 5 6 7 8 9 10 11]
>           dim: [16 13 10]
>           pos: [2080x3 double]
>          unit: 'cm'
>        inside: [1x1331 double]
>       outside: [1x749 double]
>           cfg: [1x1 struct]
>     leadfield: {1x2080 cell}
>
>
> Can you please give me a rough idea that how to concatenate the variables
> from both structure ?
>
>
> Thank you
>
> Regards ;
>
> Mushfa Yousuf
>
>
> On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
> jm.horschig at donders.ru.nl> wrote:
>
>>  Dear Mushfa,
>>
>> I think you have to compute two leadfield matrices, one for EEG (elec)
>> and one for MEG (grad), and then concatenate these (and make sure that the
>> order of sensors won't get mixed up anywhere, because  sourceanalysis just
>> expects the leadfield matrix to be ordered like your data. If that's not
>> the case, you either encounter the previous error you described or (if the
>> number of channels matches, but order is mixed up) it will just return
>> wrong source estimated activity.
>>
>> Best,
>> Jörn
>>
>>
>> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>>
>> Hello;
>>
>>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
>> of 'elec' while calculating the Leadfield.
>>
>>  Actually I am trying to calculate Combined source reconstruction from
>> both EEG and MEG sensors.
>>
>>  Do you have any idea, how to define both elec and grad definition
>> while calculating first forward then inverse solution.
>>
>>  Because in a fieldtrip either you can defined elec or grad at one time.
>>
>>
>>  Regards;
>>
>>
>>  Mushfa Yousuf
>>
>>  Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>>
>>> Hi Mushfa,
>>>
>>>  My guess is that the channels that have you used to compute .csdspctrm
>>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>>> freqPost.label, does that solve it?
>>>
>>>  Cheers,
>>> Johanna
>>>
>>>
>>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>>
>>>>   Hello Fieldtrippers,
>>>>
>>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>>
>>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>>> lead field successfully.
>>>>
>>>>  For the inverse solution using 'dics' method, I wrote the following
>>>> syntax
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>   cfg              = [];
>>>>   cfg.method       = 'dics';
>>>>  cfg.frequency    = 130;
>>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>>  cfg.grid         = grid;
>>>>  cfg.vol          = vol;
>>>>
>>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>  and I have received the following error:
>>>>
>>>>
>>>>  ??? Error using ==> mtimes
>>>> Inner matrix dimensions must agree.
>>>>
>>>>  Error in ==> beamformer_dics at 314
>>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>>         leadfield
>>>>
>>>>  Error in ==> ft_sourceanalysis at 595
>>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>>
>>>>  Error in ==> newCode at 214
>>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>
>>>>
>>>>  Any help would be appreciated.
>>>>
>>>>
>>>>  Regards;
>>>>
>>>>
>>>>  Mushfa Yousuf
>>>>
>>>>  Neurozentrum,
>>>> Universitätsklinikum Schleswig-Holstein,
>>>> Campus Kiel (UKSH), Deutschland
>>>>
>>>>
>>>>  _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mbj0310 at gmail.com  Wed May 29 11:47:14 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Wed, 29 May 2013 18:47:14 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some files
Message-ID: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>

Dear all,

Hello, my name is BJ Min from Korea.

I'm dealing with EEG data of many subjects.

When I run ft_preprocessing, the error message below shows with only some
files of my data. (not all files)

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577
??? Error using ==> ft_read_data at 149
cannot read data after the end of the file

Error in ==> ft_preprocessing at 577
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
begsample, 'endsample', endsample, 'chanindx', rawindx,
      'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
cfg.dataformat)

I think that there might be a kind of problem in data acquisition, and I
modified below scripts in the ft_read_data function with comment %.

% % test whether the requested data segment is not outside the file
% if any(begsample<1)
%   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
the file');
% elseif any(endsample>(hdr.nSamples*hdr.nTrials))
%   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the
file');
% end

After that, the ft_preprocessing worked well.

However, the files with the first problem showed additional warning message
while running ft_definetrial. (not error message)

Warning: Integer operands are required for colon operator when used as
index
> In fileio\private\loadcnt at 464
  In ft_read_header at 1450
  In ft_preprocessing at 398

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577

Also, during ft_redefinetrial, following warning message occurs.(not error
message)

Warning: removing inconsistent sampleinfo
> In ft_datatype_raw at 97
  In ft_checkdata at 213
  In ft_redefinetrial at 104

Warning: the trial definition in the configuration is inconsistent with the
actual data
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 74
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

Warning: reconstructing sampleinfo by assuming that the trials are
consecutive segments of a continuous recording
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 79
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

I wonder if these messages during ft_redefinetrial mean wrong defining
trials.
Should I continue these process like this, modifying the ft_preprocessing
function?
Or, is it better to exclude some erroneous files?

Best regards

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Wed May 29 12:01:31 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Wed, 29 May 2013 12:01:31 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
Message-ID: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>

Dear BJ Min,

what type of data are you trying to read in?
I had similar problems when reading in .CNT data.
Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.

Good Luck

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 29.05.2013 um 11:47 schrieb Beom Jun Min:

> Dear all,
> 
> Hello, my name is BJ Min from Korea.
> 
> I'm dealing with EEG data of many subjects. 
> 
> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
> 
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
> 
> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
> 
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
> % end
> 
> After that, the ft_preprocessing worked well.
> 
> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
> 
> Warning: Integer operands are required for colon operator when used as index 
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> 
> Also, during ft_redefinetrial, following warning message occurs.(not error message)
> 
> Warning: removing inconsistent sampleinfo 
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
> 
> Warning: the trial definition in the configuration is inconsistent with the actual data 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
> Should I continue these process like this, modifying the ft_preprocessing function? 
> Or, is it better to exclude some erroneous files?
> 
> Best regards
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From mbj0310 at gmail.com  Thu May 30 10:15:31 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 30 May 2013 17:15:31 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
Message-ID: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>

Dear Julian Keil,

Thank you for your reply.
I agree with that your problem was similar with mine.
My data was acquired by Neuroscan also.
There might a problem associated with .CNT file in the newer version.

Could you tell me the number of the older version you used?

Best Regards



2013/5/29 Julian Keil <julian.keil at gmail.com>

> Dear BJ Min,
>
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the
> problem, but this was in 2011, so I cannot say if the problem with .CNT
> files has been solved.
>
> Good Luck
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I'm dealing with EEG data of many subjects.
>
> When I run ft_preprocessing, the error message below shows with only some
> files of my data. (not all files)
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
>
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
> cfg.dataformat)
>
> I think that there might be a kind of problem in data acquisition, and I
> modified below scripts in the ft_read_data function with comment %.
>
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
> the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
> the file');
> % end
>
> After that, the ft_preprocessing worked well.
>
> However, the files with the first problem showed additional warning
> message while running ft_definetrial. (not error message)
>
> Warning: Integer operands are required for colon operator when used as
> index
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
>
> Also, during ft_redefinetrial, following warning message occurs.(not error
> message)
>
> Warning: removing inconsistent sampleinfo
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
>
> Warning: the trial definition in the configuration is inconsistent with
> the actual data
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> I wonder if these messages during ft_redefinetrial mean wrong defining
> trials.
> Should I continue these process like this, modifying the ft_preprocessing
> function?
> Or, is it better to exclude some erroneous files?
>
> Best regards
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Thu May 30 11:45:09 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Thu, 30 May 2013 11:45:09 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <80EC72EF-2296-47F5-97EC-197F91402C79@gmail.com>

Dear BJ Min,

I used the field trip version 20111101. I don't know if it's still available though.
To set the bitrate, you have to specify

	cfg.headerformat='ns_cnt32'; 
        cfg.dataformat='ns_cnt32'; 
        cfg.eventformat='ns_cnt32';

in ft_preprocessing

One way to check this (and also if you set your bitrate correctly), is to see if you can find easily detectable ERPs, like the visual or auditory N1 in your data. If you can't see this component, then your settings are wrong, even if data has been read into Matlab.

Good Luck,

Julian

Am 30.05.2013 um 10:15 schrieb Beom Jun Min:

> Dear Julian Keil,
> 
> Thank you for your reply. 
> I agree with that your problem was similar with mine. 
> My data was acquired by Neuroscan also. 
> There might a problem associated with .CNT file in the newer version.
> 
> Could you tell me the number of the older version you used? 
> 
> Best Regards
> 
> 
> 
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
> Dear BJ Min,
> 
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.
> 
> Good Luck
> 
> Julian
> 
> ********************
> Dr. Julian Keil
> 
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
> 
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209 
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
> 
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
> 
>> Dear all,
>> 
>> Hello, my name is BJ Min from Korea.
>> 
>> I'm dealing with EEG data of many subjects. 
>> 
>> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>> 
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
>> 
>> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
>> 
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
>> % end
>> 
>> After that, the ft_preprocessing worked well.
>> 
>> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
>> 
>> Warning: Integer operands are required for colon operator when used as index 
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> 
>> Also, during ft_redefinetrial, following warning message occurs.(not error message)
>> 
>> Warning: removing inconsistent sampleinfo 
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>> 
>> Warning: the trial definition in the configuration is inconsistent with the actual data 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
>> Should I continue these process like this, modifying the ft_preprocessing function? 
>> Or, is it better to exclude some erroneous files?
>> 
>> Best regards
>> 
>> -- 
>> BeomJun Min, M.D.
>> 
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST) 
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
>> 500-712, Republic of Korea (South) 
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From dr.chungki.lee at gmail.com  Thu May 30 11:56:02 2013
From: dr.chungki.lee at gmail.com (Chungki Lee)
Date: Thu, 30 May 2013 18:56:02 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>

Hi Min

you'd better use ft_definetrial routine before  ft_preprocessing.

example)

    cfg                              = [];
    cfg.dataset                 = filename;  % string
    cfg.trialdef.eventtype  =  your define text; % string
    cfg.trialdef.eventvalue = your label value;  % integer
    cfg.trialdef.prestim    = before onset time (sec); % positive integer,
not negative integer
    cfg.trialdef.poststim   = after onset time (sec); % positve integer
    cfg                            = ft_definetrial(cfg);
    data                          = ft_preprocessing(cfg);

have fun ^^


2013/5/30 Beom Jun Min <mbj0310 at gmail.com>

> Dear Julian Keil,
>
> Thank you for your reply.
> I agree with that your problem was similar with mine.
> My data was acquired by Neuroscan also.
> There might a problem associated with .CNT file in the newer version.
>
> Could you tell me the number of the older version you used?
>
> Best Regards
>
>
>
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>
>> Dear BJ Min,
>>
>> what type of data are you trying to read in?
>> I had similar problems when reading in .CNT data.
>> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
>> For me, reading in data with an older version of FieldTrip solved the
>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>> files has been solved.
>>
>> Good Luck
>>
>> Julian
>>
>>  ********************
>> *Dr. Julian Keil*
>> *
>> *
>> AG Multisensorische Integration
>> Psychiatrische Universitätsklinik
>> der Charité im St. Hedwig-Krankenhaus
>> Große Hamburger Straße 5-11, Raum E 307
>> 10115 Berlin
>>
>> Telefon: +49-30-2311-1879
>> Fax:        +49-30-2311-2209
>>
>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>
>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>
>> Dear all,
>>
>> Hello, my name is BJ Min from Korea.
>>
>> I'm dealing with EEG data of many subjects.
>>
>> When I run ft_preprocessing, the error message below shows with only some
>> files of my data. (not all files)
>>
>>  Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>>
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>> cfg.dataformat)
>>
>> I think that there might be a kind of problem in data acquisition, and I
>> modified below scripts in the ft_read_data function with comment %.
>>
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>> of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>> the file');
>> % end
>>
>> After that, the ft_preprocessing worked well.
>>
>> However, the files with the first problem showed additional warning
>> message while running ft_definetrial. (not error message)
>>
>> Warning: Integer operands are required for colon operator when used as
>> index
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>>
>> Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>>
>> Also, during ft_redefinetrial, following warning message occurs.(not
>> error message)
>>
>> Warning: removing inconsistent sampleinfo
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>>
>> Warning: the trial definition in the configuration is inconsistent with
>> the actual data
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> Warning: reconstructing sampleinfo by assuming that the trials are
>> consecutive segments of a continuous recording
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> I wonder if these messages during ft_redefinetrial mean wrong defining
>> trials.
>> Should I continue these process like this, modifying the ft_preprocessing
>> function?
>> Or, is it better to exclude some erroneous files?
>>
>> Best regards
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
----------------------------------------------------------------
Chungki Lee, Ph.D.
Post-doc
Biomedical Research Institute
Korea Institute of Science and Technology
E-mail: chungki at kist.re.kr
Tel:+82-2-958-5636, C.P: +82-10-5223-7309
----------------------------------------------------------------
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From lkystra at hotmail.it  Thu May 30 12:39:16 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 12:39:16 +0200
Subject: [FieldTrip] distorsion of .edf file
Message-ID: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>

Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  
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From zriouil.imane at gmail.com  Thu May 30 15:43:59 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Thu, 30 May 2013 15:43:59 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
Message-ID: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>

> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the
> use of read_edf, have a distorsion. Matlab indicate a warning for the 348
> row of read_edf . Can someone give to me a help?
>
> Best regards,
> Lucia
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 


Zriouil Imane
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From lkystra at hotmail.it  Thu May 30 17:33:55 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 17:33:55 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
Message-ID: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>

I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>




Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 

 
 
Zriouil Imane






_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu May 30 18:31:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 30 May 2013 18:31:22 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
Message-ID: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>

Hi Lucia,

Perhaps you need to be a bit more specific. 
In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.
Otherwise all of us are shooting in the dark.
Best wishes,
Jan-Mathijs


On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:

> I try and... it's not a good solution.
> 
> Date: Thu, 30 May 2013 15:43:59 +0200
> From: zriouil.imane at gmail.com
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] distorsion of .edf file
> 
> I have the same problem.
> 
> if you want to read your data. it's possible to use ft_read_data(filename')
> 
> 
> 
> 2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?
> 
> Best regards,
> Lucia
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
>  
>  
> Zriouil Imane
> 
> 
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ebrahimi_nia at yahoo.com  Thu May 30 19:14:52 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Thu, 30 May 2013 10:14:52 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
Message-ID: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>

Hi dear all,

I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.

**** Error using fread

Invalid precision.
Error in loreta2fieldtrip (line 85)
activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***

Can someone give me a help?


Best regards,
Fatemeh
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From inieuwenhuis at berkeley.edu  Thu May 30 19:30:41 2013
From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis)
Date: Thu, 30 May 2013 10:30:41 -0700
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
Message-ID: <51A78CC1.6030906@berkeley.edu>

Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug, see 
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export the 
source data as a text file. You can read that text file in with 
loreta2fieldtrip.m. It's a bit of a patch, but it worked for me.

Hope this helps,
Ingrid

On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:
> Hi dear all,
>
> I am analyzing EEG data. I have computed sLORETA (.slor) from ERP 
> data. Now I want to read and convert LORETA source reconstruction into a
> MATLAB data structure using "loreta2fieldtrip" function, But I have 
> gotten the bellow error.
>
> **** Error using fread
> Invalid precision.
> Error in loreta2fieldtrip (line 85)
> activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
> Can someone give me a help?
>
> Best regards,
> Fatemeh
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305

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From frank.ye.mei at gmail.com  Thu May 30 21:33:53 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Thu, 30 May 2013 15:33:53 -0400
Subject: [FieldTrip] error when using ctf2grad
Message-ID: <51A7A9A1.6020401@gmail.com>

Hi All,

I have some problem using ctf2grad.

The program will set   grad.balance.current = 'G3AR';,
and then do                 getfield(grad.balance, grad.balance.current)
but
grad.balance =    G1BR: [1x1 struct]
                             G2BR: [1x1 struct]
                             G3BR: [1x1 struct]

and has no G3AR in it. So an error will pop up.

Can anyone help me with that?

Also, What do G1BR,   G2BR,  G3BR, G3AR stand for?


thanks,
Ye


From politzerahless at gmail.com  Fri May 31 05:53:45 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Thu, 30 May 2013 22:53:45 -0500
Subject: [FieldTrip] Question about minimum norm estimate pipeline
Message-ID: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>

Hello all,

I have not yet gotten a response to my question below, but in the meantime
I have another question about the minimum norm estimate
workflow--specifically, about the coordinate system for the skull-stripped
anatomy in the step described at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk.
I'm confused by the following bit of code:

% ensure that the skull-stripped anatomy is expressed in the same
coordinate system as the anatomy
seg.transform = mri_tal.transform;

In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
re-aligning to Talairach in the previous step?) whereas seg.coordsys is
'ctf' (as a result of re-aligning to CTF several steps earlier). (But
mri_tal also has a field mri_tal.transformorig, which seg does not have.)
So should I really be using the same transform for both, as shown in the
tutorial?

Apologies if this question is pretty basic; I'm just trying to pinpoint
where the mis-alignment described in my message below occurred, so I want
to make sure I understand each step of the workflow correctly

Best,
Steve


> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/



On Sat, May 25, 2013 at 1:56 PM, <fieldtrip-request at science.ru.nl> wrote:
>
> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Sourcespace and volume conductor misaligned
>       (Stephen Politzer-Ahles)
>    2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
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> ------------------------------
>
> Message: 2
> Date: Sat, 25 May 2013 20:54:59 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> Message-ID:
>         <CAL4kA6eTL_TwECF62W-OoWY=
Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> 1.  Every MRI scanner is different, so I'm not familiar with that naming
> scheme, but it seems the 'GAD' at the end of the file name indicates that
> was with the Gadolinium contrast agent, so I would suggest to not use
that,
> but instead use the first (plain) T1.
>
> 2. I'm not sure what to suggest.  I assume you can see the vitamin E
marker
> clearly when viewing the DICOM file?   Is the issue that some slices are
> missing in the conversion, or that the contrast on the image is not the
> same?  or right/left flipped?
>
> Best,
> Johanna
>
>
> 2013/5/23 WangJing <13681530640 at 139.com>
>
> > Dear Johanna,
> >
> >     Thank you for your suggestion.
> >     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > t1_vibe_traGAD-5. which one is best?
> >     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> > didn't be found. what can I do?
> >
> > Best Regards,
> > Jing Wang
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-22 15:33:13
> > Subject?fieldtrip Digest, Vol 30, Issue 31
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: question About head model (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 22 May 2013 09:30:17 +0200
> > From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] question About head model
> > Message-ID:
> > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > It is best to use the T1 MRI rather than the other scans.   To open a
DICOM
> > format file, you can try one of these options:
> >
> > % read the DICOM files
> > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> >  % or use a graphical file selection[f, p] = uigetfile
> > <
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > >('*');
> > mri = ft_read_mri(fullfile
> > <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > >(p,
> > f));
> >
> >
> > I copied the above from documentation on the FieldTrip wiki:
> >
> >
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> >
> >
> > Then you can save the 'mri' into a *.mat file for future use with
FieldTrip.
> >
> > Best regards,
> > Johanna
> >
> >
> > 2013/5/22 WangJing <13681530640 at 139.com>
> >
> > > Hi
> > > I am a freshman about field trip.
> > > I am trying to build the forward model. but my mri data is different
from
> > > the data in the tutorial. So I don't know how to bulid the head
model. I
> > > use the date which is from the paper "Open Database of Epileptic EEG
with
> > > MRI and Postoperational Assessment of Foci?a Real World Verification
for
> > > the EEG Inverse Solutions",http://eeg.pl/epi
> > . MRI recordings containing a
> >
> > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain
scans
> > > with morphologic substrate of the epilepsy (mostly cortical
dysplasias,
> > > dysplastic tumors etc.). In some cases there is also a scan with the
> >
> > > gadolinium (GAD) contrast. The images were collected by Siemens
Sonata 1.5T
> > > scanner. The data is stored in the Digital Imaging and Communications
in
> > > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > > weighting.The scans have the following resolutions: T1: 512 ? 512
pixels,
> > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> >
> > > In the tutorial,the mri data stored in only one file, while the data
which
> >
> > > I used have many files, I don't know how to process. who can help
me,Thanks1
> > >  Thanks very much!
> > > Best Reagards
> > > Jing Wang
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > > To?fieldtrip<fieldtrip at science.ru.nl>
> > > Date?2013-05-21 23:59:18
> > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Thank you so much for your answer J?rn,
> > >
> > >
> >
> > > Now I got it, so, I will let the 'fourier' as input to
ft_connectivityanalysis, because for some indices I will need the
auto-spectrum, and if I fully undertood what you said, it will be the same,
as they always take the phase information from the fourier transform. And
fieltrip will automatically compute the csd if the input is the frequency
data.
> > >
> > >
> >
> > > Nevertheless, it give me some error when I tried to use the output
from 'powandcsd' of freqanalysis, always gives me a matrix dimensions
error, and when I use the output 'fourier' from connectivityanalysis, it
computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they
are signed, so this is ok), the problem are the ImC ranging from -inf to
inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier'
the values are. Which for me is really weird.
> > >
> > >
> > >
> >
> > > I have checked internally, and even when I always use the 'fourier'
as input, when it internally calculates cross-spectrum for the ImC and PLV,
the data.crsspctrm is different, e.g:
> > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > ans size(data.crsspctrm) = [1 7 59 59];
> > >
> >
> > > So, both are apparently the same, but the data inside this matrices
is different,
> > >
> > >
> >
> > > for example, when calculating the ImC the first 7 columns for the
first two rows are:
> > > val(:,:,1,1)
> > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i?
0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > >
> > > while when calculating the PLV are:
> > > val(:,:,1,1)
> > > ?[1? 1? 1? 1? 1? 1? 1]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i?
0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > >
> > >
> > >
> >
> > > I'm pretty sure I'm doing something wrong here, but I don't really
have a clue,
> > >
> > >
> >
> > > If I use the fourier transform to calculate the 'csd' in
ft_connectivity analysis and use this csd as input to all other
ft_connectivityanalysis indices all of them are set to NaN or 1, not
ranging between any numbers.
> > >
> > >
> > >
> > >
> > >
> >
> > > On the other hand, I have seen searching on the net, that fieltrip is
capable of create surrogate data, by shifting the phase information on
every trial for only one electrode of each pair while using the original
samples of each trials on the second channel, but I couldn't find on the
manual how to do such a thing. Is there any way to compute this kind of
surrogates for every sensor? or was it something that some one suggest to
somebody?
> > >
> > >
> > > Many thanks in advanced,
> > > Gabriel.
> > >
> > >
> > >
> > >
> > > ----- Mensaje original -----
> > > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > >
> > >
> > >
> > >
> > >
> > > > Dear Gabriel,
> > >        >
> > >
> >
> > >        > A) As you             see, this makes an average over the
epochs of each channel,             and not over the samples (which in this
case are the 9             frequencies of the FFT), And I would like to
have the opposite, this is, to get the imaginary part of coherence for
              each epoch (repetition) on all                   my channels
and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,
              Is this possible?
> > >                         >
> > >
> >
> > > >        No. You should think of coherence more as a measure for the
      consistency of the phase relation between channels across trials,
  so coherence is just not defined per trial,neither would it make
sense to compute coherence for a single trial.
> > >        >
> > >
> >
> > >        > B)                     Another question I have is: for the
Imaginary part                     of Coherence is not necessary to compute
the                     cross-spectrum with 'powandcsd', only the FFT, but
                    for the PLV, PPC or WPLI is that way too?       I see
some terminology issues here. Let me try to explain in a       simple (aka
least-mathematical I can think of) way:
> > >        >
> > >
> >
> > > >        For all these connectivity measures, we need the phase
information       from the Fourier transform (FFT) to compute the
cross-spectral       density matrix (CSD). The CSD can be regarded as the
equivalent in       the frequency domain to the covariance matrix in the
time domain,       thus it is a measures how a certain channels activity is
      co-modulated with another channels activity (for a particular
frequency) - makes pretty much sense to make use of this when
computing connectivity, right? :)
> > >
> >
> > > >        As you might know, a Fourier transform returns complex
numbers,       where the imaginary part of this number contains phase
information. When calling ft_freqanalysis, you can decide if it       shall
only return the (squared) real part of the frequency       spectrum
(cfg.output='pow'), or instead the full CSD (cfg.output =
'powandcsd'). Alternatively, you can also let ft_freqanalysis       return
the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier
coefficients, however, you can easily obtain the CSD       or the power
spectrum basically by multiplication the Fourier       matrix with itself
(transposed). All of these measures quantify       the phase relation
between channels across trials, and as phase       information is coded in
the imaginary part of the fourier output,       thus for
connectivityanalysis you need the CSD which can be       obtained either by
'powandcsd' or by 'fourier'.
> > >        >
> > > >        I hope that somehow clarifies your questions.
> > >        >
> > > >        Best,
> > > >        J?rn
> > >        >
> > > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > >           > Dear Fieltrip experts,
> > >          >
> > >
> >
> > > >          I have my continuous data imported to fieldtrip with
matlab, I'm         looking for performing connectivity analysis between
pairs of         sensors, I have succed as:
> > >
> >
> > > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch
with 59 channels and 2000 samples
> > > >          data.label {59x1};
> > > >          data.time {1xNepochs};
> > >          >
> > > >          then, calculate only the FFT of all sensors as:
> > > >          cfg=[];
> > > >          cfg.output='fourier';
> > > >          cfg.method='mtmfft';
> > > >          cfg.taper='hanning';
> > > >          cfg.foilim=[8.5 9.5];
> > > >          cfg.tapsmofrq=0;
> > > >          cfg.trials='all';
> > > >          cfg.keeptrials='yes';
> > > >          cfg.channel='all';
> > > >          fourier=ft_freqanalysis(cfg, data)
> > > >          as output I get:
> > > >          dimord = 'rpttap_chan_freq'
> > > >          freq= [1x9]
> > > >          fourierspctrm=[7x59x9 double]
> > >          >
> > > >          Then compute the imaginary part of coherency as:
> > >            > cfg=[];
> > >              > cfg.method ='cohe';
> > >              > cfg.complex='imag';
> > >                > cfg.channelcbm={'all'               'all'};
> > >              > coher = ft_connectivityanalysis (cfg, fourier)
> > >          > as output get:
> > >            > dimord='chan_chan_freq';
> > >              > cohspctrm=[59x59x9 double];
> > >              > dof=7;
> > >            >
> > >          > I have two main questions:
> > >          >
> > >
> >
> > >          > A) As you see, this makes an average over the
epochs of each channel, and not over the samples (which in           this
case are the 9 frequencies of the FFT), And I would like           to have
the opposite, this is, to               get the imaginary
part of coherence for each epoch (repetition)                 on all my
channels and not for each frequency, something like: chan_chan_rpt or
chancbm_rpt,               Is this possible?
> > >                  >
> > >                  >
> > >                  >
> > >
> >
> > >                  > B) Another question I have is: for the
      Imaginary part of Coherence is not necessary to
compute the cross-spectrum with 'powandcsd', only the
FFT, but for the PLV, PPC or WPLI is that way too?
> > >                  >
> > >                  >
> > >                  >
> > >                  >
> > > >                  Many thanks in advanced,
> > >                  > Gabriel.
> > >                  >
> > >                       >
> > >               >
> > >
> >
> > >        > _______________________________________________ > fieldtrip
mailing list >
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >      >
> > >
> >
> > >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for
Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging >
Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip
Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands
>  > Contact: > E-Mail:
> > > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > > http://www.ru.nl/donders
> >
> > >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
NL-6525 EN Nijmegen > The Netherlands     >
_______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > >
> >
> > > <font size="3">--------------------------<br />PhD. student Gabriel
Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain
-<br /><br />Email:
> > > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> > >
> > >
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From a.stolk at fcdonders.ru.nl  Fri May 31 08:11:23 2013
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
Subject: [FieldTrip] Question about minimum norm estimate pipeline
In-Reply-To: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>
Message-ID: <1914237354.1292588.1369980683984.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Steve, A quick guess; did you correctly align your resliced mri to Talairach space by indicating the commissures ( http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm correct, a point in the same place, e.g. between the hemispheres? This should update the transformation matrix. Best regards, Arjen ----- Oorspronkelijk bericht -----
> Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Vrijdag 31 mei 2013 05:53:45
> Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> Hello all,
> I have not yet gotten a response to my question below, but in the
> meantime I have another question about the minimum norm estimate
> workflow--specifically, about the coordinate system for the
> skull-stripped anatomy in the step described at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> . I'm confused by the following bit of code:
> % ensure that the skull-stripped anatomy is expressed in the same
> coordinate system as the anatomy
> seg.transform = mri_tal.transform;
> In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> re-aligning to Talairach in the previous step?) whereas seg.coordsys
> is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> (But mri_tal also has a field mri_tal.transformorig, which seg does
> not have.) So should I really be using the same transform for both, as
> shown in the tutorial?
> Apologies if this question is pretty basic; I'm just trying to
> pinpoint where the mis-alignment described in my message below
> occurred, so I want to make sure I understand each step of the
> workflow correctly
> Best,
> Steve
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> On Sat, May 25, 2013 at 1:56 PM, < fieldtrip-request at science.ru.nl >
> wrote:
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Sourcespace and volume conductor misaligned
> > (Stephen Politzer-Ahles)
> > 2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130525/561df14f/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sat, 25 May 2013 20:54:59 +0200
> > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> > Message-ID:
> > <CAL4kA6eTL_TwECF62W-OoWY= Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > 1. Every MRI scanner is different, so I'm not familiar with that
> > naming
> > scheme, but it seems the 'GAD' at the end of the file name indicates
> > that
> > was with the Gadolinium contrast agent, so I would suggest to not
> > use that,
> > but instead use the first (plain) T1.
> >
> > 2. I'm not sure what to suggest. I assume you can see the vitamin E
> > marker
> > clearly when viewing the DICOM file? Is the issue that some slices
> > are
> > missing in the conversion, or that the contrast on the image is not
> > the
> > same? or right/left flipped?
> >
> > Best,
> > Johanna
> >
> >
> > 2013/5/23 WangJing < 13681530640 at 139.com >
> >
> > > Dear Johanna,
> > >
> > > Thank you for your suggestion.
> > > 1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > > t1_vibe_traGAD-5. which one is best?
> > > 2.when I convert MRI from DICOM into CTF format,the vitamin E
> > > marker
> > > didn't be found. what can I do?
> > >
> > > Best Regards,
> > > Jing Wang
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > Date?2013-05-22 15:33:13
> > > Subject?fieldtrip Digest, Vol 30, Issue 31
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more
> > > specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: question About head model (Johanna Zumer)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Wed, 22 May 2013 09:30:17 +0200
> > > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > Subject: Re: [FieldTrip] question About head model
> > > Message-ID:
> > > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=
> > > HsAS_X0-w at mail.gmail.com >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Dear Jing,
> > >
> > > It is best to use the T1 MRI rather than the other scans. To open
> > > a DICOM
> > > format file, you can try one of these options:
> > >
> > > % read the DICOM files
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > % or use a graphical file selection[f, p] = uigetfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > > >('*');
> > > mri = ft_read_mri(fullfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > > >(p,
> > > f));
> > >
> > >
> > > I copied the above from documentation on the FieldTrip wiki:
> > >
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> > >
> > >
> > > Then you can save the 'mri' into a *.mat file for future use with
> > > FieldTrip.
> > >
> > > Best regards,
> > > Johanna
> > >
> > >
> > > 2013/5/22 WangJing < 13681530640 at 139.com >
> > >
> > > > Hi
> > > > I am a freshman about field trip.
> > > > I am trying to build the forward model. but my mri data is
> > > > different from
> > > > the data in the tutorial. So I don't know how to bulid the head
> > > > model. I
> > > > use the date which is from the paper "Open Database of Epileptic
> > > > EEG with
> > > > MRI and Postoperational Assessment of Foci?a Real World
> > > > Verification for
> > > > the EEG Inverse Solutions", http://eeg.pl/epi
> > > . MRI recordings containing a
> > >
> > > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted
> > > > brain scans
> > > > with morphologic substrate of the epilepsy (mostly cortical
> > > > dysplasias,
> > > > dysplastic tumors etc.). In some cases there is also a scan with
> > > > the
> > >
> > > > gadolinium (GAD) contrast. The images were collected by Siemens
> > > > Sonata 1.5T
> > > > scanner. The data is stored in the Digital Imaging and
> > > > Communications in
> > > > Medicine (DICOM) format. The name of the scan?s folder indicates
> > > > its
> > > > weighting.The scans have the following resolutions: T1: 512 ?
> > > > 512 pixels,
> > > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256
> > > > pixels,
> > > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> > >
> > > > In the tutorial,the mri data stored in only one file, while the
> > > > data which
> > >
> > > > I used have many files, I don't know how to process. who can
> > > > help me,Thanks1
> > > > Thanks very much!
> > > > Best Reagards
> > > > Jing Wang
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > > ----The following is the content of the forwarded email----
> > > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > > Date?2013-05-21 23:59:18
> > > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > > >
> > > > Send fieldtrip mailing list submissions to
> > > > fieldtrip at science.ru.nl
> > > >
> > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > or, via email, send a message with subject or body 'help' to
> > > > fieldtrip-request at science.ru.nl
> > > >
> > > > You can reach the person managing the list at
> > > > fieldtrip-owner at science.ru.nl
> > > >
> > > > When replying, please edit your Subject line so it is more
> > > > specific
> > > > than "Re: Contents of fieldtrip digest..."
> > > >
> > > >
> > > > Today's Topics:
> > > >
> > > > 1. Re: problem in connectivityanalysis (Gabriel Gonzalez
> > > > Escamilla)
> > > >
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > > From: Gabriel Gonzalez Escamilla < ggonesc at upo.es >
> > > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > > Message-ID: < 1348f6433edc26f9.519bb455 at upo.es >
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Thank you so much for your answer J?rn,
> > > >
> > > >
> > >
> > > > Now I got it, so, I will let the 'fourier' as input to
> > > > ft_connectivityanalysis, because for some indices I will need
> > > > the auto-spectrum, and if I fully undertood what you said, it
> > > > will be the same, as they always take the phase information from
> > > > the fourier transform. And fieltrip will automatically compute
> > > > the csd if the input is the frequency data.
> > > >
> > > >
> > >
> > > > Nevertheless, it give me some error when I tried to use the
> > > > output from 'powandcsd' of freqanalysis, always gives me a
> > > > matrix dimensions error, and when I use the output 'fourier'
> > > > from connectivityanalysis, it computes almost all indices to ok,
> > > > raging from? -1 to 1 (I'm saw that they are signed, so this is
> > > > ok), the problem are the ImC ranging from -inf to inf, and the
> > > > PLV values ranging from 0 to inf, but when I use the 'fourier'
> > > > the values are. Which for me is really weird.
> > > >
> > > >
> > > >
> > >
> > > > I have checked internally, and even when I always use the
> > > > 'fourier' as input, when it internally calculates cross-spectrum
> > > > for the ImC and PLV, the data.crsspctrm is different, e.g:
> > > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > > ans size(data.crsspctrm) = [1 7 59 59];
> > > >
> > >
> > > > So, both are apparently the same, but the data inside this
> > > > matrices is different,
> > > >
> > > >
> > >
> > > > for example, when calculating the ImC the first 7 columns for
> > > > the first two rows are:
> > > > val(:,:,1,1)
> > > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i?
> > > > 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > > >
> > > > while when calculating the PLV are:
> > > > val(:,:,1,1)
> > > > ?[1? 1? 1? 1? 1? 1? 1]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i?
> > > > 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > > >
> > > >
> > > >
> > >
> > > > I'm pretty sure I'm doing something wrong here, but I don't
> > > > really have a clue,
> > > >
> > > >
> > >
> > > > If I use the fourier transform to calculate the 'csd' in
> > > > ft_connectivity analysis and use this csd as input to all other
> > > > ft_connectivityanalysis indices all of them are set to NaN or 1,
> > > > not ranging between any numbers.
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > > > On the other hand, I have seen searching on the net, that
> > > > fieltrip is capable of create surrogate data, by shifting the
> > > > phase information on every trial for only one electrode of each
> > > > pair while using the original samples of each trials on the
> > > > second channel, but I couldn't find on the manual how to do such
> > > > a thing. Is there any way to compute this kind of surrogates for
> > > > every sensor? or was it something that some one suggest to
> > > > somebody?
> > > >
> > > >
> > > > Many thanks in advanced,
> > > > Gabriel.
> > > >
> > > >
> > > >
> > > >
> > > > ----- Mensaje original -----
> > > > De: "J?rn M. Horschig" < jm.horschig at donders.ru.nl >
> > > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > > A: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Dear Gabriel,
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > >
> > >
> > > > > No. You should think of coherence more as a measure for the
> > > > > consistency of the phase relation between channels across
> > > > > trials, so coherence is just not defined per trial,neither
> > > > > would it make sense to compute coherence for a single trial.
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too? I see some terminology issues here. Let me try
> > > > > to explain in a simple (aka least-mathematical I can think of)
> > > > > way:
> > > > >
> > > >
> > >
> > > > > For all these connectivity measures, we need the phase
> > > > > information from the Fourier transform (FFT) to compute the
> > > > > cross-spectral density matrix (CSD). The CSD can be regarded
> > > > > as the equivalent in the frequency domain to the covariance
> > > > > matrix in the time domain, thus it is a measures how a certain
> > > > > channels activity is co-modulated with another channels
> > > > > activity (for a particular frequency) - makes pretty much
> > > > > sense to make use of this when computing connectivity, right?
> > > > > :)
> > > >
> > >
> > > > > As you might know, a Fourier transform returns complex
> > > > > numbers, where the imaginary part of this number contains
> > > > > phase information. When calling ft_freqanalysis, you can
> > > > > decide if it shall only return the (squared) real part of the
> > > > > frequency spectrum (cfg.output='pow'), or instead the full CSD
> > > > > (cfg.output = 'powandcsd'). Alternatively, you can also let
> > > > > ft_freqanalysis return the raw Fourier coefficients
> > > > > (cfg.output='fourier'). From the Fourier coefficients,
> > > > > however, you can easily obtain the CSD or the power spectrum
> > > > > basically by multiplication the Fourier matrix with itself
> > > > > (transposed). All of these measures quantify the phase
> > > > > relation between channels across trials, and as phase
> > > > > information is coded in the imaginary part of the fourier
> > > > > output, thus for connectivityanalysis you need the CSD which
> > > > > can be obtained either by 'powandcsd' or by 'fourier'.
> > > > >
> > > > > I hope that somehow clarifies your questions.
> > > > >
> > > > > Best,
> > > > > J?rn
> > > > >
> > > > > On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > > > > Dear Fieltrip experts,
> > > > >
> > > >
> > >
> > > > > I have my continuous data imported to fieldtrip with matlab,
> > > > > I'm looking for performing connectivity analysis between pairs
> > > > > of sensors, I have succed as:
> > > >
> > >
> > > > > data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59
> > > > > channels and 2000 samples
> > > > > data.label {59x1};
> > > > > data.time {1xNepochs};
> > > > >
> > > > > then, calculate only the FFT of all sensors as:
> > > > > cfg=[];
> > > > > cfg.output='fourier';
> > > > > cfg.method='mtmfft';
> > > > > cfg.taper='hanning';
> > > > > cfg.foilim=[8.5 9.5];
> > > > > cfg.tapsmofrq=0;
> > > > > cfg.trials='all';
> > > > > cfg.keeptrials='yes';
> > > > > cfg.channel='all';
> > > > > fourier=ft_freqanalysis(cfg, data)
> > > > > as output I get:
> > > > > dimord = 'rpttap_chan_freq'
> > > > > freq= [1x9]
> > > > > fourierspctrm=[7x59x9 double]
> > > > >
> > > > > Then compute the imaginary part of coherency as:
> > > > > cfg=[];
> > > > > cfg.method ='cohe';
> > > > > cfg.complex='imag';
> > > > > cfg.channelcbm={'all' 'all'};
> > > > > coher = ft_connectivityanalysis (cfg, fourier)
> > > > > as output get:
> > > > > dimord='chan_chan_freq';
> > > > > cohspctrm=[59x59x9 double];
> > > > > dof=7;
> > > > >
> > > > > I have two main questions:
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Many thanks in advanced,
> > > > > Gabriel.
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > _______________________________________________ > fieldtrip
> > > > > mailing list >
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > >
> > > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for
> > > > > Brain, Cognition and Behaviour > Centre for Cognitive
> > > > > Neuroimaging > Radboud University Nijmegen > Neuronal
> > > > > Oscillations Group > FieldTrip Development Team > > P.O. Box
> > > > > 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: >
> > > > > E-Mail:
> > > > jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:
> > > > http://www.ru.nl/donders
> > >
> > > > > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
> > > > > > NL-6525 EN Nijmegen > The Netherlands >
> > > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > >
> > >
> > > > <font size="3">--------------------------<br />PhD. student
> > > > Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional
> > > > Neuroscience<br />Department of Physiology, Anatomy, and Cell
> > > > Biology<br />University Pablo de Olavide<br />Ctra. de Utrera,
> > > > Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > > > ggonesc at upo.es <br /> http://www.upo.es/neuroaging/es/ </font>
> > > >
> > > >
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> > > >
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> > > >
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> > > >
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> > >
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> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 30, Issue 36
> > *****************************************
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From yukaokazaki at gmail.com  Fri May 31 08:21:56 2013
From: yukaokazaki at gmail.com (Yuka Okazaki)
Date: Fri, 31 May 2013 15:21:56 +0900
Subject: [FieldTrip] single subject headmodel and mni-transformed grid
	doesn't fit
Message-ID: <CAKHP_vRT6Ad1nLLOoaUoA5UFTLK5x-yp5jm8+HtY9sD6FER4dQ@mail.gmail.com>

Dear all

I have a problem that single subject headmodel and the warped its grid to
template grid do not fit, as attached figure. I expected they are exactly
fit each other but it seems not.

I generated this figure by following steps. MEG system is yokogawa.
Any advices I should check will be very helpful and appreciated.

Yuka

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
load('~\fieldtrip\template\sourcemodel\standard_sourcemodel3d10mm.mat')
template_grid  = sourcemodel;

% Read mri data
mri2nifti('subject.mri', 'mri.nii');
mri_nifti = ft_read_mri('mri.nii');

% Define fiducial position in MRI coordinate
cfg = [];
cfg.method = 'interactive';
mri = ft_volumerealign(cfg, mri_nifti);

% segment the anatomical MRI
cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg, mri);

% construct volume conductor model (i.e. head model) for each subject
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
vol = ft_convert_units(vol, 'cm');

% create the subject specific grid, using the template grid that has just
been created
cfg = [];
cfg.grid.warpmni   = 'yes';
cfg.grid.template  =  template_grid; %sourcemodel%
cfg.grid.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri;
grid               = ft_prepare_sourcemodel(cfg);

% make a figure of the single subject headmodel, and grid positions
figure;
ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4;
ft_plot_mesh(grid.pos(grid.inside,:),'vertexcolor','r');[image: Inline
image 1]
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From politzerahless at gmail.com  Fri May 31 08:27:19 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Fri, 31 May 2013 01:27:19 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 45
In-Reply-To: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
References: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k_9EcqcEeuGM_F8O7u0047tct6P9ZP-pLf2xdJ61p1tNMA@mail.gmail.com>

Hi Arjen,

Thanks for your message; I did indeed re-align to Talairach after
reslicing, although I can't be sure it was "correct" (the page linked from
the tutorial, http://neuroimage.usc.edu/brainstorm/CoordinateSystems,
didn't give guidelines on how anterior/posteriorly to place the
interhemispheric point, so I just placed it near the top of the head on
about the same plane as the commisures). But it wasn't until the end of the
anatomical processing that I noticed the issue, so I'm wondering if there's
a way to re-align the source space and volume conduction model to each
other without going back to the beginning of the pipeline.

Best,
Steve


> Message: 1
> Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
> From: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about minimum norm estimate pipeline
> Message-ID:
>         <
1914237354.1292588.1369980683984.JavaMail.root at sculptor.zimbra.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve, A quick guess; did you correctly align your resliced mri to
Talairach space by indicating the commissures (
http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm
correct, a point in the same place, e.g. between the hemispheres? This
should update the transformation matrix. Best regards, Arjen -----
Oorspronkelijk bericht -----
> > Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> > Aan: fieldtrip at science.ru.nl
> > Verzonden: Vrijdag 31 mei 2013 05:53:45
> > Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> > Hello all,
> > I have not yet gotten a response to my question below, but in the
> > meantime I have another question about the minimum norm estimate
> > workflow--specifically, about the coordinate system for the
> > skull-stripped anatomy in the step described at
> >
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> > . I'm confused by the following bit of code:
> > % ensure that the skull-stripped anatomy is expressed in the same
> > coordinate system as the anatomy
> > seg.transform = mri_tal.transform;
> > In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> > re-aligning to Talairach in the previous step?) whereas seg.coordsys
> > is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> > (But mri_tal also has a field mri_tal.transformorig, which seg does
> > not have.) So should I really be using the same transform for both, as
> > shown in the tutorial?
> > Apologies if this question is pretty basic; I'm just trying to
> > pinpoint where the mis-alignment described in my message below
> > occurred, so I want to make sure I understand each step of the
> > workflow correctly
> > Best,
> > Steve
> > > Message: 1
> > > Date: Sat, 25 May 2013 08:11:18 -0500
> > > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > > To: fieldtrip at donders.ru.nl
> > > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > > Message-ID:
> > > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > > >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hello all,
> > >
> > > I am going through the workflow at
> > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > > making
> > > the volume conduction model using ft_prepare_headmodel(), I noticed
> > > that
> > > although the volume conduction model and sourcespace have the same
> > > orientation and overall size/shape (after I converted the volume
> > > conduction
> > > model to cm, which wasn't in the tutorial but my original model came
> > > out in
> > > mm), they don't quite line up, as you can see in this figure:
> > >
> > > http://i.imgur.com/mGEtLOa.png
> > >
> > > I did interactively re-align the data to CTF (twice--in step 2 of
> > > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > > model")
> > > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > > anatomical data"), so I'm not sure how it ended up this way. The
> > > code I've
> > > used at each step is basically the same as that in the tutorial.
> > >
> > > Is there any way to line up my volume conduction model and
> > > sourcespace now,
> > > without going back and re-running most of the workflow?
> > >
> > > Best,
> > > Steve
> > >
> > > --
> > > Stephen Politzer-Ahles
> > > University of Kansas
> > > Linguistics Department
> > > http://people.ku.edu/~sjpa/
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From stefan.debener at uni-oldenburg.de  Fri May 31 09:18:51 2013
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Fri, 31 May 2013 09:18:51 +0200
Subject: [FieldTrip] Open ostdoc position
Message-ID: <51A84EDB.6010408@uni-oldenburg.de>

The cluster of excellence Hearing4all: Models, Technology and Solutions 
for Diagnostics, Restoration and Support of Hearing at the Carl von 
Ossietzky Universität Oldenburg (in collaboration with Medizinische 
Hochschule Hannover and Leibniz Universität Hannover) is seeking to fill 
the position of a

*Postdoctoral Research Associate in the Field of Auditory 
Psychophysiology *

in the Department of Psychology, Faculty of Medicine and Health Sciences.

The position is available from 1 September 2013, for initially 2 years, 
with prospect for continuation for up to 2.5 more years. Payment is 
depending on previous experience (German TV-L E13, full time).

A paramount goal of the cluster of excellence Hearing4all 
(www.hearing4all.de) is to transform audiology into an "exact" science 
based on the interplay between experiment and theory as well as between 
basic science and clinical research. In the framework provided by the 
cluster the successful candidate is expected to contribute to the 
research goals of task group 2 "Audioneurotechnology and theragnostics" 
or task group 7 "Brain-computer interface for hearing devices", e.g., by:

- studying hearing disorder related maladaptive plasticity in the human 
auditory cortex with non-invasive techniques (EEG, MEG, NIRS);

- electrophysiological characterisation of auditory cortex adaption to 
hearing device use (hearing aids, cochlear implants);

- the role of auditory neurofeedback on speech comprehension;

- the role of multisensory processes in auditory rehabilitation.

Candidates are expected to have an academic university degree in the 
field of psychology, biology, neuroscience, or a related discipline and 
have shown their ability to perform excellent scientific work, usually 
demonstrated by the outstanding quality of their Doctorate/PhD research 
and a good publication record. We are seeking candidates with extensive 
knowledge in at least one of the following methods: advanced EEG 
recording and analysis; near-infrared spectroscopy. Excellent Matlab 
skills are mandatory and good knowledge of EEG analysis software suites 
(e.g., EEGLAB, Fieldtrip, BESA, LORETA) will be an asset. It is also 
necessary to have a background in experimental psychology, and knowledge 
of the German language is required. The Department of Psychology will 
offer an attractive scientific environment with access to research 
dedicated state-of-the-art approaches to human neurophysiological 
techniques (fMRI, NIRS, EEG, MEG, mobile EEG and mobile eye-tracking).

The University of Oldenburg strives to increase the proportion of women 
in science, so we especially encourage female candidates to apply. 
Handicapped applicants will be given preference if equally qualified.

Please send your application including a cover letter, CV, list of 
potential referees, links to recent publications, and copies of 
certificates for academic grades by email to Prof. Stefan Debener 
(Stefan.Debener at uni-oldenburg.de 
<mailto:Stefan.Debener at uni-oldenburg.de>). Feel free to contact Stefan 
Debener for further questions regarding the position. The application 
deadline is July 15, 2013.

-- 
Prof. Dr. Stefan Debener
Neuropsychology	Lab
Department of Psychology
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email: stefan.debener at uni-oldenburg.de

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From baharbahar395 at yahoo.com  Fri May 31 09:48:25 2013
From: baharbahar395 at yahoo.com (Bahar Bahar)
Date: Fri, 31 May 2013 15:48:25 +0800 (SGT)
Subject: [FieldTrip] format conversion
Message-ID: <1369986505.7865.YahooMailNeo@web192306.mail.sg3.yahoo.com>

Hi dear all,

I have a technical question about format converter module via sLORETA software (.slor file to .txt one). Can any one give me some information about the conversion procedure (and the meaning of the column and row of the output file)?

Thanks,
bahar
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From mbj0310 at gmail.com  Fri May 31 11:11:33 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Fri, 31 May 2013 18:11:33 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
	<CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
Message-ID: <CA+v9jvLXKGfwUE4TkGx9t703fQnrtJVi=0w6ZFGBYVLKAvseSw@mail.gmail.com>

Dear respondent,

Thank you for your advices.
I will try these methods.

Best regards




2013/5/30 Chungki Lee <dr.chungki.lee at gmail.com>

> Hi Min
>
> you'd better use ft_definetrial routine before  ft_preprocessing.
>
> example)
>
>     cfg                              = [];
>     cfg.dataset                 = filename;  % string
>     cfg.trialdef.eventtype  =  your define text; % string
>     cfg.trialdef.eventvalue = your label value;  % integer
>     cfg.trialdef.prestim    = before onset time (sec); % positive
> integer, not negative integer
>     cfg.trialdef.poststim   = after onset time (sec); % positve integer
>     cfg                            = ft_definetrial(cfg);
>     data                          = ft_preprocessing(cfg);
>
> have fun ^^
>
>
> 2013/5/30 Beom Jun Min <mbj0310 at gmail.com>
>
>> Dear Julian Keil,
>>
>> Thank you for your reply.
>> I agree with that your problem was similar with mine.
>> My data was acquired by Neuroscan also.
>> There might a problem associated with .CNT file in the newer version.
>>
>> Could you tell me the number of the older version you used?
>>
>> Best Regards
>>
>>
>>
>> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>>
>>> Dear BJ Min,
>>>
>>> what type of data are you trying to read in?
>>> I had similar problems when reading in .CNT data.
>>> Also, with some systems you have to specify the bit rate (e.g.
>>> Neuroscan).
>>> For me, reading in data with an older version of FieldTrip solved the
>>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>>> files has been solved.
>>>
>>> Good Luck
>>>
>>> Julian
>>>
>>>  ********************
>>> *Dr. Julian Keil*
>>> *
>>> *
>>> AG Multisensorische Integration
>>> Psychiatrische Universitätsklinik
>>> der Charité im St. Hedwig-Krankenhaus
>>> Große Hamburger Straße 5-11, Raum E 307
>>> 10115 Berlin
>>>
>>> Telefon: +49-30-2311-1879
>>> Fax:        +49-30-2311-2209
>>>
>>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>>
>>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>>
>>> Dear all,
>>>
>>> Hello, my name is BJ Min from Korea.
>>>
>>> I'm dealing with EEG data of many subjects.
>>>
>>> When I run ft_preprocessing, the error message below shows with only
>>> some files of my data. (not all files)
>>>
>>>  Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>> ??? Error using ==> ft_read_data at 149
>>> cannot read data after the end of the file
>>>
>>> Error in ==> ft_preprocessing at 577
>>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>>> cfg.dataformat)
>>>
>>> I think that there might be a kind of problem in data acquisition, and I
>>> modified below scripts in the ft_read_data function with comment %.
>>>
>>> % % test whether the requested data segment is not outside the file
>>> % if any(begsample<1)
>>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>>> of the file');
>>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>>> the file');
>>> % end
>>>
>>> After that, the ft_preprocessing worked well.
>>>
>>> However, the files with the first problem showed additional warning
>>> message while running ft_definetrial. (not error message)
>>>
>>> Warning: Integer operands are required for colon operator when used as
>>> index
>>> > In fileio\private\loadcnt at 464
>>>   In ft_read_header at 1450
>>>   In ft_preprocessing at 398
>>>
>>> Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>>
>>> Also, during ft_redefinetrial, following warning message occurs.(not
>>> error message)
>>>
>>> Warning: removing inconsistent sampleinfo
>>> > In ft_datatype_raw at 97
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 104
>>>
>>> Warning: the trial definition in the configuration is inconsistent with
>>> the actual data
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 74
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> Warning: reconstructing sampleinfo by assuming that the trials are
>>> consecutive segments of a continuous recording
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 79
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> I wonder if these messages during ft_redefinetrial mean wrong defining
>>> trials.
>>> Should I continue these process like this, modifying the
>>> ft_preprocessing function?
>>> Or, is it better to exclude some erroneous files?
>>>
>>> Best regards
>>>
>>> --
>>> BeomJun Min, M.D.
>>>
>>> Department of Medical System Engineering (DMSE)
>>> Gwangju Institute of Science and Technology (GIST)
>>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>>> 500-712, Republic of Korea (South)
>>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> ----------------------------------------------------------------
> Chungki Lee, Ph.D.
> Post-doc
> Biomedical Research Institute
> Korea Institute of Science and Technology
> E-mail: chungki at kist.re.kr
> Tel:+82-2-958-5636, C.P: +82-10-5223-7309
> ----------------------------------------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From thomas.wunderle at esi-frankfurt.de  Fri May 31 11:42:03 2013
From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas)
Date: Fri, 31 May 2013 09:42:03 +0000
Subject: [FieldTrip] channel combination problems
Message-ID: <27E5CAD9145EEC41BB9B34C01716A1983046156B@UM-EXCDAG-A01.um.gwdg.de>

Hi all,

I'm new in fieldtrip and I try to get the cfg.channelcmb to work, because I want to plot the connectivity between the channels of different laminar electrodes,
let's say the connectivity between channel 1:24 and 25:38

I tried the following:
cfg           = [];
cfg.method    = 'mtmfft';
cfg.taper     = 'dpss';
cfg.output    = 'fourier';
cfg.tapsmofrq = 1;
freq          = ft_freqanalysis(cfg, data)

The output is:
>> freq
freq =
            label: {3x1 cell}
           dimord: 'rpttap_chan_freq'
            freq: [1x101 double]
            fourierspctrm: [500x3x101 double]
            cumsumcnt: [500x1 double]
            cumtapcnt: [500x1 double]
             cfg: [1x1 struct]


I then run

cfg           = [];
cfg.method    = 'coh';
cfg.channelcmb = {freq.label{1} freq.label{2};freq.label{2} freq.label{1}};
coh= ft_connectivityanalysis(cfg, freq);

And the output here is:

>> coh
coh =
       labelcmb: {2x2 cell}
       dimord: 'chan_freq'
       cohspctrm: [2x101 double]
        freq: [1x101 double]
        dof: 500
        cfg: [1x1 struct]

As you can seen, the output of dimord is 'chan_freq' so in the subsequent call of ft_connectivityplot I get an error message:

cfg           = [];
cfg.parameter = 'cohspctrm';
ft_connectivityplot(cfg, coh);

??? Error using ==> ft_connectivityplot at 99
the data should have a dimord of chan_chan_freq or chancmb_freq


If I use in ft_freqanalysis the cfg.method = 'powandcsd', cfg.channelcmb seems to have no effect at all,
the coherence is computed for all possible pairs.

I also don't understand the difference between "cfg.channelcmb" and "cfg.labelcmb"

Can you help me in how I should correctly use the cannelcmb and labelcmb options?

Thanks for your help,
Thomas



-----
Dr. Thomas Wunderle
Ernst Strüngmann Institute (ESI) for Neuroscience<http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
in Cooperation with Max Planck Society <http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
Deutschordenstrasse 46
60528 Frankfurt am Main, Germany
www.esi-frankfurt.de<http://www.esi-frankfurt.de/>
thomas.wunderle at esi-frankfurt.de<mailto:thomas.wunderle at esi-frankfurt.de>
Tel:   +49 69 96769 519
Fax:   +49 69 96769 555

Sitz der Gesellschaft: Frankfurt am Main
Registergericht: Amtsgericht Frankfurt - HRB 84266
Geschäftsführer: Prof. Dr. Pascal Fries


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From sid.kouider at gmail.com  Fri May 31 11:56:19 2013
From: sid.kouider at gmail.com (Sid Kouider)
Date: Fri, 31 May 2013 11:56:19 +0200
Subject: [FieldTrip] postdoctoral position on EEG/BCI in Paris
Message-ID: <007701ce5de5$1b083620$5118a260$@gmail.com>

The Department of Cognitive Science at the Ecole Normale Supérieure (Paris)
invites applications for a postdoctoral position to work on Brain-Computer
Interfaces and Virtual Reality in the framework of the CEEDs European
project ( <http://ceeds-project.eu/> http://ceeds-project.eu/). 

 

The post-doc will mainly be in charge of :

1) setting a BCI loop between a virtual environment and an EEG system

2) optimize online detection of specific EEG patterns 

3) participate in the design and elaboration of research protocols.

 

The successful applicant will be affiliated to the Brain and Consciousness
team of Pr Sid Kouider (http://www.lscp.net/persons/sidk/). The Department
of Cognitive Science offers a rich research environment composed of a
multidisciplinary set of research units on philosophy, cognitive psychology,
cognitive neurosciences and computational neurosciences. Our research team,
at the interface of these disciplines, is working on the cognitive and
neural determinants of consciousness, with an emphasis on the distinction
between unconscious perception and perceptual awareness. Our lab is  located
in central Paris, within the historical Quartier Latin.

 

Candidates should have at least a PhD degree in a relevant domain and a
solid training in EEG, Brain-Computer interfaces and machine learning.
Experience with virtual reality is desirable but not a prerequisite.

 

The position will start on September 1st, 2013.

The appointment is for one year initially but can be extended later on.

The net salary will range between 2 100 and 2 500 euros/month depending on
qualifications.

 

Consideration of applicants will commence June 1st, 2013 and will continue
until the position is filled.

 

Knowledge of French is not required as the team is international and verbal
interactions are primarily in English. 

 

Please send a CV along with the names and contact information of two
references to Sid Kouider (sid.kouider at ens dot fr) and Cécile Girard
(cecilegirard20 @ gmail dot com)

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Pr Sid Kouider, CNRS research director

Ecole Normale Supérieure

LSCP, Pavillon Jardin,

29 rue d'Ulm, 75005 Paris, France

www.lscp.net/persons/sidk/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

 

 

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From haiteng.jiang at gmail.com  Fri May 31 12:15:59 2013
From: haiteng.jiang at gmail.com (Haiteng Jiang)
Date: Fri, 31 May 2013 12:15:59 +0200
Subject: [FieldTrip] time-domain granger causality in Fieldtrip?
Message-ID: <CAHSK_TRQUv9aqda123QUWA9jfWpWaJzpBnWxF0QTO08xtM58pA@mail.gmail.com>

Hi all,
   is it possible to run time-domain granger causality in Fieldtrip?
                                                         Best,
                                                          Haiteng






-- 
Haiteng Jiang
PhD candidate
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen

Visiting address
Room 2.32
Donders Centre for Cognitive Neuroimaging
Kapittelweg 29
6525 EN  Nijmegen
the Netherlands

 Tel.: +31 (0)243668291
 Web:  https://sites.google.com/site/haitengjiang/
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From d.lozanosoldevilla at fcdonders.ru.nl  Fri May 31 15:49:03 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Fri, 31 May 2013 15:49:03 +0200 (CEST)
Subject: [FieldTrip] error when using ctf2grad
In-Reply-To: <51A7A9A1.6020401@gmail.com>
Message-ID: <2006439449.1303047.1370008143778.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Ye, Are you using a recent fieldtrip version? The ctf2grad function has recently updated improving its robustness. I don't have any clue why G3AR but it basically means that your CTF system has a specific gradiometer balancing. By the way, which CTF system are you using: CTF64, CTF151, CTF275? In any case, I could have a look if you file a bug and send to me the *.res4 file and we'll figure out what's happening (but please try with a recent Fieldtrip version and tell me) Regarding your gradiometer question, I asked Robert and this is the answer we can provide (please correct me if I'm wrong here), the CTF system sensors consist in first-order axial gradiometer that measure the magnetic field gradient change in the radial direction (orthogonal to the scalp). The following is taken from the CTF documentation "MEG File Formats - release 5.2.1" appendix C. --- Higher-order gradiometer formation is a noise-cancellation technique exclusive to the CTF MEG System. It permits the MEG detectors to be sensitive to the weak signals of the brain, yet impervious to the much stronger sources from the environment. This process, which is carried out in real time, allows the system to be run without the expense of magnetic shielding, or in combination with a standard shielded room for enhanced noise reduction. In order to calculate the forward solution, the same procedure must be performed on any field data calculated from a simulated dipole. The procedure consists of calculating the field at each coil in the sensor as well as each coil in a set of reference channels. The field values at the reference channels are then multiplied by the appropriate weight and subtracted from the MEG sensor channels. --- The data set on disk contains in the header the parameters that are used to convert the data between the original (raw) representation and the higher-order gradiometer representation. This conversion can be done in real-time during acquisition, but can also be done (and undone) afterwards using CTF DataEditor, or using ft_denoise_synthetic.m function. The grad structure included in the FieldTrip representation (i.e. hdr.grad or data.grad) should be consistent with the data, hence it contains grad.balance.current grad.balance.G1BR grad.balance.G2BR grad.balance.G3BR and potentially other "balancing" schemes (your "G3AR " for instance). The grad.balance.current describes which balancing was applied to the data and to the specification of the sensor array (grad.tra) for the forward computation. In order to provide a more intuitive description, I've made a wiki FAQ to explain How does the CTF higher-order gradiometer work: http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work All the best, Diego ----- Original Message -----
> From: "Ye Mei" <frank.ye.mei at gmail.com> > To: fieldtrip at science.ru.nl > Sent: Thursday, 30 May, 2013 9:33:53 PM > Subject: [FieldTrip] error when using ctf2grad > Hi All, > > I have some problem using ctf2grad. > > The program will set grad.balance.current = 'G3AR';, > and then do getfield(grad.balance, grad.balance.current) > but > grad.balance = G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > > and has no G3AR in it. So an error will pop up. > > Can anyone help me with that? > > Also, What do G1BR, G2BR, G3BR, G3AR stand for? > > > thanks, > Ye > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/
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From lkystra at hotmail.it  Fri May 31 17:15:01 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Fri, 31 May 2013 17:15:01 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>, ,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>,
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>,
	<4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
Message-ID: <DUB107-W21B51E9DC3913CBC8A1A05D9920@phx.gbl>

Hi Jan-Mathijs,
the specifies that you asked to me, are: 

fieldtrip version: 20130401
operating system: windows 7
matlab version : I use R2011a (64bits) or R2007b (32bits)

I
 want to read a portion of my EEG signal of 3600 sec * 500 Hz. When I used
 a previous version of fieldtrip (2011-12-14), the lenght of the window wasn't 3600*500 but less. 

" Warning: Integer operands are required for colon operator when used as index 
> In read_edf at 348 "

With fieldtrip 20130401 the length of the window is right, but, when I plot the signal, I can see its distorsion.
Thank you for your attention,
Lucia

From: jan.schoffelen at donders.ru.nl
Date: Thu, 30 May 2013 18:31:22 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

Hi Lucia,
Perhaps you need to be a bit more specific. In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.Otherwise all of us are shooting in the dark.Best wishes,Jan-Mathijs

On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')


2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
Dear all,
I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
  Zriouil Imane



_______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nlTelephone: +31-24-3614793
http://www.hettaligebrein.nl



_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From ebrahimi_nia at yahoo.com  Fri May 31 17:56:55 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Fri, 31 May 2013 08:56:55 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <51A78CC1.6030906@berkeley.edu>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
	<51A78CC1.6030906@berkeley.edu>
Message-ID: <1370015815.5183.YahooMailNeo@web122402.mail.ne1.yahoo.com>

Dear respondent,

Thank you for your advices.
I have used the function that you have updated. It works out. Can you give me information about the output structure (What do the matrixes refer to?) or advise a reference to study about that please? 

Best,
Fatemeh



________________________________
 From: Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu>
To: fieldtrip at science.ru.nl 
Sent: Thursday, May 30, 2013 10:30 AM
Subject: Re: [FieldTrip] loreta2fieldtrip function error
 


Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug,
    see http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export
    the source data as a text file. You can read that text file in with
    loreta2fieldtrip.m. It's a bit of a patch, but it worked for me. 

Hope this helps,
Ingrid


On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:

Hi dear all,
>
>
>I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
>MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.
>
>
>**** Error using fread
>
>Invalid precision.
>Error in loreta2fieldtrip (line 85)
>activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
>
>Can someone give me a help?
>
>
>
>Best regards,
>Fatemeh
>
>
>
>
>_______________________________________________
fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From robince at gmail.com  Fri May 31 18:14:15 2013
From: robince at gmail.com (Robin)
Date: Fri, 31 May 2013 17:14:15 +0100
Subject: [FieldTrip] some of the requested samples occur twice
Message-ID: <CALsWBNOxcuA=LCMONaGWObU4fdZ3+vskGGFcKdTZE4jGRoW47Q@mail.gmail.com>

I have a problem in preprocessing where I am getting this error:

"""
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 262)
      dat{trlop} = ft_fetch_data(data,        'header', hdr, 'begsample',
      trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding,
      'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous,'no
Error in ft_artifact_muscle (line 158)
    [tmpcfg, artifact] = ft_artifact_zvalue(tmpcfg, data);
"""

I think this is because I am manually adding some extra padding to the
trials so that the artifact filtering can use that padding (I am doing
the artifact filtering on data in memory which is output from
ft_denoise_pca). So in this case it is not a problem if consecutive
trials overlap a bit.

I would therefore like to disable this error and wondered what is the
best way to do it. I am a bit confused because ft_artifact_zvalue
calls ft_fetch data with a "checkboundary" option which looks like it
might be what I want (and set correctly), but ft_fetch_data doesn't
seem to use that option. Instead it has an allowoverlap option.

So for now I will manually add the allowoverlap option to the call in
ft_artifact_zvalue, but I wondered what checkboundary doesn't appear
in ft_fetch_data or if this might be a bug.

Cheers

Robin


From eelke.spaak at donders.ru.nl  Wed May  1 09:40:01 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 1 May 2013 09:40:01 +0200
Subject: [FieldTrip] beggining Help
In-Reply-To: <f1d7aa427e33f400.517f0918@upo.es>
References: <f1d7aa427e33f400.517f0918@upo.es>
Message-ID: <CABPNLUosNHWq+LkeH-xUtWp4+t4aXkMyMqr=pO_HoepNpTBigg@mail.gmail.com>

Dear Gabriel,

Since you indicate that you are "completely new to fieldtrip and
almost new to EEG analysis", I would recommend you get started by
going through some of our tutorials:
http://fieldtrip.fcdonders.nl/tutorial These will help get you
acquainted with FieldTrip's work style, as well as teach you some
basics of EEG analysis. Understanding of the basics is vital if you
want to (sensibly) do connectivity analysis later on.

There are also some tutorials on connectivity, which you will find on
the same page.

As for getting your data into FieldTrip, all FT data is encapsulated
in a Matlab structure. Once your data is in Matlab, you can make a FT
structure out of it by creating a structure that resembles the output
of ft_preprocessing. Refer to the documentation for ft_datatype_raw
for details on this
(http://fieldtrip.fcdonders.nl/reference/ft_datatype_raw or "edit
ft_datatype_raw" in matlab).

Best, and good luck,
Eelke

On 29 April 2013 23:58, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear fieldtrip experts,
>
>
> I'm completely new to fieldtrip and almost new to the EEG analysis, I have
> resting-state EEG registers for my subjects in txt format, that I can load
> into matlab into something like: #timeSamples x #sensors. And I know the
> name and order of  all sensors
>
> I want to calculate the imaginary coherence, the PPC, the PLI and WPLI from
> my data, but I couldn't find how to do so in the manual. Can anyone help me
> with the steps to achieve that goal?
> I want to get those indices between all pairs of sensors, and chosen pairs
> (sensors manually selected according to my hypothesis), I hope it be
> posssible.
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jose.herrero66 at gmail.com  Wed May  1 12:08:19 2013
From: jose.herrero66 at gmail.com (Jose Herrero)
Date: Wed, 1 May 2013 06:08:19 -0400
Subject: [FieldTrip] ft_mvaranalysis with unequal length trials
Message-ID: <CA+zL3byUZEhYX3-T-Q5XQRGd1fSHEJCJu6KWT-B8Zz8bHXeNQg@mail.gmail.com>

Hi,

using ft_mvaranalysis with unequal length trials, i encountering the
following error (see below). This error does not occur after commenting out
line 241 where the data gets preprocessed. Is this ok?

mdata       = ft_mvaranalysis(cfg, trials)
the input is raw data with 25 channels and 237 trials
removing 234 trials in which no data was selected
the call to "ft_redefinetrial" took 0 seconds
preprocessing
preprocessing trial 3 from 3

the call to "ft_preprocessing" took 0 seconds
??? Index exceeds matrix dimensions.

Error in ==> ft_mvaranalysis at 293
  maxtim = max(maxtim, data.time{k}(end));


-- 
Jose L Herrero, PhD
Department of Psychiatry
Columbia University College of Physicians and Surgeons
Cognitive Neuroscience and Schizophrenia Program
Nathan S. Kline Institute for Psychiatric Research
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From robince at gmail.com  Wed May  1 18:41:37 2013
From: robince at gmail.com (Robin)
Date: Wed, 1 May 2013 17:41:37 +0100
Subject: [FieldTrip] MNE tutorial
Message-ID: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From joerg.neuberg at tu-ilmenau.de  Wed May  1 20:42:25 2013
From: joerg.neuberg at tu-ilmenau.de (=?utf-8?Q?J=C3=B6rg_Neuberg?=)
Date: Wed, 1 May 2013 20:42:25 +0200
Subject: [FieldTrip] Error: requested samples occur twice in the data
Message-ID: <27F2D05FEDC14EF9839BD48C5B218D24@JoergPC>

Hi FieldTrippers,

we are students using fieldtrip for a project at our university. Now, we have some trouble. We want to search for muscle artifacts and we receive an error message.
We started our signal processing with “ft_definetrial” to define the trials and “ft_preprocessing” to become our data. Then we cut out the stimulus artifact and interpolated the gaps. The data is saved as mat-file.

Now, we are looking for muscle artifacts with the following code:

---------- begin code --------
% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel = 'MEG*';
cfg.artfctdef.zvalue.cutoff      = 0.5;
cfg.artfctdef.zvalue.trlpadding  = 0;   
cfg.artfctdef.zvalue.fltpadding  = 0;
cfg.artfctdef.zvalue.artpadding  = 0.1;

cfg.artfctdef.muscle.bpfilter    = 'yes';
cfg.artfctdef.muscle.bpfreq      = [110 140];
cfg.artfctdef.muscle.bpfiltord   = 2;
cfg.artfctdef.muscle.bpfilttype  = 'but';
cfg.artfctdef.muscle.hilbert     = 'yes';
cfg.artfctdef.muscle.boxcar      = 0.2;

% make the process interactive
cfg.artfctdef.zvalue.interactive = 'yes';

[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);
---------- end code --------

Unfortunately there is an error and we haven’t an idea where is the problem. Maybe the overlap of the trials is a reason for this. But we can’t change this for our data because we need this trial length. Example: trial 1 from 100 to 120, trial 2 from 115 to 135.

---------- begin error --------
searching for artifacts in 306 channel
searching trials.Error using ft_fetch_data (line 123)
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 260)
      dat{trlop} = ft_fetch_data(data,        'header', hdr,
      'begsample', trl(trlop,1)-fltpadding, 'endsample',
      trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary',
      strcmp(cfg.continuous,'no
Error in muscle_artifacts (line 53)
[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);”
---------- end error --------

Do you have any idea to help us? We would be grateful for any help.

Greetings,
Joerg
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From robince at gmail.com  Thu May  2 14:04:03 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 13:04:03 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
Message-ID: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>

Running the full Freesurfer reconstruction pipeline (without the hybrid
skull stripping and Talaraich alignment on the fieldtrip side) appears to
have been successful.

However, when I try to continue with the tutorial I find that my volume and
source grid don't line up (even before any issues converting to sensor
space):

Figure: http://imgur.com/uo9uPUc (code below)

Does anyone have any idea what could be wrong?

What coordinate system is the sub-oct-6-src.fif file in (created by MNE
suite)?
If it is in talairach coordinates, how do I load the Talairach aligned
image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)

Do I need to manually include the transform from transform/talairach.xfm?
To include that can I use it directly as mri.transform in fieldtrip or do I
need to multiply it by the existing mri.transform which is there when
loading the raw anatomy scan (.img)? Come to think of it what does that
transform represent?

Sorry if these are not fieldtrip questions but I am trying to follow the
fieldtrip MNE tutorial so I was hoping someone might know.

Thanks

Robin

% load freesurfer image
mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
% load MNE grid% computed with mne_setup_source_space --ico -6
bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code
'-oct-6-src.fif']), 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
% Volume conduction model
cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
seg = ft_volumesegment(cfg, mri_fs_tal);
cfg = [];cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
% Check volume conduction
figure; hold on
ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight

On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From brungio at gmail.com  Thu May  2 14:26:10 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:26:10 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEs8D9eEdweRBGDhjGtXK_299sguhE9nqYYXG5ftRZi1pA@mail.gmail.com>

Hi Robin,

I had a similar problem during the field trip course. In my case I found
out that one set of coordinates was in mm and then other in m, so I just
had to multiply one set of coordinates.

Another thing you should be aware of is that you can segment your
anatomical using procedures other than the default ones. For example, Spm12
has new, better procedures. Importing an already prepared segmentation in
ft requires some hacking, but if you are interested I can tell you how as
soon as I get a decent internet connection.

Finally, remember that the single shell model is not that great. You should
prepare a better volume conduction model.

    Bruno
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:28:16 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:28:16 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>

Ah, I just saw that your problem might be with the origin of the anatomical
space. Have you tried to see what happens if you set its origin to the
anterior commissure before giving it in input to field trip?
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:42:08 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:42:08 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
	<CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
Message-ID: <CAGgLGEs+cJ_8Bxi=gEt=QhFv31oaRD2DfxHoosadVsiP8vU86Q@mail.gmail.com>

Sorry, my replies were not meant for the list.
On May 2, 2013 8:28 AM, "Bruno L. Giordano" <brungio at gmail.com> wrote:

> Ah, I just saw that your problem might be with the origin of the
> anatomical space. Have you tried to see what happens if you set its origin
> to the anterior commissure before giving it in input to field trip?
> On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:
>
>>  Running the full Freesurfer reconstruction pipeline (without the hybrid
>> skull stripping and Talaraich alignment on the fieldtrip side) appears to
>> have been successful.
>>
>> However, when I try to continue with the tutorial I find that my volume
>> and source grid don't line up (even before any issues converting to sensor
>> space):
>>
>> Figure: http://imgur.com/uo9uPUc (code below)
>>
>> Does anyone have any idea what could be wrong?
>>
>> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
>> suite)?
>> If it is in talairach coordinates, how do I load the Talairach aligned
>> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>>
>> Do I need to manually include the transform from transform/talairach.xfm?
>> To include that can I use it directly as mri.transform in fieldtrip or do I
>> need to multiply it by the existing mri.transform which is there when
>> loading the raw anatomy scan (.img)? Come to think of it what does that
>> transform represent?
>>
>> Sorry if these are not fieldtrip questions but I am trying to follow the
>> fieldtrip MNE tutorial so I was hoping someone might know.
>>
>> Thanks
>>
>> Robin
>>
>> % load freesurfer image
>> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
>> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
>> % load MNE grid% computed with mne_setup_source_space --ico -6
>> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
>> sourcespace = ft_convert_units(bnd, 'cm');
>> % Volume conduction model
>> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
>> seg = ft_volumesegment(cfg, mri_fs_tal);
>> cfg = [];cfg.method = 'singleshell';
>> vol = ft_prepare_headmodel(cfg, seg);
>> % Check volume conduction
>> figure; hold on
>> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
>> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>>
>> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>>
>> I am trying to run through the MNE tutorial here:
>>
>> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>>
>> Unfortunately after the volumetric processing in freesurfer my
>> intermediate result looks wrong.
>>
>> I have followed the steps (including interactive alignment to
>> Talairach) according to the tutorial. I wondered if anyone has any
>> idea what could be wrong, or could point to some more possible
>> diagnostic commands to run?
>>
>> The original Subject01.mgz file seems to have been saved correctly.
>> But if I load the orig.mgz created with:
>> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
>> and plot it with ft_sourceplot it has the same offset and upside down
>> position as the final incorrectly segments freesurfer image. Could
>> this indicate a problem?
>>
>> Thanks for any help,
>>
>> Cheers
>>
>> Robin
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
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From robince at gmail.com  Thu May  2 15:46:22 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 14:46:22 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CALsWBNOLx+KZ93GFdEi+wtdXujYwth1GniK8o3H-cJvd2KGsTA@mail.gmail.com>

By running from MNE suite:
mne_setup_mri --subject BON02 --mri T1

to create a COR.fif image from the Freesurfer output (including Talaraich
transformation) at least that COR.fir and the oct-6-src.fif mesh seem to
line up.

But now I am not sure which coordinate system they are in? (cordsys is
'neuromag' in fieldtrip) nor how to obtain the necessary inverse transform
from this space to the raw anatomy voxel space (so I can build the
transform from oct-6-src mesh to sensor space; I already have the transform
to take the original raw anatomy .img to the sensor coordinate system).

Thanks,

Robin

On Thu, May 2, 2013 at 1:04 PM, Robin <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
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From jan.schoffelen at donders.ru.nl  Thu May  2 15:57:00 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 15:57:00 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
Message-ID: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
> 
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
> 
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
> 
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
> 
> The cohspctrm looks like this:
> val(:,:,1,1) =
> 
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
> 
> I get the following warning during ft_connectivityanalysis
> 
> Warning: Divide by zero.
>> In ft_connectivity_corr at 103
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>> In ft_connectivity_corr at 104
>  In ft_connectivityanalysis at 524
> 
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
> 
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From lmelloni at gmail.com  Thu May  2 18:56:19 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 12:56:19 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
Message-ID: <-7204743264059944684@unknownmsgid>

Hi jan-mathijs

Unfortunately I get the same result whether or not I remove the mean.
Best,
-- Lucía

On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

Hi!
I am trying to calculate coherence using ft_connectivityanalysis, but
I am getting only ones and infinity as output in cohspctrm with all of
my data sets.

I first run ft_freqanalysis with
cfg.method = 'mtmfft';
cfg.taper = 'dpss';
cfg.output = 'fourier';
cfg.foilim = [1 45];
cfg.tapsmofrq = 1;
cfg.keeptrials = 'yes';
cfg.keeptapers = 'yes';
freq = ft_freqanalysis(cfg, data);

Whether I do or I do not specify cfg.channel and cfg.channelcmb here
does not seem to make a difference for my problem later on. The
spectra look absolutely fine.

I then run ft_connectivityanalysis with
cfg.method    = 'coh';
cfg.removemean= 'yes';
cfg.trials    = 'all';
cfg.feedback  = 'yes';
cfg.complex   = 'abs';
coh           = ft_connectivityanalysis(cfg, freq);

The cohspctrm looks like this:
val(:,:,1,1) =

    1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
Inf   Inf   Inf (etc.)

I get the following warning during ft_connectivityanalysis

Warning: Divide by zero.

In ft_connectivity_corr at 103

 In ft_connectivityanalysis at 524
Warning: Divide by zero.

In ft_connectivity_corr at 104

 In ft_connectivityanalysis at 524

The same happens if I try to calculate PLV through ft_connectivityanalysis.
This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
Windows 7 (64bit).

Any advice?
Thanks!
Lucia
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


Jan-Mathijs Schoffelen, MD PhD

Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From jan.schoffelen at donders.ru.nl  Thu May  2 21:12:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 21:12:22 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <-7204743264059944684@unknownmsgid>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
Message-ID: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>

Hi Lucia,

The warnings indicate that you are dividing by zero. Are you sure that your cfg is correct?

Please try

cfg = [];
cfg.method = 'coh';
coh = ft_connectivityanalysis(cfg, freq);

This should work.

Best,
Jan-Mathijs

On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:

> Hi jan-mathijs
> 
> Unfortunately I get the same result whether or not I remove the mean. 
> Best,
> -- Lucía
> 
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> 
>> Hi Lucia,
>> 
>> Could you remove cfg.removemean = 'yes' and try again?
>> 
>> Best,
>> 
>> Jan-Mathijs
>> 
>> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>> 
>>> Hi!
>>> I am trying to calculate coherence using ft_connectivityanalysis, but
>>> I am getting only ones and infinity as output in cohspctrm with all of
>>> my data sets.
>>> 
>>> I first run ft_freqanalysis with
>>> cfg.method = 'mtmfft';
>>> cfg.taper = 'dpss';
>>> cfg.output = 'fourier';
>>> cfg.foilim = [1 45];
>>> cfg.tapsmofrq = 1;
>>> cfg.keeptrials = 'yes';
>>> cfg.keeptapers = 'yes';
>>> freq = ft_freqanalysis(cfg, data);
>>> 
>>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>>> does not seem to make a difference for my problem later on. The
>>> spectra look absolutely fine.
>>> 
>>> I then run ft_connectivityanalysis with
>>> cfg.method    = 'coh';
>>> cfg.removemean= 'yes';
>>> cfg.trials    = 'all';
>>> cfg.feedback  = 'yes';
>>> cfg.complex   = 'abs';
>>> coh           = ft_connectivityanalysis(cfg, freq);
>>> 
>>> The cohspctrm looks like this:
>>> val(:,:,1,1) =
>>> 
>>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>> Inf   Inf   Inf (etc.)
>>> 
>>> I get the following warning during ft_connectivityanalysis
>>> 
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 103
>>>  In ft_connectivityanalysis at 524
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 104
>>>  In ft_connectivityanalysis at 524
>>> 
>>> The same happens if I try to calculate PLV through ft_connectivityanalysis.
>>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>>> Windows 7 (64bit).
>>> 
>>> Any advice?
>>> Thanks!
>>> Lucia
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> Jan-Mathijs Schoffelen, MD PhD 
>> 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> 
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>> 
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>> 
>> http://www.hettaligebrein.nl
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From evaladez at psych.udel.edu  Thu May  2 23:07:51 2013
From: evaladez at psych.udel.edu (Emilio Valadez)
Date: Thu, 2 May 2013 17:07:51 -0400
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
Message-ID: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>

Dear FieldTrippers,

I am trying to compute phase-amplitude coupling (PAC) between the phase of theta activity at one channel and the amplitude of gamma activity at another channel over a specific time window within trials. I have read that PAC is captured with a phase-locking value (PLV), which leads me to think that this might be computed with ft_connectivityanalysis. If this is true, what would the configuration structure and input data need to look like? Or, is there an alternative way to compute PAC using FieldTrip? Thank you in advance!

All the best,
Emilio
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From lmelloni at gmail.com  Fri May  3 00:56:30 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 18:56:30 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
Message-ID: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>

Hi Jan-Mathijs,
still the same result with the code that you suggested.

selection fourierspctrm along dimension 2
averaging crsspctrm over rpt
removing dimension rpt from crsspctrm
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 87
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 89
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 106
  In ft_connectivityanalysis at 524
the call to "ft_connectivityanalysis" took 0 seconds


Lucia

-- 
Lucia.


On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Lucia,
>
> The warnings indicate that you are dividing by zero. Are you sure that
> your cfg is correct?
>
> Please try
>
> cfg = [];
> cfg.method = 'coh';
> coh = ft_connectivityanalysis(cfg, freq);
>
> This should work.
>
> Best,
> Jan-Mathijs
>
> On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
> Hi jan-mathijs
>
> Unfortunately I get the same result whether or not I remove the mean.
> Best,
> -- Lucía
>
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
> Hi Lucia,
>
> Could you remove cfg.removemean = 'yes' and try again?
>
> Best,
>
> Jan-Mathijs
>
> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>
> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
>
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
>
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
>
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
>
> The cohspctrm looks like this:
> val(:,:,1,1) =
>
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
>
> I get the following warning during ft_connectivityanalysis
>
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 103
>
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 104
>
>  In ft_connectivityanalysis at 524
>
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
>
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jm.horschig at donders.ru.nl  Fri May  3 08:32:30 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 03 May 2013 08:32:30 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
Message-ID: <518359FE.4070207@donders.ru.nl>

Dear Lucia,

could you try whether the error persists with a recent version? If it 
does, could you go test whether this code gives the same error:

/
% ************* code starts here /
/%dummy data
cfg             = [];
cfg.ntrials     = 500;
cfg.triallength = 1;
cfg.fsample     = 200;
cfg.nsignal     = 3;
cfg.method      = 'ar';
cfg.params(:,:,1) = [ 0.8 0   0;
                       0   0.9 0.5;
                       0.4 0   0.5];
cfg.params(:,:,2) = [-0.5    0  0;
                         0 -0.8  0;
                         0    0 -0.2];
cfg.noisecov      = [0.3 0 0;
                        0 1 0;
                        0 0 0.2];

data            = ft_connectivitysimulation(cfg);


% freqanalysis
cfgf           = [];
cfgf.method    = 'mtmfft';
cfgf.output    = 'fourier';
cfgf.tapsmofrq = 2;
freq           = ft_freqanalysis(cfgf, data);

% connectivityanalysis
cfgc           = [];
cfgc.method    = 'coh';
c1             = ft_connectivityanalysis(cfgc, freq);

c1.cohspctrm//
% ************* code ends here
/
The code snippet above is part of our test suite for making sure that 
everything works fine. If it does work for you, but does not with your 
own data instead of simulated data, the error must be somewhere in your 
data, e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that 
it will all work fine if you use an updated version of FieldTrip.

Best,
Jörn


On 5/3/2013 12:56 AM, Lucia Melloni wrote:
> Hi Jan-Mathijs,
> still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
> Lucia
>
> -- 
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen 
> <jan.schoffelen at donders.ru.nl <mailto:jan.schoffelen at donders.ru.nl>> 
> wrote:
>
>     Hi Lucia,
>
>     The warnings indicate that you are dividing by zero. Are you sure
>     that your cfg is correct?
>
>     Please try
>
>     cfg = [];
>     cfg.method = 'coh';
>     coh = ft_connectivityanalysis(cfg, freq);
>
>     This should work.
>
>     Best,
>     Jan-Mathijs
>
>     On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
>>     Hi jan-mathijs
>>
>>     Unfortunately I get the same result whether or not I remove the
>>     mean.
>>     Best,
>>     -- Lucía
>>
>>     On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen
>>     <jan.schoffelen at donders.ru.nl
>>     <mailto:jan.schoffelen at donders.ru.nl>> wrote:
>>
>>>     Hi Lucia,
>>>
>>>     Could you remove cfg.removemean = 'yes' and try again?
>>>
>>>     Best,
>>>
>>>     Jan-Mathijs
>>>
>>>     On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>>
>>>>     Hi!
>>>>     I am trying to calculate coherence using
>>>>     ft_connectivityanalysis, but
>>>>     I am getting only ones and infinity as output in cohspctrm with
>>>>     all of
>>>>     my data sets.
>>>>
>>>>     I first run ft_freqanalysis with
>>>>     cfg.method = 'mtmfft';
>>>>     cfg.taper = 'dpss';
>>>>     cfg.output = 'fourier';
>>>>     cfg.foilim = [1 45];
>>>>     cfg.tapsmofrq = 1;
>>>>     cfg.keeptrials = 'yes';
>>>>     cfg.keeptapers = 'yes';
>>>>     freq = ft_freqanalysis(cfg, data);
>>>>
>>>>     Whether I do or I do not specify cfg.channel and cfg.channelcmb
>>>>     here
>>>>     does not seem to make a difference for my problem later on. The
>>>>     spectra look absolutely fine.
>>>>
>>>>     I then run ft_connectivityanalysis with
>>>>     cfg.method    = 'coh';
>>>>     cfg.removemean= 'yes';
>>>>     cfg.trials    = 'all';
>>>>     cfg.feedback  = 'yes';
>>>>     cfg.complex   = 'abs';
>>>>     coh           = ft_connectivityanalysis(cfg, freq);
>>>>
>>>>     The cohspctrm looks like this:
>>>>     val(:,:,1,1) =
>>>>
>>>>         1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>>>     Inf   Inf   Inf (etc.)
>>>>
>>>>     I get the following warning during ft_connectivityanalysis
>>>>
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 103
>>>>      In ft_connectivityanalysis at 524
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 104
>>>>      In ft_connectivityanalysis at 524
>>>>
>>>>     The same happens if I try to calculate PLV through
>>>>     ft_connectivityanalysis.
>>>>     This is with Fieldtrip version 20130422 and 20130427, Matlab
>>>>     R2009a,
>>>>     Windows 7 (64bit).
>>>>
>>>>     Any advice?
>>>>     Thanks!
>>>>     Lucia
>>>>     _______________________________________________
>>>>     fieldtrip mailing list
>>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>     Jan-Mathijs Schoffelen, MD PhD
>>>
>>>     Donders Institute for Brain, Cognition and Behaviour,
>>>     Centre for Cognitive Neuroimaging,
>>>     Radboud University Nijmegen, The Netherlands
>>>
>>>     Max Planck Institute for Psycholinguistics,
>>>     Nijmegen, The Netherlands
>>>
>>>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>>>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>>>
>>>     http://www.hettaligebrein.nl <http://www.hettaligebrein.nl/>
>>>
>>>     _______________________________________________
>>>     fieldtrip mailing list
>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>     Jan-Mathijs Schoffelen, MD PhD
>
>     Donders Institute for Brain, Cognition and Behaviour,
>     Centre for Cognitive Neuroimaging,
>     Radboud University Nijmegen, The Netherlands
>
>     Max Planck Institute for Psycholinguistics,
>     Nijmegen, The Netherlands
>
>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>
>     http://www.hettaligebrein.nl
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From gregor.volberg at psychologie.uni-regensburg.de  Fri May  3 09:35:40 2013
From: gregor.volberg at psychologie.uni-regensburg.de (Gregor Volberg)
Date: Fri, 03 May 2013 09:35:40 +0200
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
In-Reply-To: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
References: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
Message-ID: <518368CC.9030102@psychologie.uni-regensburg.de>

Dear Emilio,

I might not be fully up to date with the functionality of 
ft_connectivityanalysis, but as much as I know there is some 
preprocessing necessary to get a phase-to-amplitude coupling. A common 
strategy is to compute a Hilbert transform on the upper frequency band. 
This can be used to get the 'analytic amplitude', which is essentially a 
waveform that connects the amplitude peaks of the higher frequency. If 
the gamma amplitude is driven by the theta phase, then the analytic 
waveform  should be phase-locked with the theta cycle. The latter part 
of the analysis could be performed with the option 'plv' in 
ft_connectivityanalysis.
For the processing steps you might want to have a look at an example 
script  at http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh.

Best regards,
Gregor



Am 02.05.2013 23:07, schrieb Emilio Valadez:
> Dear FieldTrippers,
>
> I am trying to compute phase-amplitude coupling (PAC) between the phase
> of theta activity at one channel and the amplitude of gamma activity at
> another channel over a specific time window within trials. I have read
> that PAC is captured with a phase-locking value (PLV), which leads me to
> think that this might be computed with ft_connectivityanalysis. If this
> is true, what would the configuration structure and input data need to
> look like? Or, is there an alternative way to compute PAC using
> FieldTrip? Thank you in advance!
>
> All the best,
>
> Emilio
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>

-- 
Dr. rer. nat. Gregor Volberg
Institut für Psychologie
Universität Regensburg
Universitätsstraße 31
D-93053 Regensburg, Germany
Tel: +49 941 943 3862
Fax: +49 941 943 3233


From lmelloni at gmail.com  Fri May  3 14:48:01 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Fri, 3 May 2013 08:48:01 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <518359FE.4070207@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
	<518359FE.4070207@donders.ru.nl>
Message-ID: <CA+_59hd_kx38K4817yAKBnQdd6wSQsb6yTyb-0wQgU_v-8VdPw@mail.gmail.com>

Hi Jörn,
I downloaded version 20130502 and ran both my code and the test code that
you had emailed. I get 1 and inf with both.
The freq input seems to be ok, so ist must be an issue with
ft_connectivityanalysis.
Lucia

-- 
Lucia.


On Fri, May 3, 2013 at 2:32 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Lucia,
>
> could you try whether the error persists with a recent version? If it
> does, could you go test whether this code gives the same error:
>
> *
> % ************* code starts here *
> *%dummy data
> cfg             = [];
> cfg.ntrials     = 500;
> cfg.triallength = 1;
> cfg.fsample     = 200;
> cfg.nsignal     = 3;
> cfg.method      = 'ar';
> cfg.params(:,:,1) = [ 0.8 0   0;
>                       0   0.9 0.5;
>                       0.4 0   0.5];
> cfg.params(:,:,2) = [-0.5    0  0;
>                         0 -0.8  0;
>                         0    0 -0.2];
> cfg.noisecov      = [0.3 0 0;
>                        0 1 0;
>                        0 0 0.2];
>
> data            = ft_connectivitysimulation(cfg);
>
>
> % freqanalysis
> cfgf           = [];
> cfgf.method    = 'mtmfft';
> cfgf.output    = 'fourier';
> cfgf.tapsmofrq = 2;
> freq           = ft_freqanalysis(cfgf, data);
>
> % connectivityanalysis
> cfgc           = [];
> cfgc.method    = 'coh';
> c1             = ft_connectivityanalysis(cfgc, freq);
>
> c1.cohspctrm**
> % ************* code ends here
> *
> The code snippet above is part of our test suite for making sure that
> everything works fine. If it does work for you, but does not with your own
> data instead of simulated data, the error must be somewhere in your data,
> e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that it will
> all work fine if you use an updated version of FieldTrip.
>
> Best,
> Jörn
>
>
>
> On 5/3/2013 12:56 AM, Lucia Melloni wrote:
>
>  Hi Jan-Mathijs,
>  still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
>  Lucia
>
> --
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Lucia,
>>
>>  The warnings indicate that you are dividing by zero. Are you sure that
>> your cfg is correct?
>>
>>  Please try
>>
>>  cfg = [];
>> cfg.method = 'coh';
>> coh = ft_connectivityanalysis(cfg, freq);
>>
>>  This should work.
>>
>>  Best,
>> Jan-Mathijs
>>
>>  On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>>
>>  Hi jan-mathijs
>>
>>  Unfortunately I get the same result whether or not I remove the mean.
>> Best,
>> -- Lucía
>>
>> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
>> jan.schoffelen at donders.ru.nl> wrote:
>>
>>  Hi Lucia,
>>
>>  Could you remove cfg.removemean = 'yes' and try again?
>>
>>  Best,
>>
>>  Jan-Mathijs
>>
>>  On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>
>>  Hi!
>> I am trying to calculate coherence using ft_connectivityanalysis, but
>> I am getting only ones and infinity as output in cohspctrm with all of
>> my data sets.
>>
>> I first run ft_freqanalysis with
>> cfg.method = 'mtmfft';
>> cfg.taper = 'dpss';
>> cfg.output = 'fourier';
>> cfg.foilim = [1 45];
>> cfg.tapsmofrq = 1;
>> cfg.keeptrials = 'yes';
>> cfg.keeptapers = 'yes';
>> freq = ft_freqanalysis(cfg, data);
>>
>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>> does not seem to make a difference for my problem later on. The
>> spectra look absolutely fine.
>>
>> I then run ft_connectivityanalysis with
>> cfg.method    = 'coh';
>> cfg.removemean= 'yes';
>> cfg.trials    = 'all';
>> cfg.feedback  = 'yes';
>> cfg.complex   = 'abs';
>> coh           = ft_connectivityanalysis(cfg, freq);
>>
>> The cohspctrm looks like this:
>> val(:,:,1,1) =
>>
>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>> Inf   Inf   Inf (etc.)
>>
>> I get the following warning during ft_connectivityanalysis
>>
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 103
>>
>>  In ft_connectivityanalysis at 524
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 104
>>
>>  In ft_connectivityanalysis at 524
>>
>> The same happens if I try to calculate PLV through
>> ft_connectivityanalysis.
>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>> Windows 7 (64bit).
>>
>> Any advice?
>> Thanks!
>> Lucia
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>   _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From vale.niccolai at gmail.com  Fri May  3 15:09:58 2013
From: vale.niccolai at gmail.com (Valentina Niccolai)
Date: Fri, 3 May 2013 15:09:58 +0200
Subject: [FieldTrip] neuromag122_neighb
Message-ID: <CAF0jnAnVQrzd+jJPEwGO6FKKADNhdGinsQAAzfc0mrPcp0+LkQ@mail.gmail.com>

Hallo!

I would like to use the template neuromag122_neighb.mat to repair channels,
but it seems to me that this template contains labels form the neuromag306
system.  Is it right? And can I find the template somewhere?


Best,

Valentina
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From Markus.Butz at uni-duesseldorf.de  Fri May  3 16:06:24 2013
From: Markus.Butz at uni-duesseldorf.de (Markus Butz)
Date: Fri, 03 May 2013 15:06:24 +0100
Subject: [FieldTrip] Problems reading in DICOM
Message-ID: <75e09cb13160d.5183d270@uni-duesseldorf.de>




Thanks for your replies and help Robert, Jörn, and Eelke!
Finally it worked out, but the problem was rather on my side, as there where several series of different MRTs scans in one folder of which some did not work, some worked out strange as they had just some files (16-26), and some worked fine. Unfortunately I tried most intensively on the subject who came with no correct series at all. :-(  
To be fair, all the files appeared exactlty the same, but ft_read_mri is luckily mentioning which series it works on and how many files it include, which finally made me wonder. ;-) 
 
Thanks again and have a good weekend 
Markus 
  
ps: Sorry for the belated thanks! 
 
 

 
Am 13.03.13, schrieb Robert Oostenveld <r.oostenveld at donders.ru.nl>: 


> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Hi  
> 
> 
> DICOM files come with different extensions. I guess it depends on the scanner (Siemens/Philips/...). But the file format should be the same as it is a standard format, so the extension should not matter. The fileio/ft_filetype.m function detects both dcm and ima files as dicom.
> 
> 
> 
> if the files have no extension, the autodetection fails and you should explicitly specify the format as
>    mri = ft_read_mri('single_file_of_DICOM_series', 'format', 'dicom');
> I now realize that to be a hidden option. I'll get that fixed in the function documentation.
> 
> 
> 
> 
> 
> 
> I recommend that you specify a filename from somewhere in the middle of the stack of files. There are often a few localizer scans in the same directory, and these (due to the sorting of the file names) tend to end up at the beginning or end of the (alphabetical) directory listing. 
> 
> 
> cheers
> Robert
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 13 Mar 2013, at 14:22, Jörn M. Horschig wrote:
> 
> 
> 
> > 
> > 
> > Hi Markus,
> > 
> > I kept on avoiding these errors by using MRIcron's dcm2nii functionality: http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html
> > But pay attention to the coordinate system when importing it into FieldTrip afterwards, it can be quite a hassle...
> > 
> > Maybe Robert or JM know whether reading in .dcm files is possible, but I have to admit that I never tried ;) 
> > 
> > Best,
> > Jörn
> > 
> > On 3/13/2013 12:11 PM, Markus Butz wrote:
> > 
> > 
> > > 
> > > 
> > > 
> > > Dear list, 
> > > 
> > > 
> > > I am experiencing problems reading in external MRI in DICOM format from a CD (doing it the first time though). 
> > > I wanted to do it the new and easy way as described here:
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom
> > > 
> > > 
> > > % read the DICOM files 
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > 
> > > 
> > > However, I have no single slices with extension *.ima but one dataset with the extension *.dcm and the other dataset with no extension for the single slice files. I am also not sure where to copy the DICOMDIR file.
> > > 
> > > 
> > > When I try to open a single file of the *.dcm series I get:
> > > 
> > > 
> > > mri = ft_read_mri('508652C3.dcm');
> > > 
> > > 
> > > ??? Undefined function or variable "hdr".
> > > 
> > > 
> > > Error in ==> ft_read_mri at 216
> > >   hdr     = hdr(keep); 
> > > 
> > > 
> > > Trying to read in a single file of the no extension series I get:
> > > 
> > > 
> > > mri = ft_read_mri('73850486');
> > > 
> > > 
> > > ??? Error using ==> dicominfo at 41
> > > The specified file is not in DICOM format
> > > 
> > > 
> > > The Image Processing toolbox V 7.2 is installed and this is fieldtrip-20111101.
> > > 
> > > 
> > > Any help appreciated!
> > > 
> > > 
> > > Markus
> > > 
> > > 
> > > 
> > > 
> > >  
> > > 
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > 
> > 
> > 
> > 
> > -- 
> > Jörn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour 
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen 
> > Neuronal Oscillations Group
> > FieldTrip Development Team
> > 
> > P.O. Box 9101
> > NL-6500 HB Nijmegen
> > The Netherlands
> > 
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel:    +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> > 
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> > 
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 

 
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From jimparkinson at me.com  Fri May  3 22:57:26 2013
From: jimparkinson at me.com (Jim Parkinson)
Date: Fri, 03 May 2013 21:57:26 +0100
Subject: [FieldTrip] 2x2x3 Repeated Measures ANOVA in FT
Message-ID: <CACd4eMnmVjveKaT2xUf-H--Ld7PBNnkZhBQRN1JeaZ5OznppiQ@mail.gmail.com>

Hi All

Sorry for the very simplistic question here but I am finding it difficult
to construct an answer - if indeed there is one - from previous posts.

I have a study which is a 2x2x3 repeated measures design, event-related
using 64 channel EEG.  The design is  a culmination of a number of previous
studies, so in that sense is justified, and eyeballing the
data suggests that the effects are pulling in the directions we have
hypothesised.  I would really like to attempt to pull interaction effects,
main effects and then specified (a priori and justified)  contrasts from my
EEG data.  So, is it even possible using cluster permutation methods to
report 3-way, 2-way and main effect stats from such a design, and if so,
what is the best/most justifiable method? Secondly, considering the amount
of *possible*n simple contrasts available in a 2x2x3 design - even if I
don;t run them all because it is not meaningful to do so - what is the best
method to correct for multiple comparisons in the simpel contrasts I do end
up running?

Thans for any help in this confusing matter!

best,
 Jim
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From chadwick.boulay at gmail.com  Mon May  6 07:36:18 2013
From: chadwick.boulay at gmail.com (Chadwick Boulay)
Date: Mon, 06 May 2013 14:36:18 +0900
Subject: [FieldTrip] Please help me get component dipole fitting results
 using custom anatomy into normalized template for EEGLAB clustering.
Message-ID: <51874152.9090903@gmail.com>

Dear Fieldtrip users,

Using the subject's MRI and recorded EEG electrode locations, I've 
managed to segment the MRI, create the volume conduction model, align 
the electrodes, create a sourcemodel using a grid warped from the MNI 
template, create the leadfield, and perform ft_dipolefitting on IC 
weights (imported from EEGLAB). The geometry, electrode positions, and 
mri all line up (coordsys='ctf', unit='cm') and the calculated dipole 
positions are what I would expect.

[Aside: All of my topoplots have the electrodes positioned correctly 
relative to each other but the nose and ears are 90 degrees from where I 
would expect them. Do the topoplot functions not know how to deal with 
ctf coordsys?]

How can I normalize these dipole locations into the template brain so 
that I may perform component clustering in EEGLAB?
I have some ideas but I don't know how to implement them.

1) Calculate the transformation matrix to normalize the original MRI to 
the template MRI, then apply that transformation to the dipole positions 
and momentums. I'm guessing I need to use mri_norm = 
ft_volumenormalize(cfg, mri); but then I don't know how to use 
mri_norm.transform and mri_norm.initial. Further, the output of 
ft_dipolefitting doesn't seem to be suitable for ft_transform_geometry.

2) Since the sourcemodel grid is warped from the template brain, I can 
find the sourcemodel grid index closest to the dipole location then set 
the new dipole location to be the location of the template grid at the 
same index. I don't know how to do this for the momentum but I probably 
don't need the momentum for clustering.

3) Start over from the beginning, normalizing the MRI and the electrode 
locations as soon as possible then performing all subsequent 
calculations using the normalized geometry.

I searched the documentation and the list archives but I could not find 
an answer. I am surprised because I expected dipole normalisation to be 
a common requirement. Maybe I am missing something simple.
Thank you in advance for any help.
-Chad

-- 
Chadwick Boulay
JSPS Postdoctoral Fellow
Keio University
Yokohama Japan
boulay at brain.bio.keio.ac.jp




From mushfa.yousuf at googlemail.com  Mon May  6 14:47:44 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Mon, 6 May 2013 14:47:44 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
Message-ID: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>

Hello;

Yes you were right. I have defined the wrong sensors i.e 'grad' instead of
'elec' while calculating the Leadfield.

Actually I am trying to calculate Combined source reconstruction from both
EEG and MEG sensors.

Do you have any idea, how to define both elec and grad definition  while
calculating first forward then inverse solution.

Because in a fieldtrip either you can defined elec or grad at one time.


Regards;


Mushfa Yousuf

Neurozentrum,
Universitätsklinikum Schleswig-Holstein,
Campus Kiel (UKSH), Deutschland


On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:

> Hi Mushfa,
>
> My guess is that the channels that have you used to compute .csdspctrm are
> not the same as the channels in cfg.elec.    If you set cfg.channel =
> freqPost.label, does that solve it?
>
> Cheers,
> Johanna
>
>
> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>
>> Hello Fieldtrippers,
>>
>> I am doing source reconstruction using EEG channels on a fieldtrip.
>>
>> I have computed Forward solution i.e head model using  'Openmeeg' and
>> lead field successfully.
>>
>> For the inverse solution using 'dics' method, I wrote the following
>> syntax
>>
>>
>>
>>
>>
>>  cfg              = [];
>>  cfg.method       = 'dics';
>>  cfg.frequency    = 130;
>>  cfg.elec         = dataFIC12.hdr.elec;
>>  cfg.grid         = grid;
>>  cfg.vol          = vol;
>>
>>  sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>> and I have received the following error:
>>
>>
>> ??? Error using ==> mtimes
>> Inner matrix dimensions must agree.
>>
>> Error in ==> beamformer_dics at 314
>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>         leadfield
>>
>> Error in ==> ft_sourceanalysis at 595
>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>       squeeze(Cf(i,:,:)), optarg{:});
>>
>> Error in ==> newCode at 214
>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>>
>>
>> Any help would be appreciated.
>>
>>
>> Regards;
>>
>>
>> Mushfa Yousuf
>>
>> Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From chaowang0704 at gmail.com  Tue May  7 13:35:20 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 14:35:20 +0300
Subject: [FieldTrip] Some Questions on the resample design
Message-ID: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>

I
 have been using field-trip. Recently, I tried to use it for statistic
test by non-parametric method, e.g. bootstrap and permutation. As usual,
the two method involve resample original data with or without replacement.
I carefully inspected the code in the function *resampledesign* but I was
quite confused by the method in the bootstrap section:

254resample = zeros(cfg.numrandomization, Nrepl);
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From chaowang0704 at gmail.com  Tue May  7 14:08:57 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 15:08:57 +0300
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
Message-ID: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>

I'm sorry to make a mistake just now. The previous message sent didn't
fullfill my meaning.

I carefully inspected the code in the function *resampledesign* but I was
quite confused by the codes in the bootstrap section (For paired design,
the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
and design(2,N+1:2*N)=2 and N is for example the subject number; and
cfg.uvar=2):
91     Nvar  = size(design,1);   % number of factors or regressors
92     Nrepl = size(design,2);   % number of replications
...
...
248   units = design(cfg.uvar,:);
249   for k = 1:length(unique(units))
250     sel = find(units==k);
251     indx(:,k) = sel;
252     Nrep(k)   = length(sel);
253   end
254   resample = zeros(cfg.numrandomization, Nrepl);
...
...
274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
275   for i=1:cfg.numrandomization*10
276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
277   end

278   tmp = unique(tmp, 'rows');
279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
size(tmp,1), cfg.numrandomization*10);
...
...
292   for i=1:cfg.numrandomization
293      for k=1:size(indx,1)
294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
295      end
296   end

My question was on the code in 276 line. These code was to generate a
number of rand numbers (about cfg.numrandomization lines) in the range of 1
to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
If the function '*sort*' is used, then every row of matrix tmp is the same,
which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line to
the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
result is by no means what we want, I think. What we do want is several
rows numbers with same range but with distinct orders. Only in this way,
can we guarantee that each resample is not the same.



On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:

> I
> have been using field-trip. Recently, I tried to use it for statistic test
> by non-parametric method, e.g. bootstrap and permutation. As usual, the two
> method involve resample original data with or without replacement. I
> carefully inspected the code in the function *resampledesign* but I was
> quite confused by the method in the bootstrap section:
>
> 254resample = zeros(cfg.numrandomization, Nrepl);
>
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From zriouil.imane at gmail.com  Tue May  7 14:48:24 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 7 May 2013 14:48:24 +0200
Subject: [FieldTrip] convert .plx to .nex ?
Message-ID: <CABu=cReD7OPEna8o=40exmxV=QQvcWNxmbyj9w=mWzaJRPD2dg@mail.gmail.com>

Hi

i have a problem to read data with extension .plx and i want to convert
this to .nex. it's possible or no?

please respond me
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From johanna.zumer at donders.ru.nl  Tue May  7 14:53:40 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Tue, 7 May 2013 14:53:40 +0200
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
	<CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
Message-ID: <CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA@mail.gmail.com>

Dear Chao,

I'm not familiar with this piece of code, but I had a quick look.  Line
276, with the 'sort' command, is testing for the number of unique 'rows'
(line 278).  It then uses this information to modify the value of
cfg.numrandomization (line 283 which you have not displayed), which is
reduced if not enough unique information to do the requested number of
randomizations.   Then (I think) the actual randomization should be
occuring in subsequent lines of code (292-296).    Note also that this part
of code is only reached if max(design(cfg.uvar,:)) < 20.

Does that help?    Maybe someone else with more experience in this section
of code can comment as well?

Or if you still find that it indeed is not randomizing, you can file a bug
here (http://bugzilla.fcdonders.nl/), ideally with a small test script.

Cheers,
Johanna




2013/5/7 Chao Wang <chaowang0704 at gmail.com>

> I'm sorry to make a mistake just now. The previous message sent didn't
> fullfill my meaning.
>
> I carefully inspected the code in the function *resampledesign* but I was
> quite confused by the codes in the bootstrap section (For paired design,
> the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
> and design(2,N+1:2*N)=2 and N is for example the subject number; and
> cfg.uvar=2):
> 91     Nvar  = size(design,1);   % number of factors or regressors
> 92     Nrepl = size(design,2);   % number of replications
> ...
> ...
> 248   units = design(cfg.uvar,:);
> 249   for k = 1:length(unique(units))
> 250     sel = find(units==k);
> 251     indx(:,k) = sel;
> 252     Nrep(k)   = length(sel);
> 253   end
> 254   resample = zeros(cfg.numrandomization, Nrepl);
> ...
> ...
> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');
> 279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
> size(tmp,1), cfg.numrandomization*10);
> ...
> ...
> 292   for i=1:cfg.numrandomization
> 293      for k=1:size(indx,1)
> 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> 295      end
> 296   end
>
> My question was on the code in 276 line. These code was to generate a
> number of rand numbers (about cfg.numrandomization lines) in the range of 1
> to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
> If the function '*sort*' is used, then every row of matrix tmp is the
> same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line
> to the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
> result is by no means what we want, I think. What we do want is several
> rows numbers with same range but with distinct orders. Only in this way,
> can we guarantee that each resample is not the same.
>
>
>
> On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:
>
>> I
>> have been using field-trip. Recently, I tried to use it for statistic
>> test by non-parametric method, e.g. bootstrap and permutation. As usual,
>> the two method involve resample original data with or without replacement.
>> I carefully inspected the code in the function *resampledesign* but I
>> was quite confused by the method in the bootstrap section:
>>
>> 254resample = zeros(cfg.numrandomization, Nrepl);
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From antony.passaro at gmail.com  Wed May  8 23:17:21 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Wed, 8 May 2013 17:17:21 -0400
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
Message-ID: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>

 Hi Fieldtrippers,

I am trying to perform a group-level comparison of 2 conditions across 10
subjects based on the DTF connectivity. For the time being, we are looking
at the DTF for a subset of frequencies (alpha) and choosing the avgoverfreq
option which gives us a 4096 x 1 matrix since we are looking at 64 x 64
channels. Using ft_freqstatistics, I noticed that it will throw an error
explaining that there is not yet an implementation for data with channelcmb
for a cluster analysis so I took it upon myself to identify channel pairs
which should be considered neighbors and build a new neighbor structure
prior to running ft_freqstatistics. To do that, I took the basic neighbor
structure for 64 channels and then created a new neighbor structure of 4096
channel pairs based on the code below:

for i=1:4096
    label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
end

labelcmb = dtf.labelcmb;

chans=64;

%Identify the channel pairs which are neighbors with the target channel
NBtarget = {};
for ch=1:chans^2
    NBtarget(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,1},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat(x,['_' labelcmb{ch,2}]),{neighbours(
1,target).neighblabel},'UniformOutput',0);
    NBtarget(ch).neighblabel = tempnb{:};
end

%Identify the channel pairs which are neighbors with the reference channel
NBref = {};
for ch=1:chans^2
    NBref(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,2},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat([labelcmb{ch,1}
'_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
    NBref(ch).neighblabel = tempnb{:};
end


%Append both sets of neighbors (ref and target)
NBboth= {};
for ch=1:chans^2
    NBboth(ch).label = label{ch};
    NBboth(ch).neighblabel = [NBref(ch).neighblabel;
NBtarget(ch).neighblabel];
end


This seems to work and the clustering method proceeds without error. My
question is the following: is this the proper way to utilize the clustering
method using ft_freqstatistics on connectivity data or am I missing
something?

Thanks,
-Tony
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From chaowang0704 at gmail.com  Thu May  9 10:51:37 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Thu, 9 May 2013 11:51:37 +0300
Subject: [FieldTrip] Some Questions on the resample design (Johanna
	Zumer)
Message-ID: <CAGvTfVmzpDNoJ7FKbeeKHCzBPunx0J1+=b5yJKqxfs6qN9hHRw@mail.gmail.com>

Dear

Johanna,

Thank you! I understand your meaning and that's right
that
this part of code is only reached if

max(design(cfg.uvar,:)) < 20, but what I do not understand is that for what
reason,
the '20' is set to test the
max(design(cfg.uvar,:)). And besides, by using 'sort', each row of tmp will
be the same, in ascending order, which will lead the 278 line using
'unique' to have tmp only one row. That is size(tmp,1)=1; this will
lead to cfg.numrandomization=1
in 284 line.

> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');

Best regards!

Chao

Message: 4

> Date: Tue, 7 May 2013 14:53:40 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Some Questions on the resample design
> Message-ID:
>         <
> CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Chao,
>
> I'm not familiar with this piece of code, but I had a quick look.  Line
> 276, with the 'sort' command, is testing for the number of unique 'rows'
> (line 278).  It then uses this information to modify the value of
> cfg.numrandomization (line 283 which you have not displayed), which is
> reduced if not enough unique information to do the requested number of
> randomizations.   Then (I think) the actual randomization should be
> occuring in subsequent lines of code (292-296).    Note also that
> 
> this part
> of code is only reached if
> 
> max(design(cfg.uvar,:)) < 20.
>
> Does that help?    Maybe someone else with more experience in this section
> of code can comment as well?
>
> Or if you still find that it indeed is not randomizing, you can file a bug
> here (http://bugzilla.fcdonders.nl/), ideally with a small test script.
>
> Cheers,
> 
> Johanna
>
>
>
>
> 2013/5/7 Chao Wang <chaowang0704 at gmail.com>
>
> > I'm sorry to make a mistake just now. The previous message sent didn't
> > fullfill my meaning.
> >
> > I carefully inspected the code in the function *resampledesign* but I was
> > quite confused by the codes in the bootstrap section (For paired design,
> > the design matrix should be like this, design(1,:)=[1:N 1:N],
> design(2,1:N)=1
> > and design(2,N+1:2*N)=2 and N is for example the subject number; and
> > cfg.uvar=2):
> > 91     Nvar  = size(design,1);   % number of factors or regressors
> > 92     Nrepl = size(design,2);   % number of replications
> > ...
> > ...
> > 248   units = design(cfg.uvar,:);
> > 249   for k = 1:length(unique(units))
> > 250     sel = find(units==k);
> > 251     indx(:,k) = sel;
> > 252     Nrep(k)   = length(sel);
> > 253   end
> > 254   resample = zeros(cfg.numrandomization, Nrepl);
> > ...
> > ...
> > 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> > 275   for i=1:cfg.numrandomization*10
> > 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> > 277   end
> >
> > 278   tmp = unique(tmp, 'rows');
> > 279   fprintf('found %d unique rows in bootstrap matrix of %d
> bootstraps',
> > size(tmp,1), cfg.numrandomization*10);
> > ...
> > ...
> > 292   for i=1:cfg.numrandomization
> > 293      for k=1:size(indx,1)
> > 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> > 295      end
> > 296   end
> >
> > My question was on the code in 276 line. These code was to generate a
> > number of rand numbers (about cfg.numrandomization lines) in the range
> of 1
> > to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> > design and Nrep is the number of repetition (Nrep(:)=2 for paired
> design).
> > If the function '*sort*' is used, then every row of matrix tmp is the
> > same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278
> line
> > to the result: temp=1:Nrepl/Nrep(1) (because of the function unique).
> This
> > result is by no means what we want, I think. What we do want is several
> > rows numbers with same range but with distinct orders. Only in this way,
> > can we guarantee that each resample is not the same.
>
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From marianapbranco1 at gmail.com  Fri May 10 10:08:41 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Fri, 10 May 2013 10:08:41 +0200
Subject: [FieldTrip] Real-time processing
References: <9B1A8EA6-CCDE-4CED-83FD-C5D2F21607F5@student.tudelft.nl>
Message-ID: <31275A3B-B8D6-4C46-8B30-5EF745AD13BA@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From mengtongxiao at gmail.com  Fri May 10 11:39:29 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Fri, 10 May 2013 17:39:29 +0800
Subject: [FieldTrip] cooradinate
Message-ID: <CADiddyVv3S8CvCQY-RPFo4GTj1Su68U5WWdjmy2L9MwsCi1Emg@mail.gmail.com>

Dear all，

I got some ROIs from MNE. But  in MNE it use brain template that is *MNI152 .
*
I want use fieldtrip compute the spatial filter for ROIs.
For this reason ,I want got the position in sourcemodel from template in
fieldtrip.
I see the fieldtrip seem to use *MNI305  ,*isn,t it?
If fieldtrip use *MNI305 ,*  this problem is making me question whether a
transformation  is really necessary ?
The both "MNI" space cooradation * x ,y,z axis *represent right,anterior,
superior.(+x=right,+y=anterior,+z=superior)?(MNI cooradation from
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
I find infieldtrip (http://fieldtrip.fcdonders.nl/tutorial/connectivity)
sourcemodel is that *x ,y,z axis *represent anterior, right,superior?
If a transformation  is really necessary ,how should I do?

Then I am puzzed what do *x ,y,z axis *represent in stanard_1020.elc

Thanks for your help,
best,
xiao
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From mengtongxiao at gmail.com  Mon May 13 03:30:06 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Mon, 13 May 2013 09:30:06 +0800
Subject: [FieldTrip] grid-template
Message-ID: <CADiddyVrmgpO+fX+SoyY7cWHBXfc=4Tch9js+fcTV4V9QRfj_w@mail.gmail.com>

Dear all,

I want to konw what is  the MNI-template  that  constructed 3D-grids in the
fieldtrip (Template sourcemodels ) ?
is it MNI305 ,clin27 ,MNI125 or something else?

thanks,
xiao
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From jm.horschig at donders.ru.nl  Mon May 13 11:13:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 11:13:14 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
Message-ID: <5190AEAA.3020301@donders.ru.nl>

Dear Mushfa,

I think you have to compute two leadfield matrices, one for EEG (elec) 
and one for MEG (grad), and then concatenate these (and make sure that 
the order of sensors won't get mixed up anywhere, because  
sourceanalysis just expects the leadfield matrix to be ordered like your 
data. If that's not the case, you either encounter the previous error 
you described or (if the number of channels matches, but order is mixed 
up) it will just return wrong source estimated activity.

Best,
Jörn

On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
> Hello;
>
> Yes you were right. I have defined the wrong sensors i.e 'grad' 
> instead of 'elec' while calculating the Leadfield.
>
> Actually I am trying to calculate Combined source reconstruction from 
> both EEG and MEG sensors.
>
> Do you have any idea, how to define both elec and grad definition  
> while calculating first forward then inverse solution.
>
> Because in a fieldtrip either you can defined elec or grad at one time.
>
>
> Regards;
>
>
> Mushfa Yousuf
>
> Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer 
> <johanna.zumer at gmail.com <mailto:johanna.zumer at gmail.com>> wrote:
>
>     Hi Mushfa,
>
>     My guess is that the channels that have you used to compute
>     .csdspctrm are not the same as the channels in cfg.elec.    If you
>     set cfg.channel = freqPost.label, does that solve it?
>
>     Cheers,
>     Johanna
>
>
>     2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com
>     <mailto:mushfa.yousuf at googlemail.com>>
>
>         Hello Fieldtrippers,
>
>         I am doing source reconstruction using EEG channels on a
>         fieldtrip.
>
>         I have computed Forward solution i.e head model using
>          'Openmeeg' and lead field successfully.
>
>         For the inverse solution using 'dics' method, I wrote the
>         following syntax
>
>
>
>
>
>          cfg              = [];
>          cfg.method       = 'dics';
>          cfg.frequency    = 130;
>          cfg.elec         = dataFIC12.hdr.elec;
>          cfg.grid         = grid;
>          cfg.vol          = vol;
>
>          sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>         and I have received the following error:
>
>
>         ??? Error using ==> mtimes
>         Inner matrix dimensions must agree.
>
>         Error in ==> beamformer_dics at 314
>                 filt = pinv(lf' * invCf * lf) * lf' * invCf;          %
>                 Gross eqn. 3, use PINV/SVD to cover rank deficient
>                 leadfield
>
>         Error in ==> ft_sourceanalysis at 595
>               dip(i) = beamformer_dics(grid, sens, vol, [],
>         squeeze(Cf(i,:,:)), optarg{:});
>
>         Error in ==> newCode at 214
>         sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>
>
>         Any help would be appreciated.
>
>
>         Regards;
>
>
>         Mushfa Yousuf
>
>         Neurozentrum,
>         Universitätsklinikum Schleswig-Holstein,
>         Campus Kiel (UKSH), Deutschland
>
>
>         _______________________________________________
>         fieldtrip mailing list
>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From naran.kutt at gmail.com  Mon May 13 11:48:17 2013
From: naran.kutt at gmail.com (Narayanan Kutty)
Date: Mon, 13 May 2013 05:48:17 -0400
Subject: [FieldTrip] Mutual Information
Message-ID: <CAGgtWvU9tSr=6XGAt__T=mQUWQx-7h34oLjS_kgMekRkJYzdVQ@mail.gmail.com>

Hello All,

Are there any functions within fieldtrip to calculate mutual information
between channels at the sensor level. I remember that eeglab used to have a
plugin for that. Couldn't find anything in fieldtrip.

Thank you,
Naran.
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From jm.horschig at donders.ru.nl  Mon May 13 14:14:44 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 14:14:44 +0200
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
	<CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
Message-ID: <5190D934.5020407@donders.ru.nl>

Dear Tony,

I had a quick look at your code, and I think it is fine. However, I 
would define neighbours purely based on the target sensor, not on the 
reference, e.g. when computing cortico-muscular coherence on channel 
level, you  are interested in spatial clusters near the cortex and not 
in cluster on the arm where the reference sensor is.
Also check out this:

data = ft_checkdata(data, 'cmbrepresentation', 'full');

This will turn chancmb (Nx1) into chan X chan (RxS, where R*S = N).

Best,
Jörn

On 5/8/2013 11:17 PM, Antony Passaro wrote:
> Hi Fieldtrippers,
> I am trying to perform a group-level comparison of 2 conditions across 
> 10 subjects based on the DTF connectivity. For the time being, we are 
> looking at the DTF for a subset of frequencies (alpha) and choosing 
> the avgoverfreq option which gives us a 4096 x 1 matrix since we are 
> looking at 64 x 64 channels. Using ft_freqstatistics, I noticed that 
> it will throw an error explaining that there is not yet an 
> implementation for data with channelcmb for a cluster analysis so I 
> took it upon myself to identify channel pairs which should be 
> considered neighbors and build a new neighbor structure prior to 
> running ft_freqstatistics. To do that, I took the basic neighbor 
> structure for 64 channels and then created a new neighbor structure of 
> 4096 channel pairs based on the code below:
> for i=1:4096
> label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
> end
> labelcmb = dtf.labelcmb;
>
> chans=64;
> %Identify the channel pairs which are neighbors with the target channel
> NBtarget = {};
> for ch=1:chans^2
> NBtarget(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,1},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat(x,['_' 
> labelcmb{ch,2}]),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBtarget(ch).neighblabel = tempnb{:};
> end
>
> %Identify the channel pairs which are neighbors with the reference channel
> NBref = {};
> for ch=1:chans^2
> NBref(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,2},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat([labelcmb{ch,1} 
> '_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBref(ch).neighblabel = tempnb{:};
> end
>
>
> %Append both sets of neighbors (ref and target)
> NBboth= {};
> for ch=1:chans^2
> NBboth(ch).label = label{ch};
> NBboth(ch).neighblabel = [NBref(ch).neighblabel; 
> NBtarget(ch).neighblabel];
> end
> This seems to work and the clustering method proceeds without error. 
> My question is the following: is this the proper way to utilize the 
> clustering method using ft_freqstatistics on connectivity data or am I 
> missing something?
> Thanks,
> -Tony
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From sanbelluzo at gmail.com  Mon May 13 21:13:08 2013
From: sanbelluzo at gmail.com (Santiago Belluzo)
Date: Mon, 13 May 2013 16:13:08 -0300
Subject: [FieldTrip] Emotiv + FieldTrip + Matlab
In-Reply-To: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
References: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
Message-ID: <CAKkp94yg=a2VrUUSN2dxGBLTQD4E_6JOJ=VSXKrNLBVjBv8h3w@mail.gmail.com>

Hi, i´m trying to use emotiv2ft in a windows machine and Matlab return this
message

"Waiting for the device to become ready - press [Escape] to quit
EDK: User added, will now start acquisition.
Streaming 16 out of 22 channels
Could not connect to buffer server at localhost:1972."


In http://fieldtrip.fcdonders.nl/development/realtime/emotiv?s[]=emotiv said
that  "If port 1972 cannot be accessed on a Windows machine it may help to
first initialize the port from matlab, e.g., via ft_realtime_fileproxy".
But i´m not sure how to do it....
 Someone can help me?.

Santiago.


2013/3/4 Santiago Belluzo <sanbelluzo at gmail.com>

> *Hi, I'm new to FieldTrip and I'm interested in using it to capture **realtime data from the Emotiv headset using the function emotiv2ft.I`ve tried some examples like signalviewer andpowerviewer with random signal from signalproxy to check that the FieldTripBuffer works fine. Then i`ve tried to use emotiv2ft and have problems.  *
>
> *I'm not sure about how to call to this interface from within **Matlab.*
>
> *I`ve read some messages from the mailinglist with similar problem but in there is not clear for me how they solve it. *
>
> *I´ll be waiting for any help!.*
>
> *Thanks.*
>
> --
> Santiago
>



-- 
Santiago Belluzo
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From chenxiaogang1986 at 163.com  Tue May 14 03:37:29 2013
From: chenxiaogang1986 at 163.com (Xiaogang Chen)
Date: Tue, 14 May 2013 09:37:29 +0800 (CST)
Subject: [FieldTrip] ft_topoplotCC of vector
Message-ID: <5ef5e6c2.25f7.13ea0af63fd.Coremail.chenxiaogang1986@163.com>

Hi all,

 

I am trying to plot some results that are not the output from a ft function, using a ft_topoplotCC function. However, I don’t know how to use it. Would you send me some simple examples? Thanks very much.

 

Best,

 

Xiaogang Chen 
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From yoel.sher at mail.huji.ac.il  Tue May 14 18:09:37 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Tue, 14 May 2013 19:09:37 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
Message-ID: <519261C1.3020002@mail.huji.ac.il>

Dear FieldTrippers,

I would like to know if there is an option to extract the Topographic 
map (Such as the scalp in ft_topoplotER) to a matrix. I've searched 
around the functions in fieldtrip and couldn't find any..

Many Thanks,
Yoel


From eelke.spaak at donders.ru.nl  Tue May 14 19:25:40 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 14 May 2013 19:25:40 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <519261C1.3020002@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
Message-ID: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>

Dear Yoel,

I'm not sure if I understand what you mean exactly, but do you simply
want the values plotted by ft_topoplotER in case of plotting the
results of ft_timelockanalysis? In that case, you can look at the
tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
rather trivial, so I think you must mean something else.

Best,
Eelke

On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear FieldTrippers,
>
> I would like to know if there is an option to extract the Topographic map
> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
> functions in fieldtrip and couldn't find any..
>
> Many Thanks,
> Yoel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From yoel.sher at mail.huji.ac.il  Wed May 15 12:08:20 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:08:20 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
Message-ID: <51935E94.7090605@mail.huji.ac.il>

Dear Eelke,

First, thanks for you fast replay. Second, let me clarify my question. 
I'm looking for other result than the average ERP/ERF. I'm looking for a 
matrix that output the EEG value per each location (not just the 
electrodes) on the scalp. Of course that every location other than the 
electrode is an interpolated value. The plot of ft_topoplotER shows that 
matrix (but does not output, as far as I know).

Regards,
Yoel

On 05/14/2013 08:25 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> I'm not sure if I understand what you mean exactly, but do you simply
> want the values plotted by ft_topoplotER in case of plotting the
> results of ft_timelockanalysis? In that case, you can look at the
> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
> rather trivial, so I think you must mean something else.
>
> Best,
> Eelke
>
> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear FieldTrippers,
>>
>> I would like to know if there is an option to extract the Topographic map
>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
>> functions in fieldtrip and couldn't find any..
>>
>> Many Thanks,
>> Yoel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From eelke.spaak at donders.ru.nl  Wed May 15 12:22:21 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 15 May 2013 12:22:21 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <51935E94.7090605@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
Message-ID: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>

Dear Yoel,

Ah, I understand now; you want the interpolated matrix. This is not
possible with standard FieldTrip code.

However, it should not be very difficult to get this. I would
recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
Then, when the code breaks at that point, you can type in the command
window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
you have the x and y coordinates and the data (z) in variables in your
base workspace.

Getting this matrix programmatically in a script should also be
possible, but that would require custom hacks of ft_plot_topo (e.g.
you could put this assignin call in your local copy of the function,
or add Xi,Yi,Zi as output arguments, etc.)

Good luck,
best,

Eelke

On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear Eelke,
>
> First, thanks for you fast replay. Second, let me clarify my question. I'm
> looking for other result than the average ERP/ERF. I'm looking for a matrix
> that output the EEG value per each location (not just the electrodes) on the
> scalp. Of course that every location other than the electrode is an
> interpolated value. The plot of ft_topoplotER shows that matrix (but does
> not output, as far as I know).
>
> Regards,
> Yoel
>
>
> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>
>> Dear Yoel,
>>
>> I'm not sure if I understand what you mean exactly, but do you simply
>> want the values plotted by ft_topoplotER in case of plotting the
>> results of ft_timelockanalysis? In that case, you can look at the
>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>> rather trivial, so I think you must mean something else.
>>
>> Best,
>> Eelke
>>
>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>
>>> Dear FieldTrippers,
>>>
>>> I would like to know if there is an option to extract the Topographic map
>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>> the
>>> functions in fieldtrip and couldn't find any..
>>>
>>> Many Thanks,
>>> Yoel
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>


From yoel.sher at mail.huji.ac.il  Wed May 15 12:47:06 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:47:06 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
	<CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
Message-ID: <519367AA.60204@mail.huji.ac.il>

Dear Eelke,

Many thanks, I'll try it out.

Best,
- Yoel

On 05/15/2013 01:22 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> Ah, I understand now; you want the interpolated matrix. This is not
> possible with standard FieldTrip code.
>
> However, it should not be very difficult to get this. I would
> recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
> Then, when the code breaks at that point, you can type in the command
> window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
> you have the x and y coordinates and the data (z) in variables in your
> base workspace.
>
> Getting this matrix programmatically in a script should also be
> possible, but that would require custom hacks of ft_plot_topo (e.g.
> you could put this assignin call in your local copy of the function,
> or add Xi,Yi,Zi as output arguments, etc.)
>
> Good luck,
> best,
>
> Eelke
>
> On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear Eelke,
>>
>> First, thanks for you fast replay. Second, let me clarify my question. I'm
>> looking for other result than the average ERP/ERF. I'm looking for a matrix
>> that output the EEG value per each location (not just the electrodes) on the
>> scalp. Of course that every location other than the electrode is an
>> interpolated value. The plot of ft_topoplotER shows that matrix (but does
>> not output, as far as I know).
>>
>> Regards,
>> Yoel
>>
>>
>> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>> Dear Yoel,
>>>
>>> I'm not sure if I understand what you mean exactly, but do you simply
>>> want the values plotted by ft_topoplotER in case of plotting the
>>> results of ft_timelockanalysis? In that case, you can look at the
>>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>>> rather trivial, so I think you must mean something else.
>>>
>>> Best,
>>> Eelke
>>>
>>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>> Dear FieldTrippers,
>>>>
>>>> I would like to know if there is an option to extract the Topographic map
>>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>>> the
>>>> functions in fieldtrip and couldn't find any..
>>>>
>>>> Many Thanks,
>>>> Yoel
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From ggonesc at upo.es  Wed May 15 19:37:11 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 15 May 2013 19:37:11 +0200
Subject: [FieldTrip] PLV and ImC computation
Message-ID: <8d77945c28ba0f58.5193e3e7@upo.es>

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From mbj0310 at gmail.com  Thu May 16 08:28:13 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 15:28:13 +0900
Subject: [FieldTrip] About preprocessing and define trial
Message-ID: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>


Dear all,

Hello, my name is BJ Min from Korea.

I am just a beginner in the Fieldtrip.
Anyway, with the help of tutorials, I could make grand average ERP of my data finally. 

However, my question is about the order of preprocessing. According to the tutorials, and examples, it looks the ft_definetrial step is the first, then ft_preprocessing step is followed.  But, is there any method to flip these two steps? What I want to do is preprocessing (filtering, notch filtering) first then to use ft_definetrial sequentially.

Best regards


BeomJun Min, M.D.

Ph. D. student, Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST) 
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
500-712, Republic of Korea (South) 
Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr

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From eelke.spaak at donders.ru.nl  Thu May 16 08:52:02 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 08:52:02 +0200
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
Message-ID: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>

Dear BeomJun,

What you describe is definitely possible. If you specify:

cfg = [];
cfg.dataset = 'dataset';
data = ft_preprocessing(cfg);

you will get one very big 'trial' in the data structure, representing
just all your data. In the step above, you can also specify filter
options.

After this step, you can segment your data into trials by using
ft_redefinetrial (rather than ft_definetrial). However, you still need
a trl matrix containing the trial definition. The easiest way to
obtain this is to still call ft_definetrial as you used to do:

cfg = [];
cfg.dataset = 'dataset';
cfg.trialdef.....
% all the trial definition options go here
cfgout = ft_definetrial(cfg);

and then just save the output trl matrix:

trl = cfgout.trl;

now you can call ft_redefinetrial:

cfg = [];
cfg.trl = trl;
data = ft_redefinetrial(cfg, data);

and your data will be segmented.

Hope this helps,
Best,

Eelke


On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I am just a beginner in the Fieldtrip.
> Anyway, with the help of tutorials, I could make grand average ERP of my
> data finally.
>
> However, my question is about the order of preprocessing. According to the
> tutorials, and examples, it looks the ft_definetrial step is the first, then
> ft_preprocessing step is followed.  But, is there any method to flip these
> two steps? What I want to do is preprocessing (filtering, notch filtering)
> first then to use ft_definetrial sequentially.
>
> Best regards
>
>
> BeomJun Min, M.D.
>
> Ph. D. student, Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From mbj0310 at gmail.com  Thu May 16 10:06:51 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 17:06:51 +0900
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
	<CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
Message-ID: <CA+v9jvJ0bo1UFp+_qSezeO8B4LpyQ+RDiSr=2pKLWK6-8pRf4w@mail.gmail.com>

Dear Eelke Spaak

Thank you very much.
It works perfect!

Best regards.


2013/5/16 Eelke Spaak <eelke.spaak at donders.ru.nl>

> Dear BeomJun,
>
> What you describe is definitely possible. If you specify:
>
> cfg = [];
> cfg.dataset = 'dataset';
> data = ft_preprocessing(cfg);
>
> you will get one very big 'trial' in the data structure, representing
> just all your data. In the step above, you can also specify filter
> options.
>
> After this step, you can segment your data into trials by using
> ft_redefinetrial (rather than ft_definetrial). However, you still need
> a trl matrix containing the trial definition. The easiest way to
> obtain this is to still call ft_definetrial as you used to do:
>
> cfg = [];
> cfg.dataset = 'dataset';
> cfg.trialdef.....
> % all the trial definition options go here
> cfgout = ft_definetrial(cfg);
>
> and then just save the output trl matrix:
>
> trl = cfgout.trl;
>
> now you can call ft_redefinetrial:
>
> cfg = [];
> cfg.trl = trl;
> data = ft_redefinetrial(cfg, data);
>
> and your data will be segmented.
>
> Hope this helps,
> Best,
>
> Eelke
>
>
> On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
> >
> > Dear all,
> >
> > Hello, my name is BJ Min from Korea.
> >
> > I am just a beginner in the Fieldtrip.
> > Anyway, with the help of tutorials, I could make grand average ERP of my
> > data finally.
> >
> > However, my question is about the order of preprocessing. According to
> the
> > tutorials, and examples, it looks the ft_definetrial step is the first,
> then
> > ft_preprocessing step is followed.  But, is there any method to flip
> these
> > two steps? What I want to do is preprocessing (filtering, notch
> filtering)
> > first then to use ft_definetrial sequentially.
> >
> > Best regards
> >
> >
> > BeomJun Min, M.D.
> >
> > Ph. D. student, Department of Medical System Engineering (DMSE)
> > Gwangju Institute of Science and Technology (GIST)
> > 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> > 500-712, Republic of Korea (South)
> > Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> > E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From eelke.spaak at donders.ru.nl  Thu May 16 10:07:47 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 10:07:47 +0200
Subject: [FieldTrip] Second-level one-sample t test with clustering
Message-ID: <CABPNLUqSFsDCGBZCMQa2ZzQ5TDxLjH2ynmCy5jYzkQMNGJddTA@mail.gmail.com>

Dear fellow FieldTrippers,

At the moment, I want to do second-level source statistics on my data
(but the question is the same for sensor statistics). I have computed
two-sample t-scores for each subject, between the trials in conditions
A and B.

Now, the appropriate per-voxel test to do across subjects would be a
one-sample t-test. This is rather easy to do, but I would like to use
cluster permutations to correct for multiple comparisons. My idea is
to generate fake data of all zeroes, the same size as my t-score
descriptive data per subject, and then do a paired-samples t test
between the real data and these zeroes (using ft_statfun_depsamplesT).
The voxel-level t statistic of data vs 0 should be the same as a
one-sample test of course. However, I am not sure the permutations of
the data would give me a valid distribution of the cluster statistic.

The test for the real data would be (comparing column 1 to column 2):
dataA 0
dataB 0
dataC 0
dataD 0

whereas a permutation might look like so:
0 dataA
dataB 0
dataC 0
0 dataD

Intuitively, I think this makes sense, as the t score of 0 vs data
will be the negative of t(data vs 0), I should get an appropriate
randomization distribution. But I'm not completely sure of this.

So, my question: does anyone see a problem with my approach? Or is
this a valid way of cluster-correcting a one-sample T test? If not,
what would be the right way to proceed?

Many thanks,
best,
Eelke


From e.maris at psych.ru.nl  Thu May 16 16:31:15 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 16:31:15 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
Message-ID: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>

Hi Eelke,

This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.

Eric


http://www.nphyscog.com/contact
----- fieldtrip-request at science.ru.nl schreef:
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
> 
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


From eelke.spaak at donders.ru.nl  Thu May 16 16:43:32 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 16:43:32 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>

Hi Eric,

Thanks, that's what I expected. However, that approach does not take
into account the different between-trial variances in the different
subjects. What would you recommend to take those into account?

Best,
Eelke

On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> Hi Eelke,
>
> This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.
>
> Eric
>
>
> http://www.nphyscog.com/contact
> ----- fieldtrip-request at science.ru.nl schreef:
>> Send fieldtrip mailing list submissions to
>> fieldtrip at science.ru.nl
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> or, via email, send a message with subject or body 'help' to
>> fieldtrip-request at science.ru.nl
>>
>> You can reach the person managing the list at
>> fieldtrip-owner at science.ru.nl
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of fieldtrip digest..."
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From e.maris at psych.ru.nl  Thu May 16 17:28:36 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 17:28:36 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
Message-ID: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>

Hi Eelke,

It all depends on the null hypothesis that you want to test. It's better
to discuss this with you in person or at some meeting with other
colleagues (for non-Donders Discussion List readers, Eelke and I work at
the same institute), because at the end it is a matter of deciding on what
is an interesting null hypothesis (both for you and the reviewers of your
paper).

I remember a discussion with a colleague about the same issue (using
first-level t-statistics at the second level), and he was quite unhappy
when I questioned this approach (by asking whether this is really the null
hypothesis he was interested in). At the end, it turned out that he also
had tried the standard approach (using only condition means) but this did
not result in a significant p-value.

Best,

Eric


> -----Original Message-----
> From: eelke.spaak at gmail.com [mailto:eelke.spaak at gmail.com] On Behalf Of
> Eelke Spaak
> Sent: donderdag 16 mei 2013 16:44
> To: Eric Maris; FieldTrip discussion list
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
> 
> Hi Eric,
> 
> Thanks, that's what I expected. However, that approach does not take
> into account the different between-trial variances in the different
> subjects. What would you recommend to take those into account?
> 
> Best,
> Eelke
> 
> On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> > Hi Eelke,
> >
> > This not valid. At the second level, you must use the condition means
> (per subject) as the observations about which you have a hypothesis and
> which therefore have to be permuted.
> >
> > Eric
> >
> >
> > http://www.nphyscog.com/contact
> > ----- fieldtrip-request at science.ru.nl schreef:
> >> Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> or, via email, send a message with subject or body 'help' to
> >> fieldtrip-request at science.ru.nl
> >>
> >> You can reach the person managing the list at
> >> fieldtrip-owner at science.ru.nl
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of fieldtrip digest..."
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From tim.curran at Colorado.EDU  Fri May 17 14:36:54 2013
From: tim.curran at Colorado.EDU (Tim Curran)
Date: Fri, 17 May 2013 06:36:54 -0600
Subject: [FieldTrip] Postdoctoral Position, Curran Lab,
	University of Colorado Boulder
In-Reply-To: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
	<022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
Message-ID: <AEF2F5AF-5A3C-4FA3-B17D-1429D57A46FC@colorado.edu>

Postdoctoral Position
Curran Lab, University of Colorado Boulder
Postdoctoral research position available in the lab of Tim Curran at the Department of Psychology & Neuroscience, University of Colorado Boulder to work on NIH-funded ERP studies of memory and perceptual expertise.  Desirable qualifications include research experience related to memory, perceptual expertise, ERP/EEG, and/or related domains.  Anticipated start date is summer or fall of 2013.  The University of Colorado is an Equal Opportunity/Affirmative Action employer. For further information contact, tim.curran at colorado.edu<mailto:tim.curran at colorado.edu>.  Applicants must submit a CV, a statement of research experience/interests, and a cover letter including email addresses for at least three referees to contact for recommendation letters if needed. Applications will be accepted electronically at https://www.jobsatcu.com/postings/63602
http://psych.colorado.edu/~tcurran/




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From ggonesc at upo.es  Fri May 17 17:45:40 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Fri, 17 May 2013 17:45:40 +0200
Subject: [FieldTrip] problem in connectivityanalysis
Message-ID: <9f89709b303dae2.51966cc4@upo.es>

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From jessetinker at gmail.com  Fri May 17 21:36:12 2013
From: jessetinker at gmail.com (Jesse Tinker)
Date: Fri, 17 May 2013 12:36:12 -0700
Subject: [FieldTrip] Segmentation Memory Issue
Message-ID: <CACKMsgNPvYLv33cxDr0fM-SJ3QR_8y1aY+93fBmGqMOT+Lo58Q@mail.gmail.com>

Hello Fieldtrippers!

This is my first post ever and I just want to say thank you to everyone for
promoting such a vibrant and supportive intellectual community.

I have an issue which seems so simple but I am somewhat stymied by: using
fieldtrip to accomplish the coregistration. The main points of my code are:

mri = ft_read_mri( );

mri = ft_volumerealign(cfg, mri);           % Mark fiducials

mrireslice = ft_volumereslice(cfg,mri);  %To apply the resultant
transformation matrix

segmentedmri  = ft_volumesegment(cfg, mrireslice);



First, if I skip the reslice step, everything works fine. However, if I do
the reslice and then try to segment, spm_preproc tries to create a 1.8 Tb
array. Although it bravely tries, my 24 Gb of RAM inevitably fails. The
analogous array for the unsliced mri is 2Mb.

I found this confusing as the quantity of information in the resliced image
is the exact same. I traced through all the coding and the computation that
fails is based on the transformation matrix of the MRI which, of course,
changes with the reslicing. I am happy to provide details of that but won't
at the moment.

My question, has anyone else encountered this or developed a workaround?

Very much appreciated,

Jesse
British Columbia Mental Health and Research Institute
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From mengtongxiao at gmail.com  Sat May 18 16:06:20 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sat, 18 May 2013 22:06:20 +0800
Subject: [FieldTrip] a .mat file about meg data do preprocessing
Message-ID: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>

Dear all,
I have a .mat file about meg data(102*98800，channel*time,channel is
'MEG0111','MEG0121'.....'M*1' );
Then I use eeglab read it,got .set file;I want use ft_timelockanalysis then
*cfg = [];
cfg.dataset     = 'megalpha.set';
cfg.grad=grad;
data_org        = ft_preprocessing(cfg)*
>grad =
     chanori: [102x3 double]
     chanpos: [102x3 double]
    chantype: {102x1 cell}
    chanunit: {102x1 cell}
     coilori: [510x3 double]
     coilpos: [510x3 double]
       label: {102x1 cell}
         tra: [102x510 double]
        unit: 'cm'
Warning: creating default channel names
> In fileio\private\read_eeglabheader at 53
  In ft_read_header at 572
  In ft_preprocessing at 343
processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005'
'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012'
'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019'
'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026'
'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033'
'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040'
'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047'
'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054'
'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061'
'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068'
'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075'
'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082'
'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089'
'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096'
'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
reading and preprocessing
reading and preprocessing trial 1 from 1
data_org =
           hdr: [1x1 struct]
         label: {102x1 cell}
          time: {[1x98800 double]}
         trial: {[102x98800 double]}
       fsample: 1037
    sampleinfo: [1 98800]
           cfg: [1x1 struct]

*cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'M*1';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);*
timelock =
       avg: [0x98800 double]
       var: [0x98800 double]
      time: [1x98800 double]
       dof: [0x98800 double]
     label: {0x1 cell}
    dimord: 'chan_time'
       cov: []
       cfg: [1x1 struct]

there is no error displyed in command window but the timlock is empty,why?

thanks for you help,
best,
xiao
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From eeguser at hotmail.com  Sat May 18 18:21:48 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 19:21:48 +0300
Subject: [FieldTrip] computing threshold for PLV
Message-ID: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>

Dear FT Experts,



I have calculated PLV for a set of EEG data from 5 different patients. 
Now I want to convert the PLV matrix of each patient into a binary 
matrix. For this I need a threshold PLV value below which I can assume 
the phase locking is zero.

My question is, how do I compute this threshold. I know hard 
thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), 
but I guess it is not a very good option.



Can somebody suggest a better and robust (statistical) way of determining the threshold ?  		 	   		  
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From sherrykhan78 at gmail.com  Sat May 18 18:37:28 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 12:37:28 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>

You can randomly shift in time the epochs, to compute null-distribution,
and then threshold at some  p-value say p < 0.01, you can even correct
for multiple comparison in space and time using  this principle.



On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com>wrote:

> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Sat May 18 19:25:50 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 18 May 2013 19:25:50 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
Message-ID: <4EDB7A1D-4484-454B-A9CE-5AE826E2AE98@donders.ru.nl>

Dear all,

Note that shuffling the epochs with respect to one another (where for one of the channels in the pair the epoch order stays fixed) usually yields a too liberal null-distribution. The reason is that the shuffling also destroys all structure in the data that is due to electromagnetic field spread. So, even if an observed pattern of PLV is caused by a single underlying neural generator, shuffling the epochs most likely makes this pattern 'significant'. However, it still does not reflect physiological interaction between sources.

Best,
Jan-Mathijs


On May 18, 2013, at 6:37 PM, Sheraz Khan wrote:

> You can randomly shift in time the epochs, to compute null-distribution, and then threshold at some  p-value say p < 0.01, you can even correct for multiple comparison in space and time using  this principle.
> 
> 
> 
> On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com> wrote:
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From smoratti at psi.ucm.es  Sat May 18 20:11:11 2013
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Sat, 18 May 2013 20:11:11 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,

Stephan



________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From eeguser at hotmail.com  Sat May 18 21:42:05 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 22:42:05 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
Message-ID: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>




Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es
Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,
You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
Hope that helps,
Stephan



________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain
and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? _______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  
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From sherrykhan78 at gmail.com  Sun May 19 01:55:07 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 19:55:07 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
Message-ID: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>

Most of the previois discussion targeted toward event related plv for
continous data may be look at Hipp 2012 Nature Neuroscience orthogonal
correlation paper
On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:

>  Dear FT Experts
>
> Thank you for your inputs. I should add here that I have continuous EEG
> data (so effectively single trial). The way I am computing PLV is by
> dividing my data into windows of 2 seconds each and computing PLV for each
> window and then I finally average the PLV values of all the windows.
>
> So when we talk of shuffling trials, in my case should i consider each of
> 2 second window as a trial ? Sorry if this sounds stupid as I am new to
> this kind of analysis.
>
> ------------------------------
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
>
> Dear Sheraz,
>
> You might consult the following article: Lachaux, J. P. et al. 1999.
> Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208.
> In principle you have to create surrogate data that represent the null
> hypothesis that there is no phase locking between your electrodes, sources,
> etc. Then you create hundreds or thousands of surrogate data sets and
> calculate each time you PLV. That way you create a distribution of your PLV
> values under the Null hypothesis. Then you check in what percentile your
> observed PLV lies (e. g. if its beyond the 95% percentile you would reject
> the Null hypothesis).
>
> Hope that helps,
>
> Stephan
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
>
> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________ fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mengtongxiao at gmail.com  Sun May 19 09:32:37 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sun, 19 May 2013 15:32:37 +0800
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ@mail.gmail.com>

Dear all，
when I use ft_timelockanalysis like follow,there are some mistake.

cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'all';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);
the input is raw data with 102 channels and 1 trials
averaging trials
averaging trial 1 of 1

the call to "ft_timelockanalysis" took 5 seconds
??? Error using ==> mxSerialize
Error during serialization of (null)

Error in ==> ft_postamble_provenance at 76
  cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
  cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
  'UniformOutput', false), 'UniformOutput', false);

Error in ==> ft_postamble at 55
  evalin('caller', ['ft_postamble_' cmd]);
Error in ==> ft_timelockanalysis at 401
ft_postamble provenance timelock

Thank you so much for your help!!
xiao
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From eeguser at hotmail.com  Sun May 19 09:54:21 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sun, 19 May 2013 10:54:21 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>,
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>,
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <BLU176-W121107702786A05888CC94B9AE0@phx.gbl>

So, does it mean that PLV method does not make much sense for continuous data ? To be more specific, I am trying to investigate synchrony from epileptic EEG recordings.

Date: Sat, 18 May 2013 19:55:07 -0400
From: sherrykhan78 at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper

On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:







Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.

So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es

Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,
Stephan




________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/


Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain

and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982



El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.

My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From politzerahless at gmail.com  Sun May 19 14:27:37 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 19 May 2013 07:27:37 -0500
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CAJT2k_8-ndM9giikDhgz4qem475i-bf76MkE=_BSX1MOAuy+nQ@mail.gmail.com>

Hello Xiao,

I don't know if this is what is causing the error, but I did notice that
your dataset apparently only has one trial. Usually ft_timelockanalysis()
would take a dataset consisting of multiple trials and average them; you
may need to run ft_preprocessing() to divide your dataset into trials.

Best,
Steve



>
> Message: 1
> Date: Sun, 19 May 2013 15:32:37 +0800
> From: ?? <mengtongxiao at gmail.com>
> To: fieldtrip <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] help about ft_timelockanalysis
> Message-ID:
>         <
CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ at mail.gmail.com>
> Content-Type: text/plain; charset="gb2312"
>
> Dear all?
> when I use ft_timelockanalysis like follow,there are some mistake.
>
> cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'all';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);
> the input is raw data with 102 channels and 1 trials
> averaging trials
> averaging trial 1 of 1
>
> the call to "ft_timelockanalysis" took 5 seconds
> ??? Error using ==> mxSerialize
> Error during serialization of (null)
>
> Error in ==> ft_postamble_provenance at 76
>   cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
>   cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
>   'UniformOutput', false), 'UniformOutput', false);
>
> Error in ==> ft_postamble at 55
>   evalin('caller', ['ft_postamble_' cmd]);
> Error in ==> ft_timelockanalysis at 401
> ft_postamble provenance timelock
>
> Thank you so much for your help!!
> xiao
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From stephanie.ries at berkeley.edu  Mon May 20 06:32:49 2013
From: stephanie.ries at berkeley.edu (Stephanie Kathleen Ries-cornou)
Date: Sun, 19 May 2013 21:32:49 -0700
Subject: [FieldTrip] dipole modeling using field trip
Message-ID: <CAHckMuRtCLu8LGLxXX57ktWhx3DbNK2m5P4Oy9R5047GPuChFA@mail.gmail.com>

Hi,

I would like to know if it possible to reject horizontal eye movements from
scalp EEG signal using equivalent dipole modeling in Fieldtrip. I have
tried doing this using ICA but it was not possible to identify a component
reflecting saccades for all subjects. Has anyone ever done this? If yes,
any suggestion would be great!

I am trying to learn about source reconstruction using two dipoles thinking
this might be a good start and have started going through the tutorial. I
got the following error messages:

>> data = ft_dipolesimulation(cfg);
using headmodel specified in the configuration
using gradiometers specified in the configuration
computing simulated data
Error using  .*
Matrix dimensions must agree.

Error in ft_dipolesimulation (line 203)
    simulated.trial{trial}  = simulated.trial{trial} + lf(:,i:3:end) * ...

This was fixed when I removed the "..." but then I got this message:

Error using ft_fetch_vol (line 76)
no headmodel specified

Error in prepare_headmodel (line 51)
vol = ft_fetch_vol(cfg, data);

Error in ft_dipolesimulation (line 106)
[vol, sens, cfg] = prepare_headmodel(cfg, []);

The "vol" parameter is defined, so I do not know where the error is coming
from.

Best,

Stephanie


Stephanie Ries, PhD
Knight Lab - Helen Wills Neuroscience Institute
University of California at Berkeley
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From ggonesc at upo.es  Mon May 20 09:28:55 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Mon, 20 May 2013 09:28:55 +0200
Subject: [FieldTrip] problem with PLV and ImC computing
Message-ID: <1115d37d2b1643b.5199ecd7@upo.es>

I'm re-sending this, becasue searching at the fieldtrip archives, I've notice that my message was scrubbed...


Dear Fieltrip experts,

I  have my continuous data imported to fieldtrip with matlab, I'm looking  for performing connectivity analysis between pairs of sensors, I have  succed as:
data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels and 2000 samples
data.label {59x1};
data.time {1xNepochs};

then, calculate only the FFT of all sensors as:
cfg=[];
cfg.output='fourier';
cfg.method='mtmfft';
cfg.taper='hanning';
cfg.foilim=[8.5 9.5];
cfg.tapsmofrq=0;
cfg.trials='all';
cfg.keeptrials='yes';
cfg.channel='all';
fourier=ft_freqanalysis(cfg, data)
as output I get:
dimord = 'rpttap_chan_freq'
freq= [1x9]
fourierspctrm=[7x59x9 double]

Then compute the imaginary part of coherency as:
cfg=[];
cfg.method ='cohe';
cfg.complex='imag';
cfg.channelcbm={'all' 'all'};
coher = ft_connectivityanalysis (cfg, fourier)
as output get: 
dimord='chan_chan_freq';
cohspctrm=[59x59x9 double];
dof=7;

I have two main questions:

A)  As you see, this makes an average over the epochs of each channel, and  not over the samples (which in this case are the 9 frequencies of the  FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for each epoch (repetition) on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt, Is this possible?



B)  Another question I have is: for the Imaginary part of Coherence is not  necessary to compute the cross-spectrum with 'powandcsd', only the FFT,  but for the PLV, PPC or WPLI is that way too?



Many thanks in advanced,
Gabriel.
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From jan.schoffelen at donders.ru.nl  Tue May 21 08:24:48 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 21 May 2013 08:24:48 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <EF65D844-0661-44BA-8369-78933B7102A8@donders.ru.nl>

Hi all,

PLV is in principle a perfectly valid method to investigate synchrony, also in continuous data. Jörg (Hipp)'s paper introduces a connectivity metric that is insensitive to the effects of electromagnetic field spread, but it is a measure whose relationship to synchrony is hard to interpret; it quantifies amplitude envelope correlations after explicit removal of the instantaneous mixing, and does not quantify the consistency of phase relationships, as does PLV. If you are after interpreting the connectivity in terms of synchrony, you could look into using the imaginary part of coherency, or the weighted phase lag index, although neither of these methods are easy in their interpretation, either.

Best,
Jan-Mathijs

On May 19, 2013, at 1:55 AM, Sheraz Khan wrote:

> Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper
> 
> On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:
> Dear FT Experts
> 
> Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
> 
> So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.
> 
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
> 
> Dear Sheraz,
> 
> You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
> 
> Hope that helps,
> 
> Stephan
> 
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
> 
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From jm.horschig at donders.ru.nl  Tue May 21 08:31:22 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:31:22 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <9f89709b303dae2.51966cc4@upo.es>
References: <9f89709b303dae2.51966cc4@upo.es>
Message-ID: <519B14BA.9030908@donders.ru.nl>

Dear Gabriel,

> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?

No. You should think of coherence more as a measure for the consistency 
of the phase relation between channels across trials, so coherence is 
just not defined per trial,neither would it make sense to compute 
coherence for a single trial.

> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
I see some terminology issues here. Let me try to explain in a simple 
(aka least-mathematical I can think of) way:

For all these connectivity measures, we need the phase information from 
the Fourier transform (FFT) to compute the cross-spectral density matrix 
(CSD). The CSD can be regarded as the equivalent in the frequency domain 
to the covariance matrix in the time domain, thus it is a measures how a 
certain channels activity is co-modulated with another channels activity 
(for a particular frequency) - makes pretty much sense to make use of 
this when computing connectivity, right? :)
As you might know, a Fourier transform returns complex numbers, where 
the imaginary part of this number contains phase information. When 
calling ft_freqanalysis, you can decide if it shall only return the 
(squared) real part of the frequency spectrum (cfg.output='pow'), or 
instead the full CSD (cfg.output = 'powandcsd'). Alternatively, you can 
also let ft_freqanalysis return the raw Fourier coefficients 
(cfg.output='fourier'). From the Fourier coefficients, however, you can 
easily obtain the CSD or the power spectrum basically by multiplication 
the Fourier matrix with itself (transposed). All of these measures 
quantify the phase relation between channels across trials, and as phase 
information is coded in the imaginary part of the fourier output, thus 
for connectivityanalysis you need the CSD which can be obtained either 
by 'powandcsd' or by 'fourier'.

I hope that somehow clarifies your questions.

Best,
Jörn

On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> Dear Fieltrip experts,
>
> I have my continuous data imported to fieldtrip with matlab, I'm 
> looking for performing connectivity analysis between pairs of sensors, 
> I have succed as:
> data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels 
> and 2000 samples
> data.label {59x1};
> data.time {1xNepochs};
>
> then, calculate only the FFT of all sensors as:
> cfg=[];
> cfg.output='fourier';
> cfg.method='mtmfft';
> cfg.taper='hanning';
> cfg.foilim=[8.5 9.5];
> cfg.tapsmofrq=0;
> cfg.trials='all';
> cfg.keeptrials='yes';
> cfg.channel='all';
> fourier=ft_freqanalysis(cfg, data)
> as output I get:
> dimord = 'rpttap_chan_freq'
> freq= [1x9]
> fourierspctrm=[7x59x9 double]
>
> Then compute the imaginary part of coherency as:
> cfg=[];
> cfg.method ='cohe';
> cfg.complex='imag';
> cfg.channelcbm={'all' 'all'};
> coher = ft_connectivityanalysis (cfg, fourier)
> as output get:
> dimord='chan_chan_freq';
> cohspctrm=[59x59x9 double];
> dof=7;
>
> I have two main questions:
>
> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?
>
>
>
> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
>
>
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From jm.horschig at donders.ru.nl  Tue May 21 08:39:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:39:14 +0200
Subject: [FieldTrip] a .mat file about meg data do preprocessing
In-Reply-To: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
References: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
Message-ID: <519B1692.3080101@donders.ru.nl>

Dear Xiao,

Somehow your channel names seem to not be recognized by FieldTrip, and 
then it reverts to default channel names (chan001, chan002, ...). You 
will see that data_org.label will have those channel labels. 
Subsequently, you define in the cfg for timelockanalysis channel names 
that are not in your data (your channels are called chanXXX, not MEGXXXX 
now), and FieldTrip thus does not perform the operation on any channel.
I don't know much about EEGLAB and how it is integrated with FieldTrip - 
there should be an eeglab2fieldtrip function though in 
fieldtrip/external/eeglab. Maybe you can try this, or maybe someone else 
here knows why your channel labels do not get copied over to FieldTrip 
correctly.

Good luck :)
Best,
Jörn

On 5/18/2013 4:06 PM, ?? wrote:
> Dear all,
> I have a .mat file about meg data(102*98800,channel*time,channel is 
> 'MEG0111','MEG0121'.....'M*1' );
> Then I use eeglab read it,got .set file;I want use ft_timelockanalysis 
> then
> /cfg = [];
> cfg.dataset     = 'megalpha.set';
> cfg.grad=grad;
> data_org        = ft_preprocessing(cfg)/
> >grad =
>      chanori: [102x3 double]
>      chanpos: [102x3 double]
>     chantype: {102x1 cell}
>     chanunit: {102x1 cell}
>      coilori: [510x3 double]
>      coilpos: [510x3 double]
>        label: {102x1 cell}
>          tra: [102x510 double]
>         unit: 'cm'
> Warning: creating default channel names
> > In fileio\private\read_eeglabheader at 53
>   In ft_read_header at 572
>   In ft_preprocessing at 343
> processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005' 
> 'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012' 
> 'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019' 
> 'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026' 
> 'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033' 
> 'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040' 
> 'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047' 
> 'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054' 
> 'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061' 
> 'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068' 
> 'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075' 
> 'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082' 
> 'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089' 
> 'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096' 
> 'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
> reading and preprocessing
> reading and preprocessing trial 1 from 1
> data_org =
>            hdr: [1x1 struct]
>          label: {102x1 cell}
>           time: {[1x98800 double]}
>          trial: {[102x98800 double]}
>        fsample: 1037
>     sampleinfo: [1 98800]
>            cfg: [1x1 struct]
> /cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'M*1';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);/
> timelock =
>        avg: [0x98800 double]
>        var: [0x98800 double]
>       time: [1x98800 double]
>        dof: [0x98800 double]
>      label: {0x1 cell}
>     dimord: 'chan_time'
>        cov: []
>        cfg: [1x1 struct]
> there is no error displyed in command window but the timlock is empty,why?
> thanks for you help,
> best,
> xiao
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From zriouil.imane at gmail.com  Tue May 21 10:18:58 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 21 May 2013 10:18:58 +0200
Subject: [FieldTrip] ft_read_event
Message-ID: <CABu=cRdhOYn=oSy0cHADOvqgWnCR3ui5cLwy9FUkpVz7KGKK_A@mail.gmail.com>

Hello,

i have a problems in ft_read_event. if you help me please


I try to follow all instructions on the tutorial: 'Preprocessing and
analysis of spike and local field potential data'

>> spike=ft_read_spike(filename)

spike =

        label: {'Elec_1_Neuron_1'  'Elec_2_Neuron_1'  'Elec_3_Neuron_1'}
    timestamp: {[1x20246 int32]  [1x9126 int32]  [1x74291 int32]}
     waveform: {[0x20246 double]  [0x9126 double]  [0x74291 double]}
         unit: {[1x20246 double]  [1x9126 double]  [1x74291 double]}
          hdr: [1x1 struct]
       dimord: '{chan}_lead_time_spike'

>> header=ft_read_header(filename)

header =

                nChans: 94
                    Fs: 781.2500
              nSamples: 862310
               nTrials: 1
           nSamplesPre: 0
                 label: {94x1 cell}
        FirstTimeStamp: 70433310
    TimeStampPerSample: 32
                  orig: [1x1 struct]
              chantype: {94x1 cell}
              chanunit: {94x1 cell}

>>cfg=[];
cfg.dataset=filename;
cfg.trialfun='trialfun_stimon_samples';
cfg=ft_definetrial(cfg)

evaluating trialfunction 'trialfun_stimon_samples'

??? Error using ==> fseek
Not enough input arguments.

Error in ==> read_nex_event at 49
status = fseek(fid,hdr.varheader(mrkvarnum).offset,'bof');

Error in ==> ft_read_event at 1528
    event = read_nex_event(filename);

Error in ==> trialfun_stimon_samples at 3
event = ft_read_event(cfg.dataset);

Error in ==> ft_definetrial at 157
    trl   = feval(cfg.trialfun, cfg);
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From ggonesc at upo.es  Tue May 21 17:52:21 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Tue, 21 May 2013 17:52:21 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <519B14BA.9030908@donders.ru.nl>
References: <9f89709b303dae2.51966cc4@upo.es> <519B14BA.9030908@donders.ru.nl>
Message-ID: <1348f6433edc26f9.519bb455@upo.es>

Thank you so much for your answer Jörn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from  -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
 [0.9323  0.3679  0.8629  1.6436  0.6404  1.8782  0.1139] 
val(:,:,1,2)
 [0.8509-0.1555i  0.2507-0.1066i  0.8173-0.0290i  1.4328-0.2427i  0.5457-0.0500i  1.6505-0.0161i  0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
 [1  1  1  1  1  1  1] 
val(:,:,1,2)
 [0.9694-0.2133i  0.7011-0.3564i  0.9951-0.0104i  0.9014-0.3481i  0.9781-0.0819i  0.9982-0.0046i  0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        Jörn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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From antony.passaro at gmail.com  Tue May 21 18:13:28 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Tue, 21 May 2013 12:13:28 -0400
Subject: [FieldTrip] Subject-level Statistics on mvar connectivity measures
Message-ID: <CAB8wAYS-F9FiW72edUz_s84dSuobXXA6nEwZYwWEhW5bL=ggkg@mail.gmail.com>

Hi everyone,

I have had some success processing the subject-level differences between
two conditions for phase-based measures such as coherence and plv but I was
wondering what the approach would be for the directed or mvar-based
measures such as dtf, granger, or pdc? Since there are no trials to shuffle
as you normally would for the phase-based connectivity measures, what would
be the optimal statistical approach? I thought about shuffling the trials
and recomputing the mvar over and over again for each condition as a
simulation but this doesn't seem practical as it would be too
computationally intensive.

Thank you,
-Tony
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From 13681530640 at 139.com  Wed May 22 04:20:45 2013
From: 13681530640 at 139.com (WangJing)
Date: Wed, 22 May 2013 10:20:45 +0800 (CST)
Subject: [FieldTrip] question About head model
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>




Hi


I am a freshman about field trip.


I am trying to build the forward model. but my mri data is different from the data in the tutorial. So I don't know how to bulid the head model. I use the date which is from the paper "Open Database of Epileptic EEG with MRI and Postoperational Assessment of Foci—a Real World Verification for the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans with morphologic substrate of the epilepsy (mostly cortical dysplasias, dysplastic tumors etc.). In some cases there is also a scan with the gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T scanner. The data is stored in the Digital Imaging and Communications in Medicine (DICOM) format. The name of the scan’s folder indicates its weighting.The scans have the following resolutions: T1: 512 × 512 pixels, pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels, pixel spacing 0.9375 mm,slice thickness 2.5 mm.


In the tutorial,the mri data stored in only one file, while the data which I used have many files, I don't know how to process. who can help me,Thanks1





Thanks very much!


Best Reagards


Jing Wang















--------------------------------------------------------------------------------



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Today's Topics:

   1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)


----------------------------------------------------------------------

Message: 1
Date: Tue, 21 May 2013 17:52:21 +0200
From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] problem in connectivityanalysis
Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
Content-Type: text/plain; charset="iso-8859-1"

Thank you so much for your answer J?rn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139] 
val(:,:,1,2)
?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
?[1? 1? 1? 1? 1? 1? 1] 
val(:,:,1,2)
?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        J?rn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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From johanna.zumer at donders.ru.nl  Wed May 22 09:30:17 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Wed, 22 May 2013 09:30:17 +0200
Subject: [FieldTrip] question About head model
In-Reply-To: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
	<2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
Message-ID: <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w@mail.gmail.com>

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci—a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan’s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 × 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-21 23:59:18
> Subject：fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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From mushfa.yousuf at googlemail.com  Wed May 22 12:13:56 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Wed, 22 May 2013 12:13:56 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <5190AEAA.3020301@donders.ru.nl>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
Message-ID: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>

Hello Jörn;

I have calculated an indiviual leadfield for both EEG and MEG. The
structure of EEg and MEG shows the following variable

grid_meg =

        xgrid: [1x20 double]
        ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
        zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
          dim: [20 17 16]
          pos: [5440x3 double]
         unit: 'cm'
       inside: [1x3177 double]
      outside: [1x2263 double]
          cfg: [1x1 struct]
    leadfield: {1x5440 cell}


grid_eeg =

        xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
        ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
        zgrid: [2 3 4 5 6 7 8 9 10 11]
          dim: [16 13 10]
          pos: [2080x3 double]
         unit: 'cm'
       inside: [1x1331 double]
      outside: [1x749 double]
          cfg: [1x1 struct]
    leadfield: {1x2080 cell}


Can you please give me a rough idea that how to concatenate the variables
from both structure ?


Thank you

Regards ;

Mushfa Yousuf


On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Mushfa,
>
> I think you have to compute two leadfield matrices, one for EEG (elec) and
> one for MEG (grad), and then concatenate these (and make sure that the
> order of sensors won't get mixed up anywhere, because  sourceanalysis just
> expects the leadfield matrix to be ordered like your data. If that's not
> the case, you either encounter the previous error you described or (if the
> number of channels matches, but order is mixed up) it will just return
> wrong source estimated activity.
>
> Best,
> Jörn
>
>
> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>
> Hello;
>
>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
> of 'elec' while calculating the Leadfield.
>
>  Actually I am trying to calculate Combined source reconstruction from
> both EEG and MEG sensors.
>
>  Do you have any idea, how to define both elec and grad definition  while
> calculating first forward then inverse solution.
>
>  Because in a fieldtrip either you can defined elec or grad at one time.
>
>
>  Regards;
>
>
>  Mushfa Yousuf
>
>  Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>
>> Hi Mushfa,
>>
>>  My guess is that the channels that have you used to compute .csdspctrm
>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>> freqPost.label, does that solve it?
>>
>>  Cheers,
>> Johanna
>>
>>
>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>
>>>   Hello Fieldtrippers,
>>>
>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>
>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>> lead field successfully.
>>>
>>>  For the inverse solution using 'dics' method, I wrote the following
>>> syntax
>>>
>>>
>>>
>>>
>>>
>>>   cfg              = [];
>>>   cfg.method       = 'dics';
>>>  cfg.frequency    = 130;
>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>  cfg.grid         = grid;
>>>  cfg.vol          = vol;
>>>
>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>  and I have received the following error:
>>>
>>>
>>>  ??? Error using ==> mtimes
>>> Inner matrix dimensions must agree.
>>>
>>>  Error in ==> beamformer_dics at 314
>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>         leadfield
>>>
>>>  Error in ==> ft_sourceanalysis at 595
>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>
>>>  Error in ==> newCode at 214
>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>
>>>
>>>  Any help would be appreciated.
>>>
>>>
>>>  Regards;
>>>
>>>
>>>  Mushfa Yousuf
>>>
>>>  Neurozentrum,
>>> Universitätsklinikum Schleswig-Holstein,
>>> Campus Kiel (UKSH), Deutschland
>>>
>>>
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From ggonesc at upo.es  Wed May 22 19:36:08 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 22 May 2013 19:36:08 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <596f90904ed40d3b.519d1e28@upo.es>

Dear Fieldtrip experts,

I finally understood how fieltrip computes the plv, so, my last e-mail has no sense now. Given say this, I have one question:

I've followed the fieltrip implementation to compute the PLV, and found that it takes the CSD, and normalizes it for the amplitude of the replicates, this is to divide the csd by the absolute of the same csd, then makes an average of the normalized csd's, to finally take the absolute of the average-normalized-csd as the PLV.  I think it can be summarized to something like, PLV = |E( csd/abs(csd) )|

I do not see the similarity with the clasical formula that appears in the papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the cross-spectrum, and E|.| is the expected value; I cannot find the relationship between the implementation on fieltrip of the PLV and the formula on the papers.

Can anyone explain to me the relationship between the two approaches? or tell me the paper where it is explained?

Many thanks in advanced,
Gabriel

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From 13681530640 at 139.com  Thu May 23 03:38:08 2013
From: 13681530640 at 139.com (WangJing)
Date: Thu, 23 May 2013 09:38:08 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>


Dear Johanna,


 


    Thank you for your suggestion. 


    1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is t1_vibe_traGAD-5. which one is best?
    2.when I convert MRI from DICOM into CTF format,the vitamin E marker didn't be found. what can I do?


 


Best Regards,


Jing Wang














--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-22 15:33:13
Subject：fieldtrip Digest, Vol 30, Issue 31

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Today's Topics:

   1. Re: question About head model (Johanna Zumer)


----------------------------------------------------------------------

Message: 1
Date: Wed, 22 May 2013 09:30:17 +0200
From: Johanna Zumer <johanna.zumer at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] question About head model
Message-ID:
<CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci?a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan?s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> To?fieldtrip<fieldtrip at science.ru.nl>
> Date?2013-05-21 23:59:18
> Subject?fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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From eelke.spaak at donders.ru.nl  Thu May 23 10:09:17 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 23 May 2013 10:09:17 +0200
Subject: [FieldTrip] connectivity problem
In-Reply-To: <596f90904ed40d3b.519d1e28@upo.es>
References: <596f90904ed40d3b.519d1e28@upo.es>
Message-ID: <CABPNLUpec0sp=o5TWDKcU-PgQqGa_ROVSQ73uWWJbkwMHtEotA@mail.gmail.com>

Dear Gabriel,

If I am not mistaken, the classical formula in Lachaux et al. (1999)
Human Brain Mapping is PLV = 1/N * | sum(exp(i * theta(t,n))) | . This
is almost the same as the formula you mention, except, importantly,
that theta is the phase difference between two signals, so the angle
of the CSD, and *not* the imaginary part.

Note furthermore that 1 * exp(i*angle(z)) is equal to z/abs(z) for any
complex z, and you see that the implementation computes the classical
formula.

Hope this helps,
Best,
Eelke

On 22 May 2013 19:36, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear Fieldtrip experts,
>
> I finally understood how fieltrip computes the plv, so, my last e-mail has
> no sense now. Given say this, I have one question:
>
> I've followed the fieltrip implementation to compute the PLV, and found that
> it takes the CSD, and normalizes it for the amplitude of the replicates,
> this is to divide the csd by the absolute of the same csd, then makes an
> average of the normalized csd's, to finally take the absolute of the
> average-normalized-csd as the PLV.  I think it can be summarized to
> something like, PLV = |E( csd/abs(csd) )|
>
> I do not see the similarity with the clasical formula that appears in the
> papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the
> cross-spectrum, and E|.| is the expected value; I cannot find the
> relationship between the implementation on fieltrip of the PLV and the
> formula on the papers.
>
> Can anyone explain to me the relationship between the two approaches? or
> tell me the paper where it is explained?
>
> Many thanks in advanced,
> Gabriel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jeremiemattout at yahoo.fr  Thu May 23 10:19:09 2013
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Thu, 23 May 2013 09:19:09 +0100 (BST)
Subject: [FieldTrip] DCM for fMRI and EEG/MEG course - Seattle June 2013
Message-ID: <1369297149.1995.YahooMailNeo@web133005.mail.ir2.yahoo.com>

Dear Colleagues, We are pleased to announce DCM for fMRI and MEG/EEG, an intermediate-level, 3-day workshop designed for investigators having familiarity with the fundamental principles of fMRI or MEG/EEG data acquisition and analysis.. It will be held at the University of Washington in Seattle, WA from JUN 21-23, 2013, immediately following the OHBM 2013 meeting. This course will bring together investigators interested in using quantitative biophysical models to identify brain connectivity and dynamics using the tools of imaging neuroscience, including fMRI, EEG/MEG, and LFP. Presentations will include:
overviews of brain connectivity methods and models
descriptions of specifics of DCM for fMRI, EEG/MEG and LFP data
explanations of Bayesian analysis at both single-subject and group levels
explorations of DCM experimental design and other advanced issues
Each afternoon will include a laboratory session, in which participants will gather in small groups to work with the faculty through the stages of analyzing data from example experiments. Further details can be found at: http://www.neurometrika.org/DCM2013 Kind Regards, Tom Zeffiro, Jean Daunizeau & Jeremie Mattout
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From marianapbranco1 at gmail.com  Thu May 23 10:25:45 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 10:25:45 +0200
Subject: [FieldTrip] Online preprocessing
Message-ID: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From jm.horschig at donders.ru.nl  Thu May 23 11:37:59 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 11:37:59 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
Message-ID: <519DE377.1020805@donders.ru.nl>

Hi Mariana,

On 5/23/2013 10:25 AM, Mariana Branco wrote:
> Hello,
>
> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
> My questions are:
> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?

no, you should use ft_read_data directly. The way to go is to check the 
header of your buffer for new events using ft_read_event. Upon detection 
of a relevant trigger, you need to use the returned event sample to 
compute your beginning and endsample manually (this is what 
ft_definetrial, or more precisely, your trialfun, usually does).  Then 
you can use ft_read_data to read data from the buffer into memory. 
ft_read_data returns a datamatrix that can be used to create your 
data.trial field. Also, you need to manually create the rest of the 
data-structure.
> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
It is definitely possible, once you converted the matrix to a regular 
fieldtrip structure. However, since it is about speed in online 
processing, you can think about using low-level functions of FieldTrip 
directly. Note that for resampling, you can also set up the shared 
memory (eg. acq2ftx) such that is downsamples right from the start.

> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
Do not use Welch's method, use another function. I don't know about this 
particular example function, but I think you would greatly benefit from 
finding out where the error is yourself. Note that online streaming od 
data *is* complicated and requires *you* to have knowledge about this.
> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
It should be an example, yes. Usually, there should be, as explained 
above, some ft_read_event statement to read the trigger value(s). In 
that particular example, the trialfun is used rather than ft_read_data 
directly, but trialfun is basically a wrapper around ft_read_data. Also, 
in that example a bunch of trials is read in, not just one. The thing 
you need to do to adjust this is to filter out the event structure such 
that only in case of the trigger of interest some data processing is 
done (you can use ft_filter_event for this).

My best advise for you is to read all (most) example functions and 
adjust them so that they run in your lab. Then sketch a flow diagram how 
triggers/data will be sent and read, try to implement this yourself (by 
copy&pasting relevant parts out of the example functions). If you have 
specific questions, feel free to always ask, but as this stage (please 
excuse my bluntnessI think you do not really know what needs to be done. 
I could write a lot about this, but I think you will benefit more if you 
first try yourself (especially because I do not know how your lab is set 
up and how things needs to be adjusted). But, as just said, feel free to 
write again when you have other questions.

Good luck!
Best,
Jörn

>
> I am sorry for all the questions.

No problem, no  way to know everything :)

> Regards,
>
> Mariana Branco
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From marianapbranco1 at gmail.com  Thu May 23 11:57:27 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 11:57:27 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <519DE377.1020805@donders.ru.nl>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
Message-ID: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>

Hi Jörn,

Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.

Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. 
In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?

Thank you again for all the advices, I will definitely pose more question in the future.

Mariana Branco

On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:

> Hi Mariana,
> 
> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>> Hello,
>> 
>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>> My questions are:
>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
> 
> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
> 
>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
> 
> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
> 
> Good luck!
> Best,
> Jörn
> 
>> 
>> I am sorry for all the questions.
> 
> No problem, no  way to know everything :)
> 
>> Regards,
>> 
>> Mariana Branco
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
> 
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
> 
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
> 
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From jm.horschig at donders.ru.nl  Thu May 23 12:08:33 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 12:08:33 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
	<B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
Message-ID: <519DEAA1.5030402@donders.ru.nl>

Hi Mariana,

ft_preprocessing demeans by the whole time window, in your 0s to 5s. The 
baseline window you specify depends on the time axis itself, if it goes 
from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, 
then you need to define [-3 0]. Time is relative :)
Also, please check ft_timelockbaseline. But such a simple thing as 
subtracting a number from a matrix can also easily be done without 
relying on a fieldtrip function :)

Best,
Jörn

On 5/23/2013 11:57 AM, Mariana Branco wrote:
> Hi Jörn,
>
> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.
>
> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial.
> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?
>
> Thank you again for all the advices, I will definitely pose more question in the future.
>
> Mariana Branco
>
> On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
>
>> Hi Mariana,
>>
>> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>>> Hello,
>>>
>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>>> My questions are:
>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
>>
>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
>>
>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
>>
>> Good luck!
>> Best,
>> Jörn
>>
>>> I am sorry for all the questions.
>> No problem, no  way to know everything :)
>>
>>> Regards,
>>>
>>> Mariana Branco
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From andmib at gmail.com  Thu May 23 16:29:07 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Thu, 23 May 2013 10:29:07 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
Message-ID: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>

Hello all,

I am new to FieldTrip, so this is a very basic question I was hoping
someone might know an answer to.

I am using ft_read_data to read the first EPI volume after dummy scans are
thrown out. I want to write this volume to a .nii file to my disk. For some
reason, I am unable to figure out the correct structure that ft_volumewrite
wants. Using the output from ft_read_data ('dat') does not seem to work.
Does anybody have any suggestions?

[ For a longer explanation of exactly what I am aiming to do, in case you
have any suggestions: I have ROI that is defined in Talairach space. This
is the ROI I would like to pull my real-time data from for each subject in
my study. To do this, I plan to register a talairach template brain to
individual subject-space, and then apply that transformation to my ROI so
that it is in subject space. I was going to simply write out the subject's
EPI to an .nii file, and then run SPM's co-registration step which allows
for a 'child dataset' to be set (my ROI), with the source file being the
template, and the reference being the individual ROI].

Thanks
Andrew
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From ggonesc at upo.es  Thu May 23 16:46:53 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Thu, 23 May 2013 16:46:53 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <cade69b25ef8089f.519e47fd@upo.es>

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From johanna.zumer at donders.ru.nl  Fri May 24 10:21:24 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Fri, 24 May 2013 10:21:24 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
Message-ID: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>

Dear Andrew,

To read EPI (MRI) data, you should use ft_read_mri instead.   Then
hopefully the format will match what ft_volumewrite wants.

Cheers,
Johanna


2013/5/23 Andrew Brooks <andmib at gmail.com>

> Hello all,
>
> I am new to FieldTrip, so this is a very basic question I was hoping
> someone might know an answer to.
>
> I am using ft_read_data to read the first EPI volume after dummy scans are
> thrown out. I want to write this volume to a .nii file to my disk. For some
> reason, I am unable to figure out the correct structure that ft_volumewrite
> wants. Using the output from ft_read_data ('dat') does not seem to work.
> Does anybody have any suggestions?
>
> [ For a longer explanation of exactly what I am aiming to do, in case you
> have any suggestions: I have ROI that is defined in Talairach space. This
> is the ROI I would like to pull my real-time data from for each subject in
> my study. To do this, I plan to register a talairach template brain to
> individual subject-space, and then apply that transformation to my ROI so
> that it is in subject space. I was going to simply write out the subject's
> EPI to an .nii file, and then run SPM's co-registration step which allows
> for a 'child dataset' to be set (my ROI), with the source file being the
> template, and the reference being the individual ROI].
>
> Thanks
> Andrew
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From andmib at gmail.com  Fri May 24 15:15:09 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Fri, 24 May 2013 09:15:09 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
Message-ID: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>

Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
pull a single volume from the buffer using ft_read_data, and then write it
out to a nifti file using ft_volumewrite, but ft_read_data does not output
the volume in a structure that ft_volumewrite wants.


On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer
<johanna.zumer at donders.ru.nl>wrote:

> Dear Andrew,
>
> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
> hopefully the format will match what ft_volumewrite wants.
>
> Cheers,
> Johanna
>
>
> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>
>> Hello all,
>>
>> I am new to FieldTrip, so this is a very basic question I was hoping
>> someone might know an answer to.
>>
>> I am using ft_read_data to read the first EPI volume after dummy scans
>> are thrown out. I want to write this volume to a .nii file to my disk. For
>> some reason, I am unable to figure out the correct structure that
>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>> seem to work. Does anybody have any suggestions?
>>
>> [ For a longer explanation of exactly what I am aiming to do, in case you
>> have any suggestions: I have ROI that is defined in Talairach space. This
>> is the ROI I would like to pull my real-time data from for each subject in
>> my study. To do this, I plan to register a talairach template brain to
>> individual subject-space, and then apply that transformation to my ROI so
>> that it is in subject space. I was going to simply write out the subject's
>> EPI to an .nii file, and then run SPM's co-registration step which allows
>> for a 'child dataset' to be set (my ROI), with the source file being the
>> template, and the reference being the individual ROI].
>>
>> Thanks
>> Andrew
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From johanna.zumer at gmail.com  Fri May 24 16:29:00 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Fri, 24 May 2013 16:29:00 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
	<CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
Message-ID: <CAL4kA6eCbXBJAFL9q5COz_jqgqGqT2FN8wUP3n3kOqiyK7sh0w@mail.gmail.com>

I'm not familiar with the buffer, but if you can read in your data
successfully, then to convert it to the structure that ft_volumewrite
wants, you can get some information inside ft_datatype_volume for what are
required or optional fields.




2013/5/24 Andrew Brooks <andmib at gmail.com>

> Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
> pull a single volume from the buffer using ft_read_data, and then write it
> out to a nifti file using ft_volumewrite, but ft_read_data does not output
> the volume in a structure that ft_volumewrite wants.
>
>
> On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer <
> johanna.zumer at donders.ru.nl> wrote:
>
>> Dear Andrew,
>>
>> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
>> hopefully the format will match what ft_volumewrite wants.
>>
>> Cheers,
>> Johanna
>>
>>
>> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>>
>>>  Hello all,
>>>
>>> I am new to FieldTrip, so this is a very basic question I was hoping
>>> someone might know an answer to.
>>>
>>> I am using ft_read_data to read the first EPI volume after dummy scans
>>> are thrown out. I want to write this volume to a .nii file to my disk. For
>>> some reason, I am unable to figure out the correct structure that
>>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>>> seem to work. Does anybody have any suggestions?
>>>
>>> [ For a longer explanation of exactly what I am aiming to do, in case
>>> you have any suggestions: I have ROI that is defined in Talairach space.
>>> This is the ROI I would like to pull my real-time data from for each
>>> subject in my study. To do this, I plan to register a talairach template
>>> brain to individual subject-space, and then apply that transformation to my
>>> ROI so that it is in subject space. I was going to simply write out the
>>> subject's EPI to an .nii file, and then run SPM's co-registration step
>>> which allows for a 'child dataset' to be set (my ROI), with the source file
>>> being the template, and the reference being the individual ROI].
>>>
>>> Thanks
>>> Andrew
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From politzerahless at gmail.com  Sat May 25 15:11:18 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 25 May 2013 08:11:18 -0500
Subject: [FieldTrip] Sourcespace and volume conductor misaligned
Message-ID: <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=fFk0ouR0wzA@mail.gmail.com>

Hello all,

I am going through the workflow at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
the volume conduction model using ft_prepare_headmodel(), I noticed that
although the volume conduction model and sourcespace have the same
orientation and overall size/shape (after I converted the volume conduction
model to cm, which wasn't in the tutorial but my original model came out in
mm), they don't quite line up, as you can see in this figure:

http://i.imgur.com/mGEtLOa.png

I did interactively re-align the data to CTF (twice--in step 2 of
"Preprocessing of the anatomical MRI" and in step 4 of "Source model")
using fiducials, and to Talairach (step 5 of "Preprocessing of the
anatomical data"), so I'm not sure how it ended up this way. The code I've
used at each step is basically the same as that in the tutorial.

Is there any way to line up my volume conduction model and sourcespace now,
without going back and re-running most of the workflow?

Best,
Steve

-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From johanna.zumer at donders.ru.nl  Sat May 25 20:54:59 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Sat, 25 May 2013 20:54:59 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
In-Reply-To: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
	<2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
Message-ID: <CAL4kA6eTL_TwECF62W-OoWY=Y1mpBR6QoOLh+ug8AcXNbVxQ1A@mail.gmail.com>

Dear Jing,

1.  Every MRI scanner is different, so I'm not familiar with that naming
scheme, but it seems the 'GAD' at the end of the file name indicates that
was with the Gadolinium contrast agent, so I would suggest to not use that,
but instead use the first (plain) T1.

2. I'm not sure what to suggest.  I assume you can see the vitamin E marker
clearly when viewing the DICOM file?   Is the issue that some slices are
missing in the conversion, or that the contrast on the image is not the
same?  or right/left flipped?

Best,
Johanna


2013/5/23 WangJing <13681530640 at 139.com>

> Dear Johanna,
>
>     Thank you for your suggestion.
>     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> t1_vibe_traGAD-5. which one is best?
>     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> didn't be found. what can I do?
>
> Best Regards,
> Jing Wang
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-22 15:33:13
> Subject：fieldtrip Digest, Vol 30, Issue 31
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: question About head model (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 May 2013 09:30:17 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] question About head model
> Message-ID:
> <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> It is best to use the T1 MRI rather than the other scans.   To open a DICOM
> format file, you can try one of these options:
>
> % read the DICOM files
> mri = ft_read_mri('single_file_of_DICOM_series.IMA');
>  % or use a graphical file selection[f, p] = uigetfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> >('*');
> mri = ft_read_mri(fullfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> >(p,
> f));
>
>
> I copied the above from documentation on the FieldTrip wiki:
>
> http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
>
>
> Then you can save the 'mri' into a *.mat file for future use with FieldTrip.
>
> Best regards,
> Johanna
>
>
> 2013/5/22 WangJing <13681530640 at 139.com>
>
> > Hi
> > I am a freshman about field trip.
> > I am trying to build the forward model. but my mri data is different from
> > the data in the tutorial. So I don't know how to bulid the head model. I
> > use the date which is from the paper "Open Database of Epileptic EEG with
> > MRI and Postoperational Assessment of Foci?a Real World Verification for
> > the EEG Inverse Solutions",http://eeg.pl/epi
> . MRI recordings containing a
>
> > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> > with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> > dysplastic tumors etc.). In some cases there is also a scan with the
>
> > gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> > scanner. The data is stored in the Digital Imaging and Communications in
> > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
>
> > In the tutorial,the mri data stored in only one file, while the data which
>
> > I used have many files, I don't know how to process. who can help me,Thanks1
> >  Thanks very much!
> > Best Reagards
> > Jing Wang
> >
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-21 23:59:18
> > Subject?fieldtrip Digest, Vol 30, Issue 29
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 21 May 2013 17:52:21 +0200
> > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you so much for your answer J?rn,
> >
> >
>
> > Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
> >
> >
>
> > Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
> >
> >
> >
>
> > I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> > data.dimord = 'rpt_rpt_chan_chan_freq'
> > ans size(data.crsspctrm) = [1 7 59 59];
> >
>
> > So, both are apparently the same, but the data inside this matrices is different,
> >
> >
>
> > for example, when calculating the ImC the first 7 columns for the first two rows are:
> > val(:,:,1,1)
> > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > val(:,:,1,2)
> >
>
> > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> >
> > while when calculating the PLV are:
> > val(:,:,1,1)
> > ?[1? 1? 1? 1? 1? 1? 1]
> > val(:,:,1,2)
> >
>
> > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> >
> >
> >
>
> > I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
> >
> >
>
> > If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
> >
> >
> >
> >
> >
>
> > On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
> >
> >
> > Many thanks in advanced,
> > Gabriel.
> >
> >
> >
> >
> > ----- Mensaje original -----
> > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >
> >
> >
> >
> >
> > > Dear Gabriel,
> >        >
> >
>
> >        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
> >                         >
> >
>
> > >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
> >        >
> >
>
> >        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
> >        >
> >
>
> > >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
> >
>
> > >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
> >        >
> > >        I hope that somehow clarifies your questions.
> >        >
> > >        Best,
> > >        J?rn
> >        >
> > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> >           > Dear Fieltrip experts,
> >          >
> >
>
> > >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
> >
>
> > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> > >          data.label {59x1};
> > >          data.time {1xNepochs};
> >          >
> > >          then, calculate only the FFT of all sensors as:
> > >          cfg=[];
> > >          cfg.output='fourier';
> > >          cfg.method='mtmfft';
> > >          cfg.taper='hanning';
> > >          cfg.foilim=[8.5 9.5];
> > >          cfg.tapsmofrq=0;
> > >          cfg.trials='all';
> > >          cfg.keeptrials='yes';
> > >          cfg.channel='all';
> > >          fourier=ft_freqanalysis(cfg, data)
> > >          as output I get:
> > >          dimord = 'rpttap_chan_freq'
> > >          freq= [1x9]
> > >          fourierspctrm=[7x59x9 double]
> >          >
> > >          Then compute the imaginary part of coherency as:
> >            > cfg=[];
> >              > cfg.method ='cohe';
> >              > cfg.complex='imag';
> >                > cfg.channelcbm={'all'               'all'};
> >              > coher = ft_connectivityanalysis (cfg, fourier)
> >          > as output get:
> >            > dimord='chan_chan_freq';
> >              > cohspctrm=[59x59x9 double];
> >              > dof=7;
> >            >
> >          > I have two main questions:
> >          >
> >
>
> >          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
> >                  >
> >                  >
> >                  >
> >
>
> >                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
> >                  >
> >                  >
> >                  >
> >                  >
> > >                  Many thanks in advanced,
> >                  > Gabriel.
> >                  >
> >                       >
> >               >
> >
>
> >        > _______________________________________________ > fieldtrip mailing list >
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >      >
> >
>
> >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > http://www.ru.nl/donders
>
> >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
>
> > <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> >
> >
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> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> > End of fieldtrip Digest, Vol 30, Issue 29
> > *****************************************
> >
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From 13681530640 at 139.com  Sun May 26 11:26:07 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
Subject: [FieldTrip] Question about Memory requirement Of Head model
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
Message-ID: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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From julian.keil at gmail.com  Sun May 26 12:23:34 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Sun, 26 May 2013 12:23:34 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
Message-ID: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>

Dear Jing Wang,

this might be due to you using a 32bit System.
As far as I know, 32bit Windows can only use ~3 GB of Memory. At least that's what I experienced using Win XP, maybe it's different for the server.
However, I'd advise you to switch to a 64bit System and try again.

Best,

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 26.05.2013 um 11:26 schrieb WangJing:

> Hello Everyone,
>      I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.
> for example 1:
> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]
> cfg = [];
> ft_sourceplot(cfg,mri);
>  
> the result is:
> ??? Out of memory. Type HELP MEMORY for your options.
> Error in ==> ft_sourceplot at 368
>   ana  = (ana-dmin)./(dmax-dmin);
>  
> example 2:
> clear all
> mri = ft_read_mri('IM-0001-0001.dcm');
> cfg = [];
> cfg.method = 'interactive';
> cfg.coordsys = 'ctf';
> mri_realigned = ft_volumerealign(cfg,mri);
> clear mri
> cfg=[];
> mrirs = ft_volumereslice(cfg,mri_realigned);
>  
> when run to the last code, I face the same problem.
>  
> Thank you!
> Best Regards!
> Jing Wang
>  
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From 13681530640 at 139.com  Sun May 26 17:01:10 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 23:01:10 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 37
References: <mailman.9.1369562405.16243.fieldtrip@science.ru.nl>
Message-ID: <2b1851a22104e22-00005.Richmail.00025896525295133618@139.com>


Hello Everyone,


    I have resolved the problem when I ran it in computer with 64 bit OS,  thanks.


Best Regards,


Jing Wang





 













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Date：2013-05-26 18:00:05
Subject：fieldtrip Digest, Vol 30, Issue 37

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Today's Topics:

   1. Question about Memory requirement Of Head model (WangJing)


----------------------------------------------------------------------

Message: 1
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
From: WangJing <13681530640 at 139.com>
To: fieldtrip <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Question about Memory requirement Of Head model
Message-ID:
<2b1851a17ca79ab-00017.Richmail.00027836529255037638 at 139.com>
Content-Type: text/plain; charset="utf-8"


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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------------------------------

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jm.horschig at donders.ru.nl  Mon May 27 11:54:00 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 27 May 2013 11:54:00 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
	<95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
Message-ID: <51A32D38.3060908@donders.ru.nl>

Hi all,

Julian is right, that's a limit of the 32bit system (the OS does not 
matter, just the number of bits). FieldTrip itself does not have any 
requirements other than Matlab does, however the size of your data 
matters. If you want to put data with more than 3gigs into memory, it's 
just not possible with a 32bit OS or Matlab (note that even if you have 
a 64bit OS but 32bit Matlab then the 3GB limit hold). So the only way 
for you to go is to clear variables from memory or reduce the size of 
the data you want to read it (or, go to 64bit). Maybe closing background 
tasks or other programs that are running will help as well.

Best,
Jörn

On 5/26/2013 12:23 PM, Julian Keil wrote:
> Dear Jing Wang,
>
> this might be due to you using a 32bit System.
> As far as I know, 32bit Windows can only use ~3 GB of Memory. At least 
> that's what I experienced using Win XP, maybe it's different for the 
> server.
> However, I'd advise you to switch to a 64bit System and try again.
>
> Best,
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 26.05.2013 um 11:26 schrieb WangJing:
>
>> Hello Everyone,
>>      I want to know what's the requiement of fieldtrip to hardware 
>> and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is 
>> windows sever 2003, and the matlab is 2011a(32bit).I often encounter 
>> the problem of out of Memery.
>> for example 1:
>> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 
>> 512 144]
>> cfg = [];
>> ft_sourceplot(cfg,mri);
>> the result is:
>> ??? Out of memory. Type HELP MEMORY for your options.
>> Error in ==> ft_sourceplot at 368
>>   ana  = (ana-dmin)./(dmax-dmin);
>> example 2:
>> clear all
>> mri = ft_read_mri('IM-0001-0001.dcm');
>> cfg = [];
>> cfg.method = 'interactive';
>> cfg.coordsys = 'ctf';
>> mri_realigned = ft_volumerealign(cfg,mri);
>> clear mri
>> cfg=[];
>> mrirs = ft_volumereslice(cfg,mri_realigned);
>> when run to the last code, I face the same problem.
>> Thank you!
>> Best Regards!
>> Jing Wang
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From member at linkedin.com  Mon May 27 14:14:43 2013
From: member at linkedin.com (Stavros Dimitriadis)
Date: Mon, 27 May 2013 12:14:43 +0000 (UTC)
Subject: [FieldTrip] Invitation to connect on LinkedIn
Message-ID: <1730678420.35398857.1369656883124.JavaMail.app@ela4-app0128.prod>

LinkedIn
------------




    Stavros Dimitriadis requested to add you as a connection on LinkedIn:
  

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- Stavros

Accept invitation from Stavros Dimitriadis
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From johanna.zumer at gmail.com  Mon May 27 15:12:27 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Mon, 27 May 2013 15:12:27 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
	<CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
Message-ID: <CAL4kA6cbk1c8bBztUG6JD_5k1W6Ds8CY3zRqer4uVxy-Edtpsg@mail.gmail.com>

Hi Mushfa,

The values inside grid_*.leadfield are the ones that need to be
concatenated, per grid position.   So the first thing to do is figure out
which rows in grid_eeg.pos match up with which rows in grid_meg.pos, and
then only for those that match, concatenate so that the *.leadfield is of
size [(number of eeg channels + number of meg channels)  X 3].

It might be easier to first ensure that the grid used to create these
leadfields have the same 'inside' positions (inside the volume conductor).

Best,
Johanna



2013/5/22 Mushfa Yousuf <mushfa.yousuf at googlemail.com>

> Hello Jörn;
>
> I have calculated an indiviual leadfield for both EEG and MEG. The
> structure of EEg and MEG shows the following variable
>
> grid_meg =
>
>         xgrid: [1x20 double]
>         ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
>         zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
>           dim: [20 17 16]
>           pos: [5440x3 double]
>          unit: 'cm'
>        inside: [1x3177 double]
>       outside: [1x2263 double]
>           cfg: [1x1 struct]
>     leadfield: {1x5440 cell}
>
>
> grid_eeg =
>
>         xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
>         ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
>         zgrid: [2 3 4 5 6 7 8 9 10 11]
>           dim: [16 13 10]
>           pos: [2080x3 double]
>          unit: 'cm'
>        inside: [1x1331 double]
>       outside: [1x749 double]
>           cfg: [1x1 struct]
>     leadfield: {1x2080 cell}
>
>
> Can you please give me a rough idea that how to concatenate the variables
> from both structure ?
>
>
> Thank you
>
> Regards ;
>
> Mushfa Yousuf
>
>
> On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
> jm.horschig at donders.ru.nl> wrote:
>
>>  Dear Mushfa,
>>
>> I think you have to compute two leadfield matrices, one for EEG (elec)
>> and one for MEG (grad), and then concatenate these (and make sure that the
>> order of sensors won't get mixed up anywhere, because  sourceanalysis just
>> expects the leadfield matrix to be ordered like your data. If that's not
>> the case, you either encounter the previous error you described or (if the
>> number of channels matches, but order is mixed up) it will just return
>> wrong source estimated activity.
>>
>> Best,
>> Jörn
>>
>>
>> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>>
>> Hello;
>>
>>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
>> of 'elec' while calculating the Leadfield.
>>
>>  Actually I am trying to calculate Combined source reconstruction from
>> both EEG and MEG sensors.
>>
>>  Do you have any idea, how to define both elec and grad definition
>> while calculating first forward then inverse solution.
>>
>>  Because in a fieldtrip either you can defined elec or grad at one time.
>>
>>
>>  Regards;
>>
>>
>>  Mushfa Yousuf
>>
>>  Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>>
>>> Hi Mushfa,
>>>
>>>  My guess is that the channels that have you used to compute .csdspctrm
>>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>>> freqPost.label, does that solve it?
>>>
>>>  Cheers,
>>> Johanna
>>>
>>>
>>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>>
>>>>   Hello Fieldtrippers,
>>>>
>>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>>
>>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>>> lead field successfully.
>>>>
>>>>  For the inverse solution using 'dics' method, I wrote the following
>>>> syntax
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>   cfg              = [];
>>>>   cfg.method       = 'dics';
>>>>  cfg.frequency    = 130;
>>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>>  cfg.grid         = grid;
>>>>  cfg.vol          = vol;
>>>>
>>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>  and I have received the following error:
>>>>
>>>>
>>>>  ??? Error using ==> mtimes
>>>> Inner matrix dimensions must agree.
>>>>
>>>>  Error in ==> beamformer_dics at 314
>>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>>         leadfield
>>>>
>>>>  Error in ==> ft_sourceanalysis at 595
>>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>>
>>>>  Error in ==> newCode at 214
>>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>
>>>>
>>>>  Any help would be appreciated.
>>>>
>>>>
>>>>  Regards;
>>>>
>>>>
>>>>  Mushfa Yousuf
>>>>
>>>>  Neurozentrum,
>>>> Universitätsklinikum Schleswig-Holstein,
>>>> Campus Kiel (UKSH), Deutschland
>>>>
>>>>
>>>>  _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mbj0310 at gmail.com  Wed May 29 11:47:14 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Wed, 29 May 2013 18:47:14 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some files
Message-ID: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>

Dear all,

Hello, my name is BJ Min from Korea.

I'm dealing with EEG data of many subjects.

When I run ft_preprocessing, the error message below shows with only some
files of my data. (not all files)

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577
??? Error using ==> ft_read_data at 149
cannot read data after the end of the file

Error in ==> ft_preprocessing at 577
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
begsample, 'endsample', endsample, 'chanindx', rawindx,
      'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
cfg.dataformat)

I think that there might be a kind of problem in data acquisition, and I
modified below scripts in the ft_read_data function with comment %.

% % test whether the requested data segment is not outside the file
% if any(begsample<1)
%   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
the file');
% elseif any(endsample>(hdr.nSamples*hdr.nTrials))
%   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the
file');
% end

After that, the ft_preprocessing worked well.

However, the files with the first problem showed additional warning message
while running ft_definetrial. (not error message)

Warning: Integer operands are required for colon operator when used as
index
> In fileio\private\loadcnt at 464
  In ft_read_header at 1450
  In ft_preprocessing at 398

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577

Also, during ft_redefinetrial, following warning message occurs.(not error
message)

Warning: removing inconsistent sampleinfo
> In ft_datatype_raw at 97
  In ft_checkdata at 213
  In ft_redefinetrial at 104

Warning: the trial definition in the configuration is inconsistent with the
actual data
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 74
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

Warning: reconstructing sampleinfo by assuming that the trials are
consecutive segments of a continuous recording
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 79
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

I wonder if these messages during ft_redefinetrial mean wrong defining
trials.
Should I continue these process like this, modifying the ft_preprocessing
function?
Or, is it better to exclude some erroneous files?

Best regards

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Wed May 29 12:01:31 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Wed, 29 May 2013 12:01:31 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
Message-ID: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>

Dear BJ Min,

what type of data are you trying to read in?
I had similar problems when reading in .CNT data.
Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.

Good Luck

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 29.05.2013 um 11:47 schrieb Beom Jun Min:

> Dear all,
> 
> Hello, my name is BJ Min from Korea.
> 
> I'm dealing with EEG data of many subjects. 
> 
> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
> 
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
> 
> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
> 
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
> % end
> 
> After that, the ft_preprocessing worked well.
> 
> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
> 
> Warning: Integer operands are required for colon operator when used as index 
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> 
> Also, during ft_redefinetrial, following warning message occurs.(not error message)
> 
> Warning: removing inconsistent sampleinfo 
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
> 
> Warning: the trial definition in the configuration is inconsistent with the actual data 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
> Should I continue these process like this, modifying the ft_preprocessing function? 
> Or, is it better to exclude some erroneous files?
> 
> Best regards
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From mbj0310 at gmail.com  Thu May 30 10:15:31 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 30 May 2013 17:15:31 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
Message-ID: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>

Dear Julian Keil,

Thank you for your reply.
I agree with that your problem was similar with mine.
My data was acquired by Neuroscan also.
There might a problem associated with .CNT file in the newer version.

Could you tell me the number of the older version you used?

Best Regards



2013/5/29 Julian Keil <julian.keil at gmail.com>

> Dear BJ Min,
>
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the
> problem, but this was in 2011, so I cannot say if the problem with .CNT
> files has been solved.
>
> Good Luck
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I'm dealing with EEG data of many subjects.
>
> When I run ft_preprocessing, the error message below shows with only some
> files of my data. (not all files)
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
>
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
> cfg.dataformat)
>
> I think that there might be a kind of problem in data acquisition, and I
> modified below scripts in the ft_read_data function with comment %.
>
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
> the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
> the file');
> % end
>
> After that, the ft_preprocessing worked well.
>
> However, the files with the first problem showed additional warning
> message while running ft_definetrial. (not error message)
>
> Warning: Integer operands are required for colon operator when used as
> index
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
>
> Also, during ft_redefinetrial, following warning message occurs.(not error
> message)
>
> Warning: removing inconsistent sampleinfo
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
>
> Warning: the trial definition in the configuration is inconsistent with
> the actual data
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> I wonder if these messages during ft_redefinetrial mean wrong defining
> trials.
> Should I continue these process like this, modifying the ft_preprocessing
> function?
> Or, is it better to exclude some erroneous files?
>
> Best regards
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Thu May 30 11:45:09 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Thu, 30 May 2013 11:45:09 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <80EC72EF-2296-47F5-97EC-197F91402C79@gmail.com>

Dear BJ Min,

I used the field trip version 20111101. I don't know if it's still available though.
To set the bitrate, you have to specify

	cfg.headerformat='ns_cnt32'; 
        cfg.dataformat='ns_cnt32'; 
        cfg.eventformat='ns_cnt32';

in ft_preprocessing

One way to check this (and also if you set your bitrate correctly), is to see if you can find easily detectable ERPs, like the visual or auditory N1 in your data. If you can't see this component, then your settings are wrong, even if data has been read into Matlab.

Good Luck,

Julian

Am 30.05.2013 um 10:15 schrieb Beom Jun Min:

> Dear Julian Keil,
> 
> Thank you for your reply. 
> I agree with that your problem was similar with mine. 
> My data was acquired by Neuroscan also. 
> There might a problem associated with .CNT file in the newer version.
> 
> Could you tell me the number of the older version you used? 
> 
> Best Regards
> 
> 
> 
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
> Dear BJ Min,
> 
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.
> 
> Good Luck
> 
> Julian
> 
> ********************
> Dr. Julian Keil
> 
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
> 
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209 
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
> 
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
> 
>> Dear all,
>> 
>> Hello, my name is BJ Min from Korea.
>> 
>> I'm dealing with EEG data of many subjects. 
>> 
>> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>> 
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
>> 
>> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
>> 
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
>> % end
>> 
>> After that, the ft_preprocessing worked well.
>> 
>> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
>> 
>> Warning: Integer operands are required for colon operator when used as index 
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> 
>> Also, during ft_redefinetrial, following warning message occurs.(not error message)
>> 
>> Warning: removing inconsistent sampleinfo 
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>> 
>> Warning: the trial definition in the configuration is inconsistent with the actual data 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
>> Should I continue these process like this, modifying the ft_preprocessing function? 
>> Or, is it better to exclude some erroneous files?
>> 
>> Best regards
>> 
>> -- 
>> BeomJun Min, M.D.
>> 
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST) 
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
>> 500-712, Republic of Korea (South) 
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From dr.chungki.lee at gmail.com  Thu May 30 11:56:02 2013
From: dr.chungki.lee at gmail.com (Chungki Lee)
Date: Thu, 30 May 2013 18:56:02 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>

Hi Min

you'd better use ft_definetrial routine before  ft_preprocessing.

example)

    cfg                              = [];
    cfg.dataset                 = filename;  % string
    cfg.trialdef.eventtype  =  your define text; % string
    cfg.trialdef.eventvalue = your label value;  % integer
    cfg.trialdef.prestim    = before onset time (sec); % positive integer,
not negative integer
    cfg.trialdef.poststim   = after onset time (sec); % positve integer
    cfg                            = ft_definetrial(cfg);
    data                          = ft_preprocessing(cfg);

have fun ^^


2013/5/30 Beom Jun Min <mbj0310 at gmail.com>

> Dear Julian Keil,
>
> Thank you for your reply.
> I agree with that your problem was similar with mine.
> My data was acquired by Neuroscan also.
> There might a problem associated with .CNT file in the newer version.
>
> Could you tell me the number of the older version you used?
>
> Best Regards
>
>
>
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>
>> Dear BJ Min,
>>
>> what type of data are you trying to read in?
>> I had similar problems when reading in .CNT data.
>> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
>> For me, reading in data with an older version of FieldTrip solved the
>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>> files has been solved.
>>
>> Good Luck
>>
>> Julian
>>
>>  ********************
>> *Dr. Julian Keil*
>> *
>> *
>> AG Multisensorische Integration
>> Psychiatrische Universitätsklinik
>> der Charité im St. Hedwig-Krankenhaus
>> Große Hamburger Straße 5-11, Raum E 307
>> 10115 Berlin
>>
>> Telefon: +49-30-2311-1879
>> Fax:        +49-30-2311-2209
>>
>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>
>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>
>> Dear all,
>>
>> Hello, my name is BJ Min from Korea.
>>
>> I'm dealing with EEG data of many subjects.
>>
>> When I run ft_preprocessing, the error message below shows with only some
>> files of my data. (not all files)
>>
>>  Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>>
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>> cfg.dataformat)
>>
>> I think that there might be a kind of problem in data acquisition, and I
>> modified below scripts in the ft_read_data function with comment %.
>>
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>> of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>> the file');
>> % end
>>
>> After that, the ft_preprocessing worked well.
>>
>> However, the files with the first problem showed additional warning
>> message while running ft_definetrial. (not error message)
>>
>> Warning: Integer operands are required for colon operator when used as
>> index
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>>
>> Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>>
>> Also, during ft_redefinetrial, following warning message occurs.(not
>> error message)
>>
>> Warning: removing inconsistent sampleinfo
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>>
>> Warning: the trial definition in the configuration is inconsistent with
>> the actual data
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> Warning: reconstructing sampleinfo by assuming that the trials are
>> consecutive segments of a continuous recording
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> I wonder if these messages during ft_redefinetrial mean wrong defining
>> trials.
>> Should I continue these process like this, modifying the ft_preprocessing
>> function?
>> Or, is it better to exclude some erroneous files?
>>
>> Best regards
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
----------------------------------------------------------------
Chungki Lee, Ph.D.
Post-doc
Biomedical Research Institute
Korea Institute of Science and Technology
E-mail: chungki at kist.re.kr
Tel:+82-2-958-5636, C.P: +82-10-5223-7309
----------------------------------------------------------------
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From lkystra at hotmail.it  Thu May 30 12:39:16 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 12:39:16 +0200
Subject: [FieldTrip] distorsion of .edf file
Message-ID: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>

Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  
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From zriouil.imane at gmail.com  Thu May 30 15:43:59 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Thu, 30 May 2013 15:43:59 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
Message-ID: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>

> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the
> use of read_edf, have a distorsion. Matlab indicate a warning for the 348
> row of read_edf . Can someone give to me a help?
>
> Best regards,
> Lucia
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 


Zriouil Imane
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From lkystra at hotmail.it  Thu May 30 17:33:55 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 17:33:55 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
Message-ID: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>

I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>




Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 

 
 
Zriouil Imane






_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu May 30 18:31:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 30 May 2013 18:31:22 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
Message-ID: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>

Hi Lucia,

Perhaps you need to be a bit more specific. 
In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.
Otherwise all of us are shooting in the dark.
Best wishes,
Jan-Mathijs


On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:

> I try and... it's not a good solution.
> 
> Date: Thu, 30 May 2013 15:43:59 +0200
> From: zriouil.imane at gmail.com
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] distorsion of .edf file
> 
> I have the same problem.
> 
> if you want to read your data. it's possible to use ft_read_data(filename')
> 
> 
> 
> 2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?
> 
> Best regards,
> Lucia
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
>  
>  
> Zriouil Imane
> 
> 
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ebrahimi_nia at yahoo.com  Thu May 30 19:14:52 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Thu, 30 May 2013 10:14:52 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
Message-ID: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>

Hi dear all,

I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.

**** Error using fread

Invalid precision.
Error in loreta2fieldtrip (line 85)
activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***

Can someone give me a help?


Best regards,
Fatemeh
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From inieuwenhuis at berkeley.edu  Thu May 30 19:30:41 2013
From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis)
Date: Thu, 30 May 2013 10:30:41 -0700
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
Message-ID: <51A78CC1.6030906@berkeley.edu>

Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug, see 
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export the 
source data as a text file. You can read that text file in with 
loreta2fieldtrip.m. It's a bit of a patch, but it worked for me.

Hope this helps,
Ingrid

On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:
> Hi dear all,
>
> I am analyzing EEG data. I have computed sLORETA (.slor) from ERP 
> data. Now I want to read and convert LORETA source reconstruction into a
> MATLAB data structure using "loreta2fieldtrip" function, But I have 
> gotten the bellow error.
>
> **** Error using fread
> Invalid precision.
> Error in loreta2fieldtrip (line 85)
> activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
> Can someone give me a help?
>
> Best regards,
> Fatemeh
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305

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From frank.ye.mei at gmail.com  Thu May 30 21:33:53 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Thu, 30 May 2013 15:33:53 -0400
Subject: [FieldTrip] error when using ctf2grad
Message-ID: <51A7A9A1.6020401@gmail.com>

Hi All,

I have some problem using ctf2grad.

The program will set   grad.balance.current = 'G3AR';,
and then do                 getfield(grad.balance, grad.balance.current)
but
grad.balance =    G1BR: [1x1 struct]
                             G2BR: [1x1 struct]
                             G3BR: [1x1 struct]

and has no G3AR in it. So an error will pop up.

Can anyone help me with that?

Also, What do G1BR,   G2BR,  G3BR, G3AR stand for?


thanks,
Ye


From politzerahless at gmail.com  Fri May 31 05:53:45 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Thu, 30 May 2013 22:53:45 -0500
Subject: [FieldTrip] Question about minimum norm estimate pipeline
Message-ID: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>

Hello all,

I have not yet gotten a response to my question below, but in the meantime
I have another question about the minimum norm estimate
workflow--specifically, about the coordinate system for the skull-stripped
anatomy in the step described at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk.
I'm confused by the following bit of code:

% ensure that the skull-stripped anatomy is expressed in the same
coordinate system as the anatomy
seg.transform = mri_tal.transform;

In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
re-aligning to Talairach in the previous step?) whereas seg.coordsys is
'ctf' (as a result of re-aligning to CTF several steps earlier). (But
mri_tal also has a field mri_tal.transformorig, which seg does not have.)
So should I really be using the same transform for both, as shown in the
tutorial?

Apologies if this question is pretty basic; I'm just trying to pinpoint
where the mis-alignment described in my message below occurred, so I want
to make sure I understand each step of the workflow correctly

Best,
Steve


> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/



On Sat, May 25, 2013 at 1:56 PM, <fieldtrip-request at science.ru.nl> wrote:
>
> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Sourcespace and volume conductor misaligned
>       (Stephen Politzer-Ahles)
>    2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
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>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 25 May 2013 20:54:59 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> Message-ID:
>         <CAL4kA6eTL_TwECF62W-OoWY=
Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> 1.  Every MRI scanner is different, so I'm not familiar with that naming
> scheme, but it seems the 'GAD' at the end of the file name indicates that
> was with the Gadolinium contrast agent, so I would suggest to not use
that,
> but instead use the first (plain) T1.
>
> 2. I'm not sure what to suggest.  I assume you can see the vitamin E
marker
> clearly when viewing the DICOM file?   Is the issue that some slices are
> missing in the conversion, or that the contrast on the image is not the
> same?  or right/left flipped?
>
> Best,
> Johanna
>
>
> 2013/5/23 WangJing <13681530640 at 139.com>
>
> > Dear Johanna,
> >
> >     Thank you for your suggestion.
> >     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > t1_vibe_traGAD-5. which one is best?
> >     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> > didn't be found. what can I do?
> >
> > Best Regards,
> > Jing Wang
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-22 15:33:13
> > Subject?fieldtrip Digest, Vol 30, Issue 31
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: question About head model (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 22 May 2013 09:30:17 +0200
> > From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] question About head model
> > Message-ID:
> > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > It is best to use the T1 MRI rather than the other scans.   To open a
DICOM
> > format file, you can try one of these options:
> >
> > % read the DICOM files
> > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> >  % or use a graphical file selection[f, p] = uigetfile
> > <
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > >('*');
> > mri = ft_read_mri(fullfile
> > <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > >(p,
> > f));
> >
> >
> > I copied the above from documentation on the FieldTrip wiki:
> >
> >
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> >
> >
> > Then you can save the 'mri' into a *.mat file for future use with
FieldTrip.
> >
> > Best regards,
> > Johanna
> >
> >
> > 2013/5/22 WangJing <13681530640 at 139.com>
> >
> > > Hi
> > > I am a freshman about field trip.
> > > I am trying to build the forward model. but my mri data is different
from
> > > the data in the tutorial. So I don't know how to bulid the head
model. I
> > > use the date which is from the paper "Open Database of Epileptic EEG
with
> > > MRI and Postoperational Assessment of Foci?a Real World Verification
for
> > > the EEG Inverse Solutions",http://eeg.pl/epi
> > . MRI recordings containing a
> >
> > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain
scans
> > > with morphologic substrate of the epilepsy (mostly cortical
dysplasias,
> > > dysplastic tumors etc.). In some cases there is also a scan with the
> >
> > > gadolinium (GAD) contrast. The images were collected by Siemens
Sonata 1.5T
> > > scanner. The data is stored in the Digital Imaging and Communications
in
> > > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > > weighting.The scans have the following resolutions: T1: 512 ? 512
pixels,
> > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> >
> > > In the tutorial,the mri data stored in only one file, while the data
which
> >
> > > I used have many files, I don't know how to process. who can help
me,Thanks1
> > >  Thanks very much!
> > > Best Reagards
> > > Jing Wang
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > > To?fieldtrip<fieldtrip at science.ru.nl>
> > > Date?2013-05-21 23:59:18
> > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Thank you so much for your answer J?rn,
> > >
> > >
> >
> > > Now I got it, so, I will let the 'fourier' as input to
ft_connectivityanalysis, because for some indices I will need the
auto-spectrum, and if I fully undertood what you said, it will be the same,
as they always take the phase information from the fourier transform. And
fieltrip will automatically compute the csd if the input is the frequency
data.
> > >
> > >
> >
> > > Nevertheless, it give me some error when I tried to use the output
from 'powandcsd' of freqanalysis, always gives me a matrix dimensions
error, and when I use the output 'fourier' from connectivityanalysis, it
computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they
are signed, so this is ok), the problem are the ImC ranging from -inf to
inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier'
the values are. Which for me is really weird.
> > >
> > >
> > >
> >
> > > I have checked internally, and even when I always use the 'fourier'
as input, when it internally calculates cross-spectrum for the ImC and PLV,
the data.crsspctrm is different, e.g:
> > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > ans size(data.crsspctrm) = [1 7 59 59];
> > >
> >
> > > So, both are apparently the same, but the data inside this matrices
is different,
> > >
> > >
> >
> > > for example, when calculating the ImC the first 7 columns for the
first two rows are:
> > > val(:,:,1,1)
> > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i?
0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > >
> > > while when calculating the PLV are:
> > > val(:,:,1,1)
> > > ?[1? 1? 1? 1? 1? 1? 1]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i?
0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > >
> > >
> > >
> >
> > > I'm pretty sure I'm doing something wrong here, but I don't really
have a clue,
> > >
> > >
> >
> > > If I use the fourier transform to calculate the 'csd' in
ft_connectivity analysis and use this csd as input to all other
ft_connectivityanalysis indices all of them are set to NaN or 1, not
ranging between any numbers.
> > >
> > >
> > >
> > >
> > >
> >
> > > On the other hand, I have seen searching on the net, that fieltrip is
capable of create surrogate data, by shifting the phase information on
every trial for only one electrode of each pair while using the original
samples of each trials on the second channel, but I couldn't find on the
manual how to do such a thing. Is there any way to compute this kind of
surrogates for every sensor? or was it something that some one suggest to
somebody?
> > >
> > >
> > > Many thanks in advanced,
> > > Gabriel.
> > >
> > >
> > >
> > >
> > > ----- Mensaje original -----
> > > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > >
> > >
> > >
> > >
> > >
> > > > Dear Gabriel,
> > >        >
> > >
> >
> > >        > A) As you             see, this makes an average over the
epochs of each channel,             and not over the samples (which in this
case are the 9             frequencies of the FFT), And I would like to
have the opposite, this is, to get the imaginary part of coherence for
              each epoch (repetition) on all                   my channels
and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,
              Is this possible?
> > >                         >
> > >
> >
> > > >        No. You should think of coherence more as a measure for the
      consistency of the phase relation between channels across trials,
  so coherence is just not defined per trial,neither would it make
sense to compute coherence for a single trial.
> > >        >
> > >
> >
> > >        > B)                     Another question I have is: for the
Imaginary part                     of Coherence is not necessary to compute
the                     cross-spectrum with 'powandcsd', only the FFT, but
                    for the PLV, PPC or WPLI is that way too?       I see
some terminology issues here. Let me try to explain in a       simple (aka
least-mathematical I can think of) way:
> > >        >
> > >
> >
> > > >        For all these connectivity measures, we need the phase
information       from the Fourier transform (FFT) to compute the
cross-spectral       density matrix (CSD). The CSD can be regarded as the
equivalent in       the frequency domain to the covariance matrix in the
time domain,       thus it is a measures how a certain channels activity is
      co-modulated with another channels activity (for a particular
frequency) - makes pretty much sense to make use of this when
computing connectivity, right? :)
> > >
> >
> > > >        As you might know, a Fourier transform returns complex
numbers,       where the imaginary part of this number contains phase
information. When calling ft_freqanalysis, you can decide if it       shall
only return the (squared) real part of the frequency       spectrum
(cfg.output='pow'), or instead the full CSD (cfg.output =
'powandcsd'). Alternatively, you can also let ft_freqanalysis       return
the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier
coefficients, however, you can easily obtain the CSD       or the power
spectrum basically by multiplication the Fourier       matrix with itself
(transposed). All of these measures quantify       the phase relation
between channels across trials, and as phase       information is coded in
the imaginary part of the fourier output,       thus for
connectivityanalysis you need the CSD which can be       obtained either by
'powandcsd' or by 'fourier'.
> > >        >
> > > >        I hope that somehow clarifies your questions.
> > >        >
> > > >        Best,
> > > >        J?rn
> > >        >
> > > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > >           > Dear Fieltrip experts,
> > >          >
> > >
> >
> > > >          I have my continuous data imported to fieldtrip with
matlab, I'm         looking for performing connectivity analysis between
pairs of         sensors, I have succed as:
> > >
> >
> > > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch
with 59 channels and 2000 samples
> > > >          data.label {59x1};
> > > >          data.time {1xNepochs};
> > >          >
> > > >          then, calculate only the FFT of all sensors as:
> > > >          cfg=[];
> > > >          cfg.output='fourier';
> > > >          cfg.method='mtmfft';
> > > >          cfg.taper='hanning';
> > > >          cfg.foilim=[8.5 9.5];
> > > >          cfg.tapsmofrq=0;
> > > >          cfg.trials='all';
> > > >          cfg.keeptrials='yes';
> > > >          cfg.channel='all';
> > > >          fourier=ft_freqanalysis(cfg, data)
> > > >          as output I get:
> > > >          dimord = 'rpttap_chan_freq'
> > > >          freq= [1x9]
> > > >          fourierspctrm=[7x59x9 double]
> > >          >
> > > >          Then compute the imaginary part of coherency as:
> > >            > cfg=[];
> > >              > cfg.method ='cohe';
> > >              > cfg.complex='imag';
> > >                > cfg.channelcbm={'all'               'all'};
> > >              > coher = ft_connectivityanalysis (cfg, fourier)
> > >          > as output get:
> > >            > dimord='chan_chan_freq';
> > >              > cohspctrm=[59x59x9 double];
> > >              > dof=7;
> > >            >
> > >          > I have two main questions:
> > >          >
> > >
> >
> > >          > A) As you see, this makes an average over the
epochs of each channel, and not over the samples (which in           this
case are the 9 frequencies of the FFT), And I would like           to have
the opposite, this is, to               get the imaginary
part of coherence for each epoch (repetition)                 on all my
channels and not for each frequency, something like: chan_chan_rpt or
chancbm_rpt,               Is this possible?
> > >                  >
> > >                  >
> > >                  >
> > >
> >
> > >                  > B) Another question I have is: for the
      Imaginary part of Coherence is not necessary to
compute the cross-spectrum with 'powandcsd', only the
FFT, but for the PLV, PPC or WPLI is that way too?
> > >                  >
> > >                  >
> > >                  >
> > >                  >
> > > >                  Many thanks in advanced,
> > >                  > Gabriel.
> > >                  >
> > >                       >
> > >               >
> > >
> >
> > >        > _______________________________________________ > fieldtrip
mailing list >
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >      >
> > >
> >
> > >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for
Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging >
Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip
Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands
>  > Contact: > E-Mail:
> > > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > > http://www.ru.nl/donders
> >
> > >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
NL-6525 EN Nijmegen > The Netherlands     >
_______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > >
> >
> > > <font size="3">--------------------------<br />PhD. student Gabriel
Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain
-<br /><br />Email:
> > > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> > >
> > >
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From a.stolk at fcdonders.ru.nl  Fri May 31 08:11:23 2013
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
Subject: [FieldTrip] Question about minimum norm estimate pipeline
In-Reply-To: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>
Message-ID: <1914237354.1292588.1369980683984.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Steve, A quick guess; did you correctly align your resliced mri to Talairach space by indicating the commissures ( http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm correct, a point in the same place, e.g. between the hemispheres? This should update the transformation matrix. Best regards, Arjen ----- Oorspronkelijk bericht -----
> Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Vrijdag 31 mei 2013 05:53:45
> Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> Hello all,
> I have not yet gotten a response to my question below, but in the
> meantime I have another question about the minimum norm estimate
> workflow--specifically, about the coordinate system for the
> skull-stripped anatomy in the step described at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> . I'm confused by the following bit of code:
> % ensure that the skull-stripped anatomy is expressed in the same
> coordinate system as the anatomy
> seg.transform = mri_tal.transform;
> In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> re-aligning to Talairach in the previous step?) whereas seg.coordsys
> is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> (But mri_tal also has a field mri_tal.transformorig, which seg does
> not have.) So should I really be using the same transform for both, as
> shown in the tutorial?
> Apologies if this question is pretty basic; I'm just trying to
> pinpoint where the mis-alignment described in my message below
> occurred, so I want to make sure I understand each step of the
> workflow correctly
> Best,
> Steve
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> On Sat, May 25, 2013 at 1:56 PM, < fieldtrip-request at science.ru.nl >
> wrote:
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Sourcespace and volume conductor misaligned
> > (Stephen Politzer-Ahles)
> > 2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sat, 25 May 2013 20:54:59 +0200
> > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> > Message-ID:
> > <CAL4kA6eTL_TwECF62W-OoWY= Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > 1. Every MRI scanner is different, so I'm not familiar with that
> > naming
> > scheme, but it seems the 'GAD' at the end of the file name indicates
> > that
> > was with the Gadolinium contrast agent, so I would suggest to not
> > use that,
> > but instead use the first (plain) T1.
> >
> > 2. I'm not sure what to suggest. I assume you can see the vitamin E
> > marker
> > clearly when viewing the DICOM file? Is the issue that some slices
> > are
> > missing in the conversion, or that the contrast on the image is not
> > the
> > same? or right/left flipped?
> >
> > Best,
> > Johanna
> >
> >
> > 2013/5/23 WangJing < 13681530640 at 139.com >
> >
> > > Dear Johanna,
> > >
> > > Thank you for your suggestion.
> > > 1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > > t1_vibe_traGAD-5. which one is best?
> > > 2.when I convert MRI from DICOM into CTF format,the vitamin E
> > > marker
> > > didn't be found. what can I do?
> > >
> > > Best Regards,
> > > Jing Wang
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > Date?2013-05-22 15:33:13
> > > Subject?fieldtrip Digest, Vol 30, Issue 31
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more
> > > specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: question About head model (Johanna Zumer)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Wed, 22 May 2013 09:30:17 +0200
> > > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > Subject: Re: [FieldTrip] question About head model
> > > Message-ID:
> > > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=
> > > HsAS_X0-w at mail.gmail.com >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Dear Jing,
> > >
> > > It is best to use the T1 MRI rather than the other scans. To open
> > > a DICOM
> > > format file, you can try one of these options:
> > >
> > > % read the DICOM files
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > % or use a graphical file selection[f, p] = uigetfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > > >('*');
> > > mri = ft_read_mri(fullfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > > >(p,
> > > f));
> > >
> > >
> > > I copied the above from documentation on the FieldTrip wiki:
> > >
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> > >
> > >
> > > Then you can save the 'mri' into a *.mat file for future use with
> > > FieldTrip.
> > >
> > > Best regards,
> > > Johanna
> > >
> > >
> > > 2013/5/22 WangJing < 13681530640 at 139.com >
> > >
> > > > Hi
> > > > I am a freshman about field trip.
> > > > I am trying to build the forward model. but my mri data is
> > > > different from
> > > > the data in the tutorial. So I don't know how to bulid the head
> > > > model. I
> > > > use the date which is from the paper "Open Database of Epileptic
> > > > EEG with
> > > > MRI and Postoperational Assessment of Foci?a Real World
> > > > Verification for
> > > > the EEG Inverse Solutions", http://eeg.pl/epi
> > > . MRI recordings containing a
> > >
> > > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted
> > > > brain scans
> > > > with morphologic substrate of the epilepsy (mostly cortical
> > > > dysplasias,
> > > > dysplastic tumors etc.). In some cases there is also a scan with
> > > > the
> > >
> > > > gadolinium (GAD) contrast. The images were collected by Siemens
> > > > Sonata 1.5T
> > > > scanner. The data is stored in the Digital Imaging and
> > > > Communications in
> > > > Medicine (DICOM) format. The name of the scan?s folder indicates
> > > > its
> > > > weighting.The scans have the following resolutions: T1: 512 ?
> > > > 512 pixels,
> > > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256
> > > > pixels,
> > > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> > >
> > > > In the tutorial,the mri data stored in only one file, while the
> > > > data which
> > >
> > > > I used have many files, I don't know how to process. who can
> > > > help me,Thanks1
> > > > Thanks very much!
> > > > Best Reagards
> > > > Jing Wang
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > > ----The following is the content of the forwarded email----
> > > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > > Date?2013-05-21 23:59:18
> > > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > > >
> > > > Send fieldtrip mailing list submissions to
> > > > fieldtrip at science.ru.nl
> > > >
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> > > > Today's Topics:
> > > >
> > > > 1. Re: problem in connectivityanalysis (Gabriel Gonzalez
> > > > Escamilla)
> > > >
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > > From: Gabriel Gonzalez Escamilla < ggonesc at upo.es >
> > > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > > Message-ID: < 1348f6433edc26f9.519bb455 at upo.es >
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Thank you so much for your answer J?rn,
> > > >
> > > >
> > >
> > > > Now I got it, so, I will let the 'fourier' as input to
> > > > ft_connectivityanalysis, because for some indices I will need
> > > > the auto-spectrum, and if I fully undertood what you said, it
> > > > will be the same, as they always take the phase information from
> > > > the fourier transform. And fieltrip will automatically compute
> > > > the csd if the input is the frequency data.
> > > >
> > > >
> > >
> > > > Nevertheless, it give me some error when I tried to use the
> > > > output from 'powandcsd' of freqanalysis, always gives me a
> > > > matrix dimensions error, and when I use the output 'fourier'
> > > > from connectivityanalysis, it computes almost all indices to ok,
> > > > raging from? -1 to 1 (I'm saw that they are signed, so this is
> > > > ok), the problem are the ImC ranging from -inf to inf, and the
> > > > PLV values ranging from 0 to inf, but when I use the 'fourier'
> > > > the values are. Which for me is really weird.
> > > >
> > > >
> > > >
> > >
> > > > I have checked internally, and even when I always use the
> > > > 'fourier' as input, when it internally calculates cross-spectrum
> > > > for the ImC and PLV, the data.crsspctrm is different, e.g:
> > > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > > ans size(data.crsspctrm) = [1 7 59 59];
> > > >
> > >
> > > > So, both are apparently the same, but the data inside this
> > > > matrices is different,
> > > >
> > > >
> > >
> > > > for example, when calculating the ImC the first 7 columns for
> > > > the first two rows are:
> > > > val(:,:,1,1)
> > > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i?
> > > > 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > > >
> > > > while when calculating the PLV are:
> > > > val(:,:,1,1)
> > > > ?[1? 1? 1? 1? 1? 1? 1]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i?
> > > > 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > > >
> > > >
> > > >
> > >
> > > > I'm pretty sure I'm doing something wrong here, but I don't
> > > > really have a clue,
> > > >
> > > >
> > >
> > > > If I use the fourier transform to calculate the 'csd' in
> > > > ft_connectivity analysis and use this csd as input to all other
> > > > ft_connectivityanalysis indices all of them are set to NaN or 1,
> > > > not ranging between any numbers.
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > > > On the other hand, I have seen searching on the net, that
> > > > fieltrip is capable of create surrogate data, by shifting the
> > > > phase information on every trial for only one electrode of each
> > > > pair while using the original samples of each trials on the
> > > > second channel, but I couldn't find on the manual how to do such
> > > > a thing. Is there any way to compute this kind of surrogates for
> > > > every sensor? or was it something that some one suggest to
> > > > somebody?
> > > >
> > > >
> > > > Many thanks in advanced,
> > > > Gabriel.
> > > >
> > > >
> > > >
> > > >
> > > > ----- Mensaje original -----
> > > > De: "J?rn M. Horschig" < jm.horschig at donders.ru.nl >
> > > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > > A: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Dear Gabriel,
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > >
> > >
> > > > > No. You should think of coherence more as a measure for the
> > > > > consistency of the phase relation between channels across
> > > > > trials, so coherence is just not defined per trial,neither
> > > > > would it make sense to compute coherence for a single trial.
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too? I see some terminology issues here. Let me try
> > > > > to explain in a simple (aka least-mathematical I can think of)
> > > > > way:
> > > > >
> > > >
> > >
> > > > > For all these connectivity measures, we need the phase
> > > > > information from the Fourier transform (FFT) to compute the
> > > > > cross-spectral density matrix (CSD). The CSD can be regarded
> > > > > as the equivalent in the frequency domain to the covariance
> > > > > matrix in the time domain, thus it is a measures how a certain
> > > > > channels activity is co-modulated with another channels
> > > > > activity (for a particular frequency) - makes pretty much
> > > > > sense to make use of this when computing connectivity, right?
> > > > > :)
> > > >
> > >
> > > > > As you might know, a Fourier transform returns complex
> > > > > numbers, where the imaginary part of this number contains
> > > > > phase information. When calling ft_freqanalysis, you can
> > > > > decide if it shall only return the (squared) real part of the
> > > > > frequency spectrum (cfg.output='pow'), or instead the full CSD
> > > > > (cfg.output = 'powandcsd'). Alternatively, you can also let
> > > > > ft_freqanalysis return the raw Fourier coefficients
> > > > > (cfg.output='fourier'). From the Fourier coefficients,
> > > > > however, you can easily obtain the CSD or the power spectrum
> > > > > basically by multiplication the Fourier matrix with itself
> > > > > (transposed). All of these measures quantify the phase
> > > > > relation between channels across trials, and as phase
> > > > > information is coded in the imaginary part of the fourier
> > > > > output, thus for connectivityanalysis you need the CSD which
> > > > > can be obtained either by 'powandcsd' or by 'fourier'.
> > > > >
> > > > > I hope that somehow clarifies your questions.
> > > > >
> > > > > Best,
> > > > > J?rn
> > > > >
> > > > > On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > > > > Dear Fieltrip experts,
> > > > >
> > > >
> > >
> > > > > I have my continuous data imported to fieldtrip with matlab,
> > > > > I'm looking for performing connectivity analysis between pairs
> > > > > of sensors, I have succed as:
> > > >
> > >
> > > > > data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59
> > > > > channels and 2000 samples
> > > > > data.label {59x1};
> > > > > data.time {1xNepochs};
> > > > >
> > > > > then, calculate only the FFT of all sensors as:
> > > > > cfg=[];
> > > > > cfg.output='fourier';
> > > > > cfg.method='mtmfft';
> > > > > cfg.taper='hanning';
> > > > > cfg.foilim=[8.5 9.5];
> > > > > cfg.tapsmofrq=0;
> > > > > cfg.trials='all';
> > > > > cfg.keeptrials='yes';
> > > > > cfg.channel='all';
> > > > > fourier=ft_freqanalysis(cfg, data)
> > > > > as output I get:
> > > > > dimord = 'rpttap_chan_freq'
> > > > > freq= [1x9]
> > > > > fourierspctrm=[7x59x9 double]
> > > > >
> > > > > Then compute the imaginary part of coherency as:
> > > > > cfg=[];
> > > > > cfg.method ='cohe';
> > > > > cfg.complex='imag';
> > > > > cfg.channelcbm={'all' 'all'};
> > > > > coher = ft_connectivityanalysis (cfg, fourier)
> > > > > as output get:
> > > > > dimord='chan_chan_freq';
> > > > > cohspctrm=[59x59x9 double];
> > > > > dof=7;
> > > > >
> > > > > I have two main questions:
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Many thanks in advanced,
> > > > > Gabriel.
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > _______________________________________________ > fieldtrip
> > > > > mailing list >
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > >
> > > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for
> > > > > Brain, Cognition and Behaviour > Centre for Cognitive
> > > > > Neuroimaging > Radboud University Nijmegen > Neuronal
> > > > > Oscillations Group > FieldTrip Development Team > > P.O. Box
> > > > > 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: >
> > > > > E-Mail:
> > > > jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:
> > > > http://www.ru.nl/donders
> > >
> > > > > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
> > > > > > NL-6525 EN Nijmegen > The Netherlands >
> > > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > >
> > >
> > > > <font size="3">--------------------------<br />PhD. student
> > > > Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional
> > > > Neuroscience<br />Department of Physiology, Anatomy, and Cell
> > > > Biology<br />University Pablo de Olavide<br />Ctra. de Utrera,
> > > > Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > > > ggonesc at upo.es <br /> http://www.upo.es/neuroaging/es/ </font>
> > > >
> > > >
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> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> > > > End of fieldtrip Digest, Vol 30, Issue 29
> > > > *****************************************
> > > >
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> > >
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> > *****************************************
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From yukaokazaki at gmail.com  Fri May 31 08:21:56 2013
From: yukaokazaki at gmail.com (Yuka Okazaki)
Date: Fri, 31 May 2013 15:21:56 +0900
Subject: [FieldTrip] single subject headmodel and mni-transformed grid
	doesn't fit
Message-ID: <CAKHP_vRT6Ad1nLLOoaUoA5UFTLK5x-yp5jm8+HtY9sD6FER4dQ@mail.gmail.com>

Dear all

I have a problem that single subject headmodel and the warped its grid to
template grid do not fit, as attached figure. I expected they are exactly
fit each other but it seems not.

I generated this figure by following steps. MEG system is yokogawa.
Any advices I should check will be very helpful and appreciated.

Yuka

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
load('~\fieldtrip\template\sourcemodel\standard_sourcemodel3d10mm.mat')
template_grid  = sourcemodel;

% Read mri data
mri2nifti('subject.mri', 'mri.nii');
mri_nifti = ft_read_mri('mri.nii');

% Define fiducial position in MRI coordinate
cfg = [];
cfg.method = 'interactive';
mri = ft_volumerealign(cfg, mri_nifti);

% segment the anatomical MRI
cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg, mri);

% construct volume conductor model (i.e. head model) for each subject
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
vol = ft_convert_units(vol, 'cm');

% create the subject specific grid, using the template grid that has just
been created
cfg = [];
cfg.grid.warpmni   = 'yes';
cfg.grid.template  =  template_grid; %sourcemodel%
cfg.grid.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri;
grid               = ft_prepare_sourcemodel(cfg);

% make a figure of the single subject headmodel, and grid positions
figure;
ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4;
ft_plot_mesh(grid.pos(grid.inside,:),'vertexcolor','r');[image: Inline
image 1]
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From politzerahless at gmail.com  Fri May 31 08:27:19 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Fri, 31 May 2013 01:27:19 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 45
In-Reply-To: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
References: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k_9EcqcEeuGM_F8O7u0047tct6P9ZP-pLf2xdJ61p1tNMA@mail.gmail.com>

Hi Arjen,

Thanks for your message; I did indeed re-align to Talairach after
reslicing, although I can't be sure it was "correct" (the page linked from
the tutorial, http://neuroimage.usc.edu/brainstorm/CoordinateSystems,
didn't give guidelines on how anterior/posteriorly to place the
interhemispheric point, so I just placed it near the top of the head on
about the same plane as the commisures). But it wasn't until the end of the
anatomical processing that I noticed the issue, so I'm wondering if there's
a way to re-align the source space and volume conduction model to each
other without going back to the beginning of the pipeline.

Best,
Steve


> Message: 1
> Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
> From: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about minimum norm estimate pipeline
> Message-ID:
>         <
1914237354.1292588.1369980683984.JavaMail.root at sculptor.zimbra.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve, A quick guess; did you correctly align your resliced mri to
Talairach space by indicating the commissures (
http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm
correct, a point in the same place, e.g. between the hemispheres? This
should update the transformation matrix. Best regards, Arjen -----
Oorspronkelijk bericht -----
> > Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> > Aan: fieldtrip at science.ru.nl
> > Verzonden: Vrijdag 31 mei 2013 05:53:45
> > Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> > Hello all,
> > I have not yet gotten a response to my question below, but in the
> > meantime I have another question about the minimum norm estimate
> > workflow--specifically, about the coordinate system for the
> > skull-stripped anatomy in the step described at
> >
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> > . I'm confused by the following bit of code:
> > % ensure that the skull-stripped anatomy is expressed in the same
> > coordinate system as the anatomy
> > seg.transform = mri_tal.transform;
> > In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> > re-aligning to Talairach in the previous step?) whereas seg.coordsys
> > is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> > (But mri_tal also has a field mri_tal.transformorig, which seg does
> > not have.) So should I really be using the same transform for both, as
> > shown in the tutorial?
> > Apologies if this question is pretty basic; I'm just trying to
> > pinpoint where the mis-alignment described in my message below
> > occurred, so I want to make sure I understand each step of the
> > workflow correctly
> > Best,
> > Steve
> > > Message: 1
> > > Date: Sat, 25 May 2013 08:11:18 -0500
> > > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > > To: fieldtrip at donders.ru.nl
> > > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > > Message-ID:
> > > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > > >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hello all,
> > >
> > > I am going through the workflow at
> > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > > making
> > > the volume conduction model using ft_prepare_headmodel(), I noticed
> > > that
> > > although the volume conduction model and sourcespace have the same
> > > orientation and overall size/shape (after I converted the volume
> > > conduction
> > > model to cm, which wasn't in the tutorial but my original model came
> > > out in
> > > mm), they don't quite line up, as you can see in this figure:
> > >
> > > http://i.imgur.com/mGEtLOa.png
> > >
> > > I did interactively re-align the data to CTF (twice--in step 2 of
> > > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > > model")
> > > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > > anatomical data"), so I'm not sure how it ended up this way. The
> > > code I've
> > > used at each step is basically the same as that in the tutorial.
> > >
> > > Is there any way to line up my volume conduction model and
> > > sourcespace now,
> > > without going back and re-running most of the workflow?
> > >
> > > Best,
> > > Steve
> > >
> > > --
> > > Stephen Politzer-Ahles
> > > University of Kansas
> > > Linguistics Department
> > > http://people.ku.edu/~sjpa/
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From stefan.debener at uni-oldenburg.de  Fri May 31 09:18:51 2013
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Fri, 31 May 2013 09:18:51 +0200
Subject: [FieldTrip] Open ostdoc position
Message-ID: <51A84EDB.6010408@uni-oldenburg.de>

The cluster of excellence Hearing4all: Models, Technology and Solutions 
for Diagnostics, Restoration and Support of Hearing at the Carl von 
Ossietzky Universität Oldenburg (in collaboration with Medizinische 
Hochschule Hannover and Leibniz Universität Hannover) is seeking to fill 
the position of a

*Postdoctoral Research Associate in the Field of Auditory 
Psychophysiology *

in the Department of Psychology, Faculty of Medicine and Health Sciences.

The position is available from 1 September 2013, for initially 2 years, 
with prospect for continuation for up to 2.5 more years. Payment is 
depending on previous experience (German TV-L E13, full time).

A paramount goal of the cluster of excellence Hearing4all 
(www.hearing4all.de) is to transform audiology into an "exact" science 
based on the interplay between experiment and theory as well as between 
basic science and clinical research. In the framework provided by the 
cluster the successful candidate is expected to contribute to the 
research goals of task group 2 "Audioneurotechnology and theragnostics" 
or task group 7 "Brain-computer interface for hearing devices", e.g., by:

- studying hearing disorder related maladaptive plasticity in the human 
auditory cortex with non-invasive techniques (EEG, MEG, NIRS);

- electrophysiological characterisation of auditory cortex adaption to 
hearing device use (hearing aids, cochlear implants);

- the role of auditory neurofeedback on speech comprehension;

- the role of multisensory processes in auditory rehabilitation.

Candidates are expected to have an academic university degree in the 
field of psychology, biology, neuroscience, or a related discipline and 
have shown their ability to perform excellent scientific work, usually 
demonstrated by the outstanding quality of their Doctorate/PhD research 
and a good publication record. We are seeking candidates with extensive 
knowledge in at least one of the following methods: advanced EEG 
recording and analysis; near-infrared spectroscopy. Excellent Matlab 
skills are mandatory and good knowledge of EEG analysis software suites 
(e.g., EEGLAB, Fieldtrip, BESA, LORETA) will be an asset. It is also 
necessary to have a background in experimental psychology, and knowledge 
of the German language is required. The Department of Psychology will 
offer an attractive scientific environment with access to research 
dedicated state-of-the-art approaches to human neurophysiological 
techniques (fMRI, NIRS, EEG, MEG, mobile EEG and mobile eye-tracking).

The University of Oldenburg strives to increase the proportion of women 
in science, so we especially encourage female candidates to apply. 
Handicapped applicants will be given preference if equally qualified.

Please send your application including a cover letter, CV, list of 
potential referees, links to recent publications, and copies of 
certificates for academic grades by email to Prof. Stefan Debener 
(Stefan.Debener at uni-oldenburg.de 
<mailto:Stefan.Debener at uni-oldenburg.de>). Feel free to contact Stefan 
Debener for further questions regarding the position. The application 
deadline is July 15, 2013.

-- 
Prof. Dr. Stefan Debener
Neuropsychology	Lab
Department of Psychology
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email: stefan.debener at uni-oldenburg.de

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From baharbahar395 at yahoo.com  Fri May 31 09:48:25 2013
From: baharbahar395 at yahoo.com (Bahar Bahar)
Date: Fri, 31 May 2013 15:48:25 +0800 (SGT)
Subject: [FieldTrip] format conversion
Message-ID: <1369986505.7865.YahooMailNeo@web192306.mail.sg3.yahoo.com>

Hi dear all,

I have a technical question about format converter module via sLORETA software (.slor file to .txt one). Can any one give me some information about the conversion procedure (and the meaning of the column and row of the output file)?

Thanks,
bahar
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From mbj0310 at gmail.com  Fri May 31 11:11:33 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Fri, 31 May 2013 18:11:33 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
	<CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
Message-ID: <CA+v9jvLXKGfwUE4TkGx9t703fQnrtJVi=0w6ZFGBYVLKAvseSw@mail.gmail.com>

Dear respondent,

Thank you for your advices.
I will try these methods.

Best regards




2013/5/30 Chungki Lee <dr.chungki.lee at gmail.com>

> Hi Min
>
> you'd better use ft_definetrial routine before  ft_preprocessing.
>
> example)
>
>     cfg                              = [];
>     cfg.dataset                 = filename;  % string
>     cfg.trialdef.eventtype  =  your define text; % string
>     cfg.trialdef.eventvalue = your label value;  % integer
>     cfg.trialdef.prestim    = before onset time (sec); % positive
> integer, not negative integer
>     cfg.trialdef.poststim   = after onset time (sec); % positve integer
>     cfg                            = ft_definetrial(cfg);
>     data                          = ft_preprocessing(cfg);
>
> have fun ^^
>
>
> 2013/5/30 Beom Jun Min <mbj0310 at gmail.com>
>
>> Dear Julian Keil,
>>
>> Thank you for your reply.
>> I agree with that your problem was similar with mine.
>> My data was acquired by Neuroscan also.
>> There might a problem associated with .CNT file in the newer version.
>>
>> Could you tell me the number of the older version you used?
>>
>> Best Regards
>>
>>
>>
>> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>>
>>> Dear BJ Min,
>>>
>>> what type of data are you trying to read in?
>>> I had similar problems when reading in .CNT data.
>>> Also, with some systems you have to specify the bit rate (e.g.
>>> Neuroscan).
>>> For me, reading in data with an older version of FieldTrip solved the
>>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>>> files has been solved.
>>>
>>> Good Luck
>>>
>>> Julian
>>>
>>>  ********************
>>> *Dr. Julian Keil*
>>> *
>>> *
>>> AG Multisensorische Integration
>>> Psychiatrische Universitätsklinik
>>> der Charité im St. Hedwig-Krankenhaus
>>> Große Hamburger Straße 5-11, Raum E 307
>>> 10115 Berlin
>>>
>>> Telefon: +49-30-2311-1879
>>> Fax:        +49-30-2311-2209
>>>
>>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>>
>>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>>
>>> Dear all,
>>>
>>> Hello, my name is BJ Min from Korea.
>>>
>>> I'm dealing with EEG data of many subjects.
>>>
>>> When I run ft_preprocessing, the error message below shows with only
>>> some files of my data. (not all files)
>>>
>>>  Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>> ??? Error using ==> ft_read_data at 149
>>> cannot read data after the end of the file
>>>
>>> Error in ==> ft_preprocessing at 577
>>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>>> cfg.dataformat)
>>>
>>> I think that there might be a kind of problem in data acquisition, and I
>>> modified below scripts in the ft_read_data function with comment %.
>>>
>>> % % test whether the requested data segment is not outside the file
>>> % if any(begsample<1)
>>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>>> of the file');
>>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>>> the file');
>>> % end
>>>
>>> After that, the ft_preprocessing worked well.
>>>
>>> However, the files with the first problem showed additional warning
>>> message while running ft_definetrial. (not error message)
>>>
>>> Warning: Integer operands are required for colon operator when used as
>>> index
>>> > In fileio\private\loadcnt at 464
>>>   In ft_read_header at 1450
>>>   In ft_preprocessing at 398
>>>
>>> Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>>
>>> Also, during ft_redefinetrial, following warning message occurs.(not
>>> error message)
>>>
>>> Warning: removing inconsistent sampleinfo
>>> > In ft_datatype_raw at 97
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 104
>>>
>>> Warning: the trial definition in the configuration is inconsistent with
>>> the actual data
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 74
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> Warning: reconstructing sampleinfo by assuming that the trials are
>>> consecutive segments of a continuous recording
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 79
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> I wonder if these messages during ft_redefinetrial mean wrong defining
>>> trials.
>>> Should I continue these process like this, modifying the
>>> ft_preprocessing function?
>>> Or, is it better to exclude some erroneous files?
>>>
>>> Best regards
>>>
>>> --
>>> BeomJun Min, M.D.
>>>
>>> Department of Medical System Engineering (DMSE)
>>> Gwangju Institute of Science and Technology (GIST)
>>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>>> 500-712, Republic of Korea (South)
>>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> ----------------------------------------------------------------
> Chungki Lee, Ph.D.
> Post-doc
> Biomedical Research Institute
> Korea Institute of Science and Technology
> E-mail: chungki at kist.re.kr
> Tel:+82-2-958-5636, C.P: +82-10-5223-7309
> ----------------------------------------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From thomas.wunderle at esi-frankfurt.de  Fri May 31 11:42:03 2013
From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas)
Date: Fri, 31 May 2013 09:42:03 +0000
Subject: [FieldTrip] channel combination problems
Message-ID: <27E5CAD9145EEC41BB9B34C01716A1983046156B@UM-EXCDAG-A01.um.gwdg.de>

Hi all,

I'm new in fieldtrip and I try to get the cfg.channelcmb to work, because I want to plot the connectivity between the channels of different laminar electrodes,
let's say the connectivity between channel 1:24 and 25:38

I tried the following:
cfg           = [];
cfg.method    = 'mtmfft';
cfg.taper     = 'dpss';
cfg.output    = 'fourier';
cfg.tapsmofrq = 1;
freq          = ft_freqanalysis(cfg, data)

The output is:
>> freq
freq =
            label: {3x1 cell}
           dimord: 'rpttap_chan_freq'
            freq: [1x101 double]
            fourierspctrm: [500x3x101 double]
            cumsumcnt: [500x1 double]
            cumtapcnt: [500x1 double]
             cfg: [1x1 struct]


I then run

cfg           = [];
cfg.method    = 'coh';
cfg.channelcmb = {freq.label{1} freq.label{2};freq.label{2} freq.label{1}};
coh= ft_connectivityanalysis(cfg, freq);

And the output here is:

>> coh
coh =
       labelcmb: {2x2 cell}
       dimord: 'chan_freq'
       cohspctrm: [2x101 double]
        freq: [1x101 double]
        dof: 500
        cfg: [1x1 struct]

As you can seen, the output of dimord is 'chan_freq' so in the subsequent call of ft_connectivityplot I get an error message:

cfg           = [];
cfg.parameter = 'cohspctrm';
ft_connectivityplot(cfg, coh);

??? Error using ==> ft_connectivityplot at 99
the data should have a dimord of chan_chan_freq or chancmb_freq


If I use in ft_freqanalysis the cfg.method = 'powandcsd', cfg.channelcmb seems to have no effect at all,
the coherence is computed for all possible pairs.

I also don't understand the difference between "cfg.channelcmb" and "cfg.labelcmb"

Can you help me in how I should correctly use the cannelcmb and labelcmb options?

Thanks for your help,
Thomas



-----
Dr. Thomas Wunderle
Ernst Strüngmann Institute (ESI) for Neuroscience<http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
in Cooperation with Max Planck Society <http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
Deutschordenstrasse 46
60528 Frankfurt am Main, Germany
www.esi-frankfurt.de<http://www.esi-frankfurt.de/>
thomas.wunderle at esi-frankfurt.de<mailto:thomas.wunderle at esi-frankfurt.de>
Tel:   +49 69 96769 519
Fax:   +49 69 96769 555

Sitz der Gesellschaft: Frankfurt am Main
Registergericht: Amtsgericht Frankfurt - HRB 84266
Geschäftsführer: Prof. Dr. Pascal Fries


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From sid.kouider at gmail.com  Fri May 31 11:56:19 2013
From: sid.kouider at gmail.com (Sid Kouider)
Date: Fri, 31 May 2013 11:56:19 +0200
Subject: [FieldTrip] postdoctoral position on EEG/BCI in Paris
Message-ID: <007701ce5de5$1b083620$5118a260$@gmail.com>

The Department of Cognitive Science at the Ecole Normale Supérieure (Paris)
invites applications for a postdoctoral position to work on Brain-Computer
Interfaces and Virtual Reality in the framework of the CEEDs European
project ( <http://ceeds-project.eu/> http://ceeds-project.eu/). 

 

The post-doc will mainly be in charge of :

1) setting a BCI loop between a virtual environment and an EEG system

2) optimize online detection of specific EEG patterns 

3) participate in the design and elaboration of research protocols.

 

The successful applicant will be affiliated to the Brain and Consciousness
team of Pr Sid Kouider (http://www.lscp.net/persons/sidk/). The Department
of Cognitive Science offers a rich research environment composed of a
multidisciplinary set of research units on philosophy, cognitive psychology,
cognitive neurosciences and computational neurosciences. Our research team,
at the interface of these disciplines, is working on the cognitive and
neural determinants of consciousness, with an emphasis on the distinction
between unconscious perception and perceptual awareness. Our lab is  located
in central Paris, within the historical Quartier Latin.

 

Candidates should have at least a PhD degree in a relevant domain and a
solid training in EEG, Brain-Computer interfaces and machine learning.
Experience with virtual reality is desirable but not a prerequisite.

 

The position will start on September 1st, 2013.

The appointment is for one year initially but can be extended later on.

The net salary will range between 2 100 and 2 500 euros/month depending on
qualifications.

 

Consideration of applicants will commence June 1st, 2013 and will continue
until the position is filled.

 

Knowledge of French is not required as the team is international and verbal
interactions are primarily in English. 

 

Please send a CV along with the names and contact information of two
references to Sid Kouider (sid.kouider at ens dot fr) and Cécile Girard
(cecilegirard20 @ gmail dot com)

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Pr Sid Kouider, CNRS research director

Ecole Normale Supérieure

LSCP, Pavillon Jardin,

29 rue d'Ulm, 75005 Paris, France

www.lscp.net/persons/sidk/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

 

 

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From haiteng.jiang at gmail.com  Fri May 31 12:15:59 2013
From: haiteng.jiang at gmail.com (Haiteng Jiang)
Date: Fri, 31 May 2013 12:15:59 +0200
Subject: [FieldTrip] time-domain granger causality in Fieldtrip?
Message-ID: <CAHSK_TRQUv9aqda123QUWA9jfWpWaJzpBnWxF0QTO08xtM58pA@mail.gmail.com>

Hi all,
   is it possible to run time-domain granger causality in Fieldtrip?
                                                         Best,
                                                          Haiteng






-- 
Haiteng Jiang
PhD candidate
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen

Visiting address
Room 2.32
Donders Centre for Cognitive Neuroimaging
Kapittelweg 29
6525 EN  Nijmegen
the Netherlands

 Tel.: +31 (0)243668291
 Web:  https://sites.google.com/site/haitengjiang/
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From d.lozanosoldevilla at fcdonders.ru.nl  Fri May 31 15:49:03 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Fri, 31 May 2013 15:49:03 +0200 (CEST)
Subject: [FieldTrip] error when using ctf2grad
In-Reply-To: <51A7A9A1.6020401@gmail.com>
Message-ID: <2006439449.1303047.1370008143778.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Ye, Are you using a recent fieldtrip version? The ctf2grad function has recently updated improving its robustness. I don't have any clue why G3AR but it basically means that your CTF system has a specific gradiometer balancing. By the way, which CTF system are you using: CTF64, CTF151, CTF275? In any case, I could have a look if you file a bug and send to me the *.res4 file and we'll figure out what's happening (but please try with a recent Fieldtrip version and tell me) Regarding your gradiometer question, I asked Robert and this is the answer we can provide (please correct me if I'm wrong here), the CTF system sensors consist in first-order axial gradiometer that measure the magnetic field gradient change in the radial direction (orthogonal to the scalp). The following is taken from the CTF documentation "MEG File Formats - release 5.2.1" appendix C. --- Higher-order gradiometer formation is a noise-cancellation technique exclusive to the CTF MEG System. It permits the MEG detectors to be sensitive to the weak signals of the brain, yet impervious to the much stronger sources from the environment. This process, which is carried out in real time, allows the system to be run without the expense of magnetic shielding, or in combination with a standard shielded room for enhanced noise reduction. In order to calculate the forward solution, the same procedure must be performed on any field data calculated from a simulated dipole. The procedure consists of calculating the field at each coil in the sensor as well as each coil in a set of reference channels. The field values at the reference channels are then multiplied by the appropriate weight and subtracted from the MEG sensor channels. --- The data set on disk contains in the header the parameters that are used to convert the data between the original (raw) representation and the higher-order gradiometer representation. This conversion can be done in real-time during acquisition, but can also be done (and undone) afterwards using CTF DataEditor, or using ft_denoise_synthetic.m function. The grad structure included in the FieldTrip representation (i.e. hdr.grad or data.grad) should be consistent with the data, hence it contains grad.balance.current grad.balance.G1BR grad.balance.G2BR grad.balance.G3BR and potentially other "balancing" schemes (your "G3AR " for instance). The grad.balance.current describes which balancing was applied to the data and to the specification of the sensor array (grad.tra) for the forward computation. In order to provide a more intuitive description, I've made a wiki FAQ to explain How does the CTF higher-order gradiometer work: http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work All the best, Diego ----- Original Message -----
> From: "Ye Mei" <frank.ye.mei at gmail.com> > To: fieldtrip at science.ru.nl > Sent: Thursday, 30 May, 2013 9:33:53 PM > Subject: [FieldTrip] error when using ctf2grad > Hi All, > > I have some problem using ctf2grad. > > The program will set grad.balance.current = 'G3AR';, > and then do getfield(grad.balance, grad.balance.current) > but > grad.balance = G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > > and has no G3AR in it. So an error will pop up. > > Can anyone help me with that? > > Also, What do G1BR, G2BR, G3BR, G3AR stand for? > > > thanks, > Ye > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/
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From lkystra at hotmail.it  Fri May 31 17:15:01 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Fri, 31 May 2013 17:15:01 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>, ,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>,
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>,
	<4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
Message-ID: <DUB107-W21B51E9DC3913CBC8A1A05D9920@phx.gbl>

Hi Jan-Mathijs,
the specifies that you asked to me, are: 

fieldtrip version: 20130401
operating system: windows 7
matlab version : I use R2011a (64bits) or R2007b (32bits)

I
 want to read a portion of my EEG signal of 3600 sec * 500 Hz. When I used
 a previous version of fieldtrip (2011-12-14), the lenght of the window wasn't 3600*500 but less. 

" Warning: Integer operands are required for colon operator when used as index 
> In read_edf at 348 "

With fieldtrip 20130401 the length of the window is right, but, when I plot the signal, I can see its distorsion.
Thank you for your attention,
Lucia

From: jan.schoffelen at donders.ru.nl
Date: Thu, 30 May 2013 18:31:22 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

Hi Lucia,
Perhaps you need to be a bit more specific. In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.Otherwise all of us are shooting in the dark.Best wishes,Jan-Mathijs

On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')


2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
Dear all,
I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
  Zriouil Imane



_______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nlTelephone: +31-24-3614793
http://www.hettaligebrein.nl



_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From ebrahimi_nia at yahoo.com  Fri May 31 17:56:55 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Fri, 31 May 2013 08:56:55 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <51A78CC1.6030906@berkeley.edu>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
	<51A78CC1.6030906@berkeley.edu>
Message-ID: <1370015815.5183.YahooMailNeo@web122402.mail.ne1.yahoo.com>

Dear respondent,

Thank you for your advices.
I have used the function that you have updated. It works out. Can you give me information about the output structure (What do the matrixes refer to?) or advise a reference to study about that please? 

Best,
Fatemeh



________________________________
 From: Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu>
To: fieldtrip at science.ru.nl 
Sent: Thursday, May 30, 2013 10:30 AM
Subject: Re: [FieldTrip] loreta2fieldtrip function error
 


Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug,
    see http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export
    the source data as a text file. You can read that text file in with
    loreta2fieldtrip.m. It's a bit of a patch, but it worked for me. 

Hope this helps,
Ingrid


On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:

Hi dear all,
>
>
>I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
>MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.
>
>
>**** Error using fread
>
>Invalid precision.
>Error in loreta2fieldtrip (line 85)
>activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
>
>Can someone give me a help?
>
>
>
>Best regards,
>Fatemeh
>
>
>
>
>_______________________________________________
fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From robince at gmail.com  Fri May 31 18:14:15 2013
From: robince at gmail.com (Robin)
Date: Fri, 31 May 2013 17:14:15 +0100
Subject: [FieldTrip] some of the requested samples occur twice
Message-ID: <CALsWBNOxcuA=LCMONaGWObU4fdZ3+vskGGFcKdTZE4jGRoW47Q@mail.gmail.com>

I have a problem in preprocessing where I am getting this error:

"""
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 262)
      dat{trlop} = ft_fetch_data(data,        'header', hdr, 'begsample',
      trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding,
      'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous,'no
Error in ft_artifact_muscle (line 158)
    [tmpcfg, artifact] = ft_artifact_zvalue(tmpcfg, data);
"""

I think this is because I am manually adding some extra padding to the
trials so that the artifact filtering can use that padding (I am doing
the artifact filtering on data in memory which is output from
ft_denoise_pca). So in this case it is not a problem if consecutive
trials overlap a bit.

I would therefore like to disable this error and wondered what is the
best way to do it. I am a bit confused because ft_artifact_zvalue
calls ft_fetch data with a "checkboundary" option which looks like it
might be what I want (and set correctly), but ft_fetch_data doesn't
seem to use that option. Instead it has an allowoverlap option.

So for now I will manually add the allowoverlap option to the call in
ft_artifact_zvalue, but I wondered what checkboundary doesn't appear
in ft_fetch_data or if this might be a bug.

Cheers

Robin


From eelke.spaak at donders.ru.nl  Wed May  1 09:40:01 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 1 May 2013 09:40:01 +0200
Subject: [FieldTrip] beggining Help
In-Reply-To: <f1d7aa427e33f400.517f0918@upo.es>
References: <f1d7aa427e33f400.517f0918@upo.es>
Message-ID: <CABPNLUosNHWq+LkeH-xUtWp4+t4aXkMyMqr=pO_HoepNpTBigg@mail.gmail.com>

Dear Gabriel,

Since you indicate that you are "completely new to fieldtrip and
almost new to EEG analysis", I would recommend you get started by
going through some of our tutorials:
http://fieldtrip.fcdonders.nl/tutorial These will help get you
acquainted with FieldTrip's work style, as well as teach you some
basics of EEG analysis. Understanding of the basics is vital if you
want to (sensibly) do connectivity analysis later on.

There are also some tutorials on connectivity, which you will find on
the same page.

As for getting your data into FieldTrip, all FT data is encapsulated
in a Matlab structure. Once your data is in Matlab, you can make a FT
structure out of it by creating a structure that resembles the output
of ft_preprocessing. Refer to the documentation for ft_datatype_raw
for details on this
(http://fieldtrip.fcdonders.nl/reference/ft_datatype_raw or "edit
ft_datatype_raw" in matlab).

Best, and good luck,
Eelke

On 29 April 2013 23:58, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear fieldtrip experts,
>
>
> I'm completely new to fieldtrip and almost new to the EEG analysis, I have
> resting-state EEG registers for my subjects in txt format, that I can load
> into matlab into something like: #timeSamples x #sensors. And I know the
> name and order of  all sensors
>
> I want to calculate the imaginary coherence, the PPC, the PLI and WPLI from
> my data, but I couldn't find how to do so in the manual. Can anyone help me
> with the steps to achieve that goal?
> I want to get those indices between all pairs of sensors, and chosen pairs
> (sensors manually selected according to my hypothesis), I hope it be
> posssible.
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jose.herrero66 at gmail.com  Wed May  1 12:08:19 2013
From: jose.herrero66 at gmail.com (Jose Herrero)
Date: Wed, 1 May 2013 06:08:19 -0400
Subject: [FieldTrip] ft_mvaranalysis with unequal length trials
Message-ID: <CA+zL3byUZEhYX3-T-Q5XQRGd1fSHEJCJu6KWT-B8Zz8bHXeNQg@mail.gmail.com>

Hi,

using ft_mvaranalysis with unequal length trials, i encountering the
following error (see below). This error does not occur after commenting out
line 241 where the data gets preprocessed. Is this ok?

mdata       = ft_mvaranalysis(cfg, trials)
the input is raw data with 25 channels and 237 trials
removing 234 trials in which no data was selected
the call to "ft_redefinetrial" took 0 seconds
preprocessing
preprocessing trial 3 from 3

the call to "ft_preprocessing" took 0 seconds
??? Index exceeds matrix dimensions.

Error in ==> ft_mvaranalysis at 293
  maxtim = max(maxtim, data.time{k}(end));


-- 
Jose L Herrero, PhD
Department of Psychiatry
Columbia University College of Physicians and Surgeons
Cognitive Neuroscience and Schizophrenia Program
Nathan S. Kline Institute for Psychiatric Research
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From robince at gmail.com  Wed May  1 18:41:37 2013
From: robince at gmail.com (Robin)
Date: Wed, 1 May 2013 17:41:37 +0100
Subject: [FieldTrip] MNE tutorial
Message-ID: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From joerg.neuberg at tu-ilmenau.de  Wed May  1 20:42:25 2013
From: joerg.neuberg at tu-ilmenau.de (=?utf-8?Q?J=C3=B6rg_Neuberg?=)
Date: Wed, 1 May 2013 20:42:25 +0200
Subject: [FieldTrip] Error: requested samples occur twice in the data
Message-ID: <27F2D05FEDC14EF9839BD48C5B218D24@JoergPC>

Hi FieldTrippers,

we are students using fieldtrip for a project at our university. Now, we have some trouble. We want to search for muscle artifacts and we receive an error message.
We started our signal processing with “ft_definetrial” to define the trials and “ft_preprocessing” to become our data. Then we cut out the stimulus artifact and interpolated the gaps. The data is saved as mat-file.

Now, we are looking for muscle artifacts with the following code:

---------- begin code --------
% channel selection, cutoff and padding
cfg.artfctdef.zvalue.channel = 'MEG*';
cfg.artfctdef.zvalue.cutoff      = 0.5;
cfg.artfctdef.zvalue.trlpadding  = 0;   
cfg.artfctdef.zvalue.fltpadding  = 0;
cfg.artfctdef.zvalue.artpadding  = 0.1;

cfg.artfctdef.muscle.bpfilter    = 'yes';
cfg.artfctdef.muscle.bpfreq      = [110 140];
cfg.artfctdef.muscle.bpfiltord   = 2;
cfg.artfctdef.muscle.bpfilttype  = 'but';
cfg.artfctdef.muscle.hilbert     = 'yes';
cfg.artfctdef.muscle.boxcar      = 0.2;

% make the process interactive
cfg.artfctdef.zvalue.interactive = 'yes';

[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);
---------- end code --------

Unfortunately there is an error and we haven’t an idea where is the problem. Maybe the overlap of the trials is a reason for this. But we can’t change this for our data because we need this trial length. Example: trial 1 from 100 to 120, trial 2 from 115 to 135.

---------- begin error --------
searching for artifacts in 306 channel
searching trials.Error using ft_fetch_data (line 123)
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 260)
      dat{trlop} = ft_fetch_data(data,        'header', hdr,
      'begsample', trl(trlop,1)-fltpadding, 'endsample',
      trl(trlop,2)+fltpadding, 'chanindx', sgnind, 'checkboundary',
      strcmp(cfg.continuous,'no
Error in muscle_artifacts (line 53)
[cfg, artifact_muscle] = ft_artifact_zvalue(cfg, data);”
---------- end error --------

Do you have any idea to help us? We would be grateful for any help.

Greetings,
Joerg
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From robince at gmail.com  Thu May  2 14:04:03 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 13:04:03 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
Message-ID: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>

Running the full Freesurfer reconstruction pipeline (without the hybrid
skull stripping and Talaraich alignment on the fieldtrip side) appears to
have been successful.

However, when I try to continue with the tutorial I find that my volume and
source grid don't line up (even before any issues converting to sensor
space):

Figure: http://imgur.com/uo9uPUc (code below)

Does anyone have any idea what could be wrong?

What coordinate system is the sub-oct-6-src.fif file in (created by MNE
suite)?
If it is in talairach coordinates, how do I load the Talairach aligned
image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)

Do I need to manually include the transform from transform/talairach.xfm?
To include that can I use it directly as mri.transform in fieldtrip or do I
need to multiply it by the existing mri.transform which is there when
loading the raw anatomy scan (.img)? Come to think of it what does that
transform represent?

Sorry if these are not fieldtrip questions but I am trying to follow the
fieldtrip MNE tutorial so I was hoping someone might know.

Thanks

Robin

% load freesurfer image
mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
% load MNE grid% computed with mne_setup_source_space --ico -6
bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code
'-oct-6-src.fif']), 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
% Volume conduction model
cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
seg = ft_volumesegment(cfg, mri_fs_tal);
cfg = [];cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
% Check volume conduction
figure; hold on
ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight

On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:

I am trying to run through the MNE tutorial here:

http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate

Unfortunately after the volumetric processing in freesurfer my
intermediate result looks wrong.

I have followed the steps (including interactive alignment to
Talairach) according to the tutorial. I wondered if anyone has any
idea what could be wrong, or could point to some more possible
diagnostic commands to run?

The original Subject01.mgz file seems to have been saved correctly.
But if I load the orig.mgz created with:
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
and plot it with ft_sourceplot it has the same offset and upside down
position as the final incorrectly segments freesurfer image. Could
this indicate a problem?

Thanks for any help,

Cheers

Robin
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From brungio at gmail.com  Thu May  2 14:26:10 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:26:10 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEs8D9eEdweRBGDhjGtXK_299sguhE9nqYYXG5ftRZi1pA@mail.gmail.com>

Hi Robin,

I had a similar problem during the field trip course. In my case I found
out that one set of coordinates was in mm and then other in m, so I just
had to multiply one set of coordinates.

Another thing you should be aware of is that you can segment your
anatomical using procedures other than the default ones. For example, Spm12
has new, better procedures. Importing an already prepared segmentation in
ft requires some hacking, but if you are interested I can tell you how as
soon as I get a decent internet connection.

Finally, remember that the single shell model is not that great. You should
prepare a better volume conduction model.

    Bruno
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:28:16 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:28:16 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>

Ah, I just saw that your problem might be with the origin of the anatomical
space. Have you tried to see what happens if you set its origin to the
anterior commissure before giving it in input to field trip?
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From brungio at gmail.com  Thu May  2 14:42:08 2013
From: brungio at gmail.com (Bruno L. Giordano)
Date: Thu, 2 May 2013 08:42:08 -0400
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
	<CAGgLGEse+krfhAv+DyOGgs=XexG1Mg0hDe9aYM0dsXuvZ+mZ5g@mail.gmail.com>
Message-ID: <CAGgLGEs+cJ_8Bxi=gEt=QhFv31oaRD2DfxHoosadVsiP8vU86Q@mail.gmail.com>

Sorry, my replies were not meant for the list.
On May 2, 2013 8:28 AM, "Bruno L. Giordano" <brungio at gmail.com> wrote:

> Ah, I just saw that your problem might be with the origin of the
> anatomical space. Have you tried to see what happens if you set its origin
> to the anterior commissure before giving it in input to field trip?
> On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:
>
>>  Running the full Freesurfer reconstruction pipeline (without the hybrid
>> skull stripping and Talaraich alignment on the fieldtrip side) appears to
>> have been successful.
>>
>> However, when I try to continue with the tutorial I find that my volume
>> and source grid don't line up (even before any issues converting to sensor
>> space):
>>
>> Figure: http://imgur.com/uo9uPUc (code below)
>>
>> Does anyone have any idea what could be wrong?
>>
>> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
>> suite)?
>> If it is in talairach coordinates, how do I load the Talairach aligned
>> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>>
>> Do I need to manually include the transform from transform/talairach.xfm?
>> To include that can I use it directly as mri.transform in fieldtrip or do I
>> need to multiply it by the existing mri.transform which is there when
>> loading the raw anatomy scan (.img)? Come to think of it what does that
>> transform represent?
>>
>> Sorry if these are not fieldtrip questions but I am trying to follow the
>> fieldtrip MNE tutorial so I was hoping someone might know.
>>
>> Thanks
>>
>> Robin
>>
>> % load freesurfer image
>> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
>> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
>> % load MNE grid% computed with mne_setup_source_space --ico -6
>> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
>> sourcespace = ft_convert_units(bnd, 'cm');
>> % Volume conduction model
>> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
>> seg = ft_volumesegment(cfg, mri_fs_tal);
>> cfg = [];cfg.method = 'singleshell';
>> vol = ft_prepare_headmodel(cfg, seg);
>> % Check volume conduction
>> figure; hold on
>> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
>> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>>
>> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>>
>> I am trying to run through the MNE tutorial here:
>>
>> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>>
>> Unfortunately after the volumetric processing in freesurfer my
>> intermediate result looks wrong.
>>
>> I have followed the steps (including interactive alignment to
>> Talairach) according to the tutorial. I wondered if anyone has any
>> idea what could be wrong, or could point to some more possible
>> diagnostic commands to run?
>>
>> The original Subject01.mgz file seems to have been saved correctly.
>> But if I load the orig.mgz created with:
>> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
>> and plot it with ft_sourceplot it has the same offset and upside down
>> position as the final incorrectly segments freesurfer image. Could
>> this indicate a problem?
>>
>> Thanks for any help,
>>
>> Cheers
>>
>> Robin
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
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From robince at gmail.com  Thu May  2 15:46:22 2013
From: robince at gmail.com (Robin)
Date: Thu, 2 May 2013 14:46:22 +0100
Subject: [FieldTrip] MNE tutorial
In-Reply-To: <CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
References: <CALsWBNPPzu=B27R68PZr0SKRod=gGD0Y8ntpZ+Z=CP2N161vhA@mail.gmail.com>
	<CALsWBNM94Lb1NNQ7rXCK5rMKx2_UADcCZqLRT5VCdqaFFqZ+yw@mail.gmail.com>
Message-ID: <CALsWBNOLx+KZ93GFdEi+wtdXujYwth1GniK8o3H-cJvd2KGsTA@mail.gmail.com>

By running from MNE suite:
mne_setup_mri --subject BON02 --mri T1

to create a COR.fif image from the Freesurfer output (including Talaraich
transformation) at least that COR.fir and the oct-6-src.fif mesh seem to
line up.

But now I am not sure which coordinate system they are in? (cordsys is
'neuromag' in fieldtrip) nor how to obtain the necessary inverse transform
from this space to the raw anatomy voxel space (so I can build the
transform from oct-6-src mesh to sensor space; I already have the transform
to take the original raw anatomy .img to the sensor coordinate system).

Thanks,

Robin

On Thu, May 2, 2013 at 1:04 PM, Robin <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
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From jan.schoffelen at donders.ru.nl  Thu May  2 15:57:00 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 15:57:00 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
Message-ID: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
> 
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
> 
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
> 
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
> 
> The cohspctrm looks like this:
> val(:,:,1,1) =
> 
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
> 
> I get the following warning during ft_connectivityanalysis
> 
> Warning: Divide by zero.
>> In ft_connectivity_corr at 103
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>> In ft_connectivity_corr at 104
>  In ft_connectivityanalysis at 524
> 
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
> 
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From lmelloni at gmail.com  Thu May  2 18:56:19 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 12:56:19 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
Message-ID: <-7204743264059944684@unknownmsgid>

Hi jan-mathijs

Unfortunately I get the same result whether or not I remove the mean.
Best,
-- Lucía

On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

Hi Lucia,

Could you remove cfg.removemean = 'yes' and try again?

Best,

Jan-Mathijs

On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:

Hi!
I am trying to calculate coherence using ft_connectivityanalysis, but
I am getting only ones and infinity as output in cohspctrm with all of
my data sets.

I first run ft_freqanalysis with
cfg.method = 'mtmfft';
cfg.taper = 'dpss';
cfg.output = 'fourier';
cfg.foilim = [1 45];
cfg.tapsmofrq = 1;
cfg.keeptrials = 'yes';
cfg.keeptapers = 'yes';
freq = ft_freqanalysis(cfg, data);

Whether I do or I do not specify cfg.channel and cfg.channelcmb here
does not seem to make a difference for my problem later on. The
spectra look absolutely fine.

I then run ft_connectivityanalysis with
cfg.method    = 'coh';
cfg.removemean= 'yes';
cfg.trials    = 'all';
cfg.feedback  = 'yes';
cfg.complex   = 'abs';
coh           = ft_connectivityanalysis(cfg, freq);

The cohspctrm looks like this:
val(:,:,1,1) =

    1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
Inf   Inf   Inf (etc.)

I get the following warning during ft_connectivityanalysis

Warning: Divide by zero.

In ft_connectivity_corr at 103

 In ft_connectivityanalysis at 524
Warning: Divide by zero.

In ft_connectivity_corr at 104

 In ft_connectivityanalysis at 524

The same happens if I try to calculate PLV through ft_connectivityanalysis.
This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
Windows 7 (64bit).

Any advice?
Thanks!
Lucia
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


Jan-Mathijs Schoffelen, MD PhD

Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From jan.schoffelen at donders.ru.nl  Thu May  2 21:12:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 2 May 2013 21:12:22 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <-7204743264059944684@unknownmsgid>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
Message-ID: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>

Hi Lucia,

The warnings indicate that you are dividing by zero. Are you sure that your cfg is correct?

Please try

cfg = [];
cfg.method = 'coh';
coh = ft_connectivityanalysis(cfg, freq);

This should work.

Best,
Jan-Mathijs

On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:

> Hi jan-mathijs
> 
> Unfortunately I get the same result whether or not I remove the mean. 
> Best,
> -- Lucía
> 
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> wrote:
> 
>> Hi Lucia,
>> 
>> Could you remove cfg.removemean = 'yes' and try again?
>> 
>> Best,
>> 
>> Jan-Mathijs
>> 
>> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>> 
>>> Hi!
>>> I am trying to calculate coherence using ft_connectivityanalysis, but
>>> I am getting only ones and infinity as output in cohspctrm with all of
>>> my data sets.
>>> 
>>> I first run ft_freqanalysis with
>>> cfg.method = 'mtmfft';
>>> cfg.taper = 'dpss';
>>> cfg.output = 'fourier';
>>> cfg.foilim = [1 45];
>>> cfg.tapsmofrq = 1;
>>> cfg.keeptrials = 'yes';
>>> cfg.keeptapers = 'yes';
>>> freq = ft_freqanalysis(cfg, data);
>>> 
>>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>>> does not seem to make a difference for my problem later on. The
>>> spectra look absolutely fine.
>>> 
>>> I then run ft_connectivityanalysis with
>>> cfg.method    = 'coh';
>>> cfg.removemean= 'yes';
>>> cfg.trials    = 'all';
>>> cfg.feedback  = 'yes';
>>> cfg.complex   = 'abs';
>>> coh           = ft_connectivityanalysis(cfg, freq);
>>> 
>>> The cohspctrm looks like this:
>>> val(:,:,1,1) =
>>> 
>>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>> Inf   Inf   Inf (etc.)
>>> 
>>> I get the following warning during ft_connectivityanalysis
>>> 
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 103
>>>  In ft_connectivityanalysis at 524
>>> Warning: Divide by zero.
>>>> In ft_connectivity_corr at 104
>>>  In ft_connectivityanalysis at 524
>>> 
>>> The same happens if I try to calculate PLV through ft_connectivityanalysis.
>>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>>> Windows 7 (64bit).
>>> 
>>> Any advice?
>>> Thanks!
>>> Lucia
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> Jan-Mathijs Schoffelen, MD PhD 
>> 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> 
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>> 
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>> 
>> http://www.hettaligebrein.nl
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From evaladez at psych.udel.edu  Thu May  2 23:07:51 2013
From: evaladez at psych.udel.edu (Emilio Valadez)
Date: Thu, 2 May 2013 17:07:51 -0400
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
Message-ID: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>

Dear FieldTrippers,

I am trying to compute phase-amplitude coupling (PAC) between the phase of theta activity at one channel and the amplitude of gamma activity at another channel over a specific time window within trials. I have read that PAC is captured with a phase-locking value (PLV), which leads me to think that this might be computed with ft_connectivityanalysis. If this is true, what would the configuration structure and input data need to look like? Or, is there an alternative way to compute PAC using FieldTrip? Thank you in advance!

All the best,
Emilio
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From lmelloni at gmail.com  Fri May  3 00:56:30 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Thu, 2 May 2013 18:56:30 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
Message-ID: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>

Hi Jan-Mathijs,
still the same result with the code that you suggested.

selection fourierspctrm along dimension 2
averaging crsspctrm over rpt
removing dimension rpt from crsspctrm
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 87
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 89
  In ft_connectivityanalysis at 524
Warning: PROGRESS is only a compatibility wrapper, which will soon be
removed. Please instead call FT_PROGRESS.
> In progress at 16
  In ft_connectivity_corr at 106
  In ft_connectivityanalysis at 524
the call to "ft_connectivityanalysis" took 0 seconds


Lucia

-- 
Lucia.


On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Lucia,
>
> The warnings indicate that you are dividing by zero. Are you sure that
> your cfg is correct?
>
> Please try
>
> cfg = [];
> cfg.method = 'coh';
> coh = ft_connectivityanalysis(cfg, freq);
>
> This should work.
>
> Best,
> Jan-Mathijs
>
> On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
> Hi jan-mathijs
>
> Unfortunately I get the same result whether or not I remove the mean.
> Best,
> -- Lucía
>
> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
> Hi Lucia,
>
> Could you remove cfg.removemean = 'yes' and try again?
>
> Best,
>
> Jan-Mathijs
>
> On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>
> Hi!
> I am trying to calculate coherence using ft_connectivityanalysis, but
> I am getting only ones and infinity as output in cohspctrm with all of
> my data sets.
>
> I first run ft_freqanalysis with
> cfg.method = 'mtmfft';
> cfg.taper = 'dpss';
> cfg.output = 'fourier';
> cfg.foilim = [1 45];
> cfg.tapsmofrq = 1;
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'yes';
> freq = ft_freqanalysis(cfg, data);
>
> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
> does not seem to make a difference for my problem later on. The
> spectra look absolutely fine.
>
> I then run ft_connectivityanalysis with
> cfg.method    = 'coh';
> cfg.removemean= 'yes';
> cfg.trials    = 'all';
> cfg.feedback  = 'yes';
> cfg.complex   = 'abs';
> coh           = ft_connectivityanalysis(cfg, freq);
>
> The cohspctrm looks like this:
> val(:,:,1,1) =
>
>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
> Inf   Inf   Inf (etc.)
>
> I get the following warning during ft_connectivityanalysis
>
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 103
>
>  In ft_connectivityanalysis at 524
> Warning: Divide by zero.
>
> In ft_connectivity_corr at 104
>
>  In ft_connectivityanalysis at 524
>
> The same happens if I try to calculate PLV through ft_connectivityanalysis.
> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
> Windows 7 (64bit).
>
> Any advice?
> Thanks!
> Lucia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jm.horschig at donders.ru.nl  Fri May  3 08:32:30 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 03 May 2013 08:32:30 +0200
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
Message-ID: <518359FE.4070207@donders.ru.nl>

Dear Lucia,

could you try whether the error persists with a recent version? If it 
does, could you go test whether this code gives the same error:

/
% ************* code starts here /
/%dummy data
cfg             = [];
cfg.ntrials     = 500;
cfg.triallength = 1;
cfg.fsample     = 200;
cfg.nsignal     = 3;
cfg.method      = 'ar';
cfg.params(:,:,1) = [ 0.8 0   0;
                       0   0.9 0.5;
                       0.4 0   0.5];
cfg.params(:,:,2) = [-0.5    0  0;
                         0 -0.8  0;
                         0    0 -0.2];
cfg.noisecov      = [0.3 0 0;
                        0 1 0;
                        0 0 0.2];

data            = ft_connectivitysimulation(cfg);


% freqanalysis
cfgf           = [];
cfgf.method    = 'mtmfft';
cfgf.output    = 'fourier';
cfgf.tapsmofrq = 2;
freq           = ft_freqanalysis(cfgf, data);

% connectivityanalysis
cfgc           = [];
cfgc.method    = 'coh';
c1             = ft_connectivityanalysis(cfgc, freq);

c1.cohspctrm//
% ************* code ends here
/
The code snippet above is part of our test suite for making sure that 
everything works fine. If it does work for you, but does not with your 
own data instead of simulated data, the error must be somewhere in your 
data, e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that 
it will all work fine if you use an updated version of FieldTrip.

Best,
Jörn


On 5/3/2013 12:56 AM, Lucia Melloni wrote:
> Hi Jan-Mathijs,
> still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be 
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
> Lucia
>
> -- 
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen 
> <jan.schoffelen at donders.ru.nl <mailto:jan.schoffelen at donders.ru.nl>> 
> wrote:
>
>     Hi Lucia,
>
>     The warnings indicate that you are dividing by zero. Are you sure
>     that your cfg is correct?
>
>     Please try
>
>     cfg = [];
>     cfg.method = 'coh';
>     coh = ft_connectivityanalysis(cfg, freq);
>
>     This should work.
>
>     Best,
>     Jan-Mathijs
>
>     On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>
>>     Hi jan-mathijs
>>
>>     Unfortunately I get the same result whether or not I remove the
>>     mean.
>>     Best,
>>     -- Lucía
>>
>>     On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen
>>     <jan.schoffelen at donders.ru.nl
>>     <mailto:jan.schoffelen at donders.ru.nl>> wrote:
>>
>>>     Hi Lucia,
>>>
>>>     Could you remove cfg.removemean = 'yes' and try again?
>>>
>>>     Best,
>>>
>>>     Jan-Mathijs
>>>
>>>     On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>>
>>>>     Hi!
>>>>     I am trying to calculate coherence using
>>>>     ft_connectivityanalysis, but
>>>>     I am getting only ones and infinity as output in cohspctrm with
>>>>     all of
>>>>     my data sets.
>>>>
>>>>     I first run ft_freqanalysis with
>>>>     cfg.method = 'mtmfft';
>>>>     cfg.taper = 'dpss';
>>>>     cfg.output = 'fourier';
>>>>     cfg.foilim = [1 45];
>>>>     cfg.tapsmofrq = 1;
>>>>     cfg.keeptrials = 'yes';
>>>>     cfg.keeptapers = 'yes';
>>>>     freq = ft_freqanalysis(cfg, data);
>>>>
>>>>     Whether I do or I do not specify cfg.channel and cfg.channelcmb
>>>>     here
>>>>     does not seem to make a difference for my problem later on. The
>>>>     spectra look absolutely fine.
>>>>
>>>>     I then run ft_connectivityanalysis with
>>>>     cfg.method    = 'coh';
>>>>     cfg.removemean= 'yes';
>>>>     cfg.trials    = 'all';
>>>>     cfg.feedback  = 'yes';
>>>>     cfg.complex   = 'abs';
>>>>     coh           = ft_connectivityanalysis(cfg, freq);
>>>>
>>>>     The cohspctrm looks like this:
>>>>     val(:,:,1,1) =
>>>>
>>>>         1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>>>>     Inf   Inf   Inf (etc.)
>>>>
>>>>     I get the following warning during ft_connectivityanalysis
>>>>
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 103
>>>>      In ft_connectivityanalysis at 524
>>>>     Warning: Divide by zero.
>>>>>     In ft_connectivity_corr at 104
>>>>      In ft_connectivityanalysis at 524
>>>>
>>>>     The same happens if I try to calculate PLV through
>>>>     ft_connectivityanalysis.
>>>>     This is with Fieldtrip version 20130422 and 20130427, Matlab
>>>>     R2009a,
>>>>     Windows 7 (64bit).
>>>>
>>>>     Any advice?
>>>>     Thanks!
>>>>     Lucia
>>>>     _______________________________________________
>>>>     fieldtrip mailing list
>>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>     Jan-Mathijs Schoffelen, MD PhD
>>>
>>>     Donders Institute for Brain, Cognition and Behaviour,
>>>     Centre for Cognitive Neuroimaging,
>>>     Radboud University Nijmegen, The Netherlands
>>>
>>>     Max Planck Institute for Psycholinguistics,
>>>     Nijmegen, The Netherlands
>>>
>>>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>>>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>>>
>>>     http://www.hettaligebrein.nl <http://www.hettaligebrein.nl/>
>>>
>>>     _______________________________________________
>>>     fieldtrip mailing list
>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>     Jan-Mathijs Schoffelen, MD PhD
>
>     Donders Institute for Brain, Cognition and Behaviour,
>     Centre for Cognitive Neuroimaging,
>     Radboud University Nijmegen, The Netherlands
>
>     Max Planck Institute for Psycholinguistics,
>     Nijmegen, The Netherlands
>
>     J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>     Telephone: +31-24-3614793 <tel:%2B31-24-3614793>
>
>     http://www.hettaligebrein.nl
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From gregor.volberg at psychologie.uni-regensburg.de  Fri May  3 09:35:40 2013
From: gregor.volberg at psychologie.uni-regensburg.de (Gregor Volberg)
Date: Fri, 03 May 2013 09:35:40 +0200
Subject: [FieldTrip] Phase-amplitude coupling (PAC)
In-Reply-To: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
References: <10DBEA48DAE8BB4F8F588B1254C0D92E01B8763E014C@razor.psych.udel.edu>
Message-ID: <518368CC.9030102@psychologie.uni-regensburg.de>

Dear Emilio,

I might not be fully up to date with the functionality of 
ft_connectivityanalysis, but as much as I know there is some 
preprocessing necessary to get a phase-to-amplitude coupling. A common 
strategy is to compute a Hilbert transform on the upper frequency band. 
This can be used to get the 'analytic amplitude', which is essentially a 
waveform that connects the amplitude peaks of the higher frequency. If 
the gamma amplitude is driven by the theta phase, then the analytic 
waveform  should be phase-locked with the theta cycle. The latter part 
of the analysis could be performed with the option 'plv' in 
ft_connectivityanalysis.
For the processing steps you might want to have a look at an example 
script  at http://fieldtrip.fcdonders.nl/example/crossfreq/phalow_amphigh.

Best regards,
Gregor



Am 02.05.2013 23:07, schrieb Emilio Valadez:
> Dear FieldTrippers,
>
> I am trying to compute phase-amplitude coupling (PAC) between the phase
> of theta activity at one channel and the amplitude of gamma activity at
> another channel over a specific time window within trials. I have read
> that PAC is captured with a phase-locking value (PLV), which leads me to
> think that this might be computed with ft_connectivityanalysis. If this
> is true, what would the configuration structure and input data need to
> look like? Or, is there an alternative way to compute PAC using
> FieldTrip? Thank you in advance!
>
> All the best,
>
> Emilio
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>

-- 
Dr. rer. nat. Gregor Volberg
Institut für Psychologie
Universität Regensburg
Universitätsstraße 31
D-93053 Regensburg, Germany
Tel: +49 941 943 3862
Fax: +49 941 943 3233


From lmelloni at gmail.com  Fri May  3 14:48:01 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Fri, 3 May 2013 08:48:01 -0400
Subject: [FieldTrip] Only 1 and Inf as output of ft_connectivityanalysis
In-Reply-To: <518359FE.4070207@donders.ru.nl>
References: <CA+_59hcb0B691e6wh4TZWGFApkth2WRTVQhAfkE6-sMZTwNLFA@mail.gmail.com>
	<9A3D199E-0816-4CBC-AE43-65F768C84EA6@donders.ru.nl>
	<-7204743264059944684@unknownmsgid>
	<4B415E50-71DE-42C8-893D-54F991DC616A@donders.ru.nl>
	<CA+_59hf1=MVDvYkiFCqqZR=HC-nDv0_J7vNJ5z5a0wCQHv_STw@mail.gmail.com>
	<518359FE.4070207@donders.ru.nl>
Message-ID: <CA+_59hd_kx38K4817yAKBnQdd6wSQsb6yTyb-0wQgU_v-8VdPw@mail.gmail.com>

Hi Jörn,
I downloaded version 20130502 and ran both my code and the test code that
you had emailed. I get 1 and inf with both.
The freq input seems to be ok, so ist must be an issue with
ft_connectivityanalysis.
Lucia

-- 
Lucia.


On Fri, May 3, 2013 at 2:32 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Lucia,
>
> could you try whether the error persists with a recent version? If it
> does, could you go test whether this code gives the same error:
>
> *
> % ************* code starts here *
> *%dummy data
> cfg             = [];
> cfg.ntrials     = 500;
> cfg.triallength = 1;
> cfg.fsample     = 200;
> cfg.nsignal     = 3;
> cfg.method      = 'ar';
> cfg.params(:,:,1) = [ 0.8 0   0;
>                       0   0.9 0.5;
>                       0.4 0   0.5];
> cfg.params(:,:,2) = [-0.5    0  0;
>                         0 -0.8  0;
>                         0    0 -0.2];
> cfg.noisecov      = [0.3 0 0;
>                        0 1 0;
>                        0 0 0.2];
>
> data            = ft_connectivitysimulation(cfg);
>
>
> % freqanalysis
> cfgf           = [];
> cfgf.method    = 'mtmfft';
> cfgf.output    = 'fourier';
> cfgf.tapsmofrq = 2;
> freq           = ft_freqanalysis(cfgf, data);
>
> % connectivityanalysis
> cfgc           = [];
> cfgc.method    = 'coh';
> c1             = ft_connectivityanalysis(cfgc, freq);
>
> c1.cohspctrm**
> % ************* code ends here
> *
> The code snippet above is part of our test suite for making sure that
> everything works fine. If it does work for you, but does not with your own
> data instead of simulated data, the error must be somewhere in your data,
> e.g. powspctrm consists of nans or 0s etc. Anyway, I assume that it will
> all work fine if you use an updated version of FieldTrip.
>
> Best,
> Jörn
>
>
>
> On 5/3/2013 12:56 AM, Lucia Melloni wrote:
>
>  Hi Jan-Mathijs,
>  still the same result with the code that you suggested.
>
> selection fourierspctrm along dimension 2
> averaging crsspctrm over rpt
> removing dimension rpt from crsspctrm
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 87
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 89
>   In ft_connectivityanalysis at 524
> Warning: PROGRESS is only a compatibility wrapper, which will soon be
> removed. Please instead call FT_PROGRESS.
> > In progress at 16
>   In ft_connectivity_corr at 106
>   In ft_connectivityanalysis at 524
> the call to "ft_connectivityanalysis" took 0 seconds
>
>
>  Lucia
>
> --
> Lucia.
>
>
> On Thu, May 2, 2013 at 3:12 PM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Lucia,
>>
>>  The warnings indicate that you are dividing by zero. Are you sure that
>> your cfg is correct?
>>
>>  Please try
>>
>>  cfg = [];
>> cfg.method = 'coh';
>> coh = ft_connectivityanalysis(cfg, freq);
>>
>>  This should work.
>>
>>  Best,
>> Jan-Mathijs
>>
>>  On May 2, 2013, at 6:56 PM, Lucia Melloni wrote:
>>
>>  Hi jan-mathijs
>>
>>  Unfortunately I get the same result whether or not I remove the mean.
>> Best,
>> -- Lucía
>>
>> On May 2, 2013, at 9:57 AM, jan-mathijs schoffelen <
>> jan.schoffelen at donders.ru.nl> wrote:
>>
>>  Hi Lucia,
>>
>>  Could you remove cfg.removemean = 'yes' and try again?
>>
>>  Best,
>>
>>  Jan-Mathijs
>>
>>  On Apr 29, 2013, at 2:38 AM, Lucia Melloni wrote:
>>
>>  Hi!
>> I am trying to calculate coherence using ft_connectivityanalysis, but
>> I am getting only ones and infinity as output in cohspctrm with all of
>> my data sets.
>>
>> I first run ft_freqanalysis with
>> cfg.method = 'mtmfft';
>> cfg.taper = 'dpss';
>> cfg.output = 'fourier';
>> cfg.foilim = [1 45];
>> cfg.tapsmofrq = 1;
>> cfg.keeptrials = 'yes';
>> cfg.keeptapers = 'yes';
>> freq = ft_freqanalysis(cfg, data);
>>
>> Whether I do or I do not specify cfg.channel and cfg.channelcmb here
>> does not seem to make a difference for my problem later on. The
>> spectra look absolutely fine.
>>
>> I then run ft_connectivityanalysis with
>> cfg.method    = 'coh';
>> cfg.removemean= 'yes';
>> cfg.trials    = 'all';
>> cfg.feedback  = 'yes';
>> cfg.complex   = 'abs';
>> coh           = ft_connectivityanalysis(cfg, freq);
>>
>> The cohspctrm looks like this:
>> val(:,:,1,1) =
>>
>>     1   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf   Inf
>> Inf   Inf   Inf (etc.)
>>
>> I get the following warning during ft_connectivityanalysis
>>
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 103
>>
>>  In ft_connectivityanalysis at 524
>> Warning: Divide by zero.
>>
>> In ft_connectivity_corr at 104
>>
>>  In ft_connectivityanalysis at 524
>>
>> The same happens if I try to calculate PLV through
>> ft_connectivityanalysis.
>> This is with Fieldtrip version 20130422 and 20130427, Matlab R2009a,
>> Windows 7 (64bit).
>>
>> Any advice?
>> Thanks!
>> Lucia
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>   _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>          Jan-Mathijs Schoffelen, MD PhD
>>
>>  Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>>  Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>>  J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>>  http://www.hettaligebrein.nl
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From vale.niccolai at gmail.com  Fri May  3 15:09:58 2013
From: vale.niccolai at gmail.com (Valentina Niccolai)
Date: Fri, 3 May 2013 15:09:58 +0200
Subject: [FieldTrip] neuromag122_neighb
Message-ID: <CAF0jnAnVQrzd+jJPEwGO6FKKADNhdGinsQAAzfc0mrPcp0+LkQ@mail.gmail.com>

Hallo!

I would like to use the template neuromag122_neighb.mat to repair channels,
but it seems to me that this template contains labels form the neuromag306
system.  Is it right? And can I find the template somewhere?


Best,

Valentina
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From Markus.Butz at uni-duesseldorf.de  Fri May  3 16:06:24 2013
From: Markus.Butz at uni-duesseldorf.de (Markus Butz)
Date: Fri, 03 May 2013 15:06:24 +0100
Subject: [FieldTrip] Problems reading in DICOM
Message-ID: <75e09cb13160d.5183d270@uni-duesseldorf.de>




Thanks for your replies and help Robert, Jörn, and Eelke!
Finally it worked out, but the problem was rather on my side, as there where several series of different MRTs scans in one folder of which some did not work, some worked out strange as they had just some files (16-26), and some worked fine. Unfortunately I tried most intensively on the subject who came with no correct series at all. :-(  
To be fair, all the files appeared exactlty the same, but ft_read_mri is luckily mentioning which series it works on and how many files it include, which finally made me wonder. ;-) 
 
Thanks again and have a good weekend 
Markus 
  
ps: Sorry for the belated thanks! 
 
 

 
Am 13.03.13, schrieb Robert Oostenveld <r.oostenveld at donders.ru.nl>: 


> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Hi  
> 
> 
> DICOM files come with different extensions. I guess it depends on the scanner (Siemens/Philips/...). But the file format should be the same as it is a standard format, so the extension should not matter. The fileio/ft_filetype.m function detects both dcm and ima files as dicom.
> 
> 
> 
> if the files have no extension, the autodetection fails and you should explicitly specify the format as
>    mri = ft_read_mri('single_file_of_DICOM_series', 'format', 'dicom');
> I now realize that to be a hidden option. I'll get that fixed in the function documentation.
> 
> 
> 
> 
> 
> 
> I recommend that you specify a filename from somewhere in the middle of the stack of files. There are often a few localizer scans in the same directory, and these (due to the sorting of the file names) tend to end up at the beginning or end of the (alphabetical) directory listing. 
> 
> 
> cheers
> Robert
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 13 Mar 2013, at 14:22, Jörn M. Horschig wrote:
> 
> 
> 
> > 
> > 
> > Hi Markus,
> > 
> > I kept on avoiding these errors by using MRIcron's dcm2nii functionality: http://www.mccauslandcenter.sc.edu/mricro/mricron/index.html
> > But pay attention to the coordinate system when importing it into FieldTrip afterwards, it can be quite a hassle...
> > 
> > Maybe Robert or JM know whether reading in .dcm files is possible, but I have to admit that I never tried ;) 
> > 
> > Best,
> > Jörn
> > 
> > On 3/13/2013 12:11 PM, Markus Butz wrote:
> > 
> > 
> > > 
> > > 
> > > 
> > > Dear list, 
> > > 
> > > 
> > > I am experiencing problems reading in external MRI in DICOM format from a CD (doing it the first time though). 
> > > I wanted to do it the new and easy way as described here:
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format?s[]=dicom
> > > 
> > > 
> > > % read the DICOM files 
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > 
> > > 
> > > However, I have no single slices with extension *.ima but one dataset with the extension *.dcm and the other dataset with no extension for the single slice files. I am also not sure where to copy the DICOMDIR file.
> > > 
> > > 
> > > When I try to open a single file of the *.dcm series I get:
> > > 
> > > 
> > > mri = ft_read_mri('508652C3.dcm');
> > > 
> > > 
> > > ??? Undefined function or variable "hdr".
> > > 
> > > 
> > > Error in ==> ft_read_mri at 216
> > >   hdr     = hdr(keep); 
> > > 
> > > 
> > > Trying to read in a single file of the no extension series I get:
> > > 
> > > 
> > > mri = ft_read_mri('73850486');
> > > 
> > > 
> > > ??? Error using ==> dicominfo at 41
> > > The specified file is not in DICOM format
> > > 
> > > 
> > > The Image Processing toolbox V 7.2 is installed and this is fieldtrip-20111101.
> > > 
> > > 
> > > Any help appreciated!
> > > 
> > > 
> > > Markus
> > > 
> > > 
> > > 
> > > 
> > >  
> > > 
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > 
> > 
> > 
> > 
> > -- 
> > Jörn M. Horschig
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour 
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen 
> > Neuronal Oscillations Group
> > FieldTrip Development Team
> > 
> > P.O. Box 9101
> > NL-6500 HB Nijmegen
> > The Netherlands
> > 
> > Contact:
> > E-Mail: jm.horschig at donders.ru.nl
> > Tel:    +31-(0)24-36-68493
> > Web: http://www.ru.nl/donders
> > 
> > Visiting address:
> > Trigon, room 2.30
> > Kapittelweg 29
> > NL-6525 EN Nijmegen
> > The Netherlands
> > 
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 

 
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From jimparkinson at me.com  Fri May  3 22:57:26 2013
From: jimparkinson at me.com (Jim Parkinson)
Date: Fri, 03 May 2013 21:57:26 +0100
Subject: [FieldTrip] 2x2x3 Repeated Measures ANOVA in FT
Message-ID: <CACd4eMnmVjveKaT2xUf-H--Ld7PBNnkZhBQRN1JeaZ5OznppiQ@mail.gmail.com>

Hi All

Sorry for the very simplistic question here but I am finding it difficult
to construct an answer - if indeed there is one - from previous posts.

I have a study which is a 2x2x3 repeated measures design, event-related
using 64 channel EEG.  The design is  a culmination of a number of previous
studies, so in that sense is justified, and eyeballing the
data suggests that the effects are pulling in the directions we have
hypothesised.  I would really like to attempt to pull interaction effects,
main effects and then specified (a priori and justified)  contrasts from my
EEG data.  So, is it even possible using cluster permutation methods to
report 3-way, 2-way and main effect stats from such a design, and if so,
what is the best/most justifiable method? Secondly, considering the amount
of *possible*n simple contrasts available in a 2x2x3 design - even if I
don;t run them all because it is not meaningful to do so - what is the best
method to correct for multiple comparisons in the simpel contrasts I do end
up running?

Thans for any help in this confusing matter!

best,
 Jim
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From chadwick.boulay at gmail.com  Mon May  6 07:36:18 2013
From: chadwick.boulay at gmail.com (Chadwick Boulay)
Date: Mon, 06 May 2013 14:36:18 +0900
Subject: [FieldTrip] Please help me get component dipole fitting results
 using custom anatomy into normalized template for EEGLAB clustering.
Message-ID: <51874152.9090903@gmail.com>

Dear Fieldtrip users,

Using the subject's MRI and recorded EEG electrode locations, I've 
managed to segment the MRI, create the volume conduction model, align 
the electrodes, create a sourcemodel using a grid warped from the MNI 
template, create the leadfield, and perform ft_dipolefitting on IC 
weights (imported from EEGLAB). The geometry, electrode positions, and 
mri all line up (coordsys='ctf', unit='cm') and the calculated dipole 
positions are what I would expect.

[Aside: All of my topoplots have the electrodes positioned correctly 
relative to each other but the nose and ears are 90 degrees from where I 
would expect them. Do the topoplot functions not know how to deal with 
ctf coordsys?]

How can I normalize these dipole locations into the template brain so 
that I may perform component clustering in EEGLAB?
I have some ideas but I don't know how to implement them.

1) Calculate the transformation matrix to normalize the original MRI to 
the template MRI, then apply that transformation to the dipole positions 
and momentums. I'm guessing I need to use mri_norm = 
ft_volumenormalize(cfg, mri); but then I don't know how to use 
mri_norm.transform and mri_norm.initial. Further, the output of 
ft_dipolefitting doesn't seem to be suitable for ft_transform_geometry.

2) Since the sourcemodel grid is warped from the template brain, I can 
find the sourcemodel grid index closest to the dipole location then set 
the new dipole location to be the location of the template grid at the 
same index. I don't know how to do this for the momentum but I probably 
don't need the momentum for clustering.

3) Start over from the beginning, normalizing the MRI and the electrode 
locations as soon as possible then performing all subsequent 
calculations using the normalized geometry.

I searched the documentation and the list archives but I could not find 
an answer. I am surprised because I expected dipole normalisation to be 
a common requirement. Maybe I am missing something simple.
Thank you in advance for any help.
-Chad

-- 
Chadwick Boulay
JSPS Postdoctoral Fellow
Keio University
Yokohama Japan
boulay at brain.bio.keio.ac.jp




From mushfa.yousuf at googlemail.com  Mon May  6 14:47:44 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Mon, 6 May 2013 14:47:44 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
Message-ID: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>

Hello;

Yes you were right. I have defined the wrong sensors i.e 'grad' instead of
'elec' while calculating the Leadfield.

Actually I am trying to calculate Combined source reconstruction from both
EEG and MEG sensors.

Do you have any idea, how to define both elec and grad definition  while
calculating first forward then inverse solution.

Because in a fieldtrip either you can defined elec or grad at one time.


Regards;


Mushfa Yousuf

Neurozentrum,
Universitätsklinikum Schleswig-Holstein,
Campus Kiel (UKSH), Deutschland


On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:

> Hi Mushfa,
>
> My guess is that the channels that have you used to compute .csdspctrm are
> not the same as the channels in cfg.elec.    If you set cfg.channel =
> freqPost.label, does that solve it?
>
> Cheers,
> Johanna
>
>
> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>
>> Hello Fieldtrippers,
>>
>> I am doing source reconstruction using EEG channels on a fieldtrip.
>>
>> I have computed Forward solution i.e head model using  'Openmeeg' and
>> lead field successfully.
>>
>> For the inverse solution using 'dics' method, I wrote the following
>> syntax
>>
>>
>>
>>
>>
>>  cfg              = [];
>>  cfg.method       = 'dics';
>>  cfg.frequency    = 130;
>>  cfg.elec         = dataFIC12.hdr.elec;
>>  cfg.grid         = grid;
>>  cfg.vol          = vol;
>>
>>  sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>> and I have received the following error:
>>
>>
>> ??? Error using ==> mtimes
>> Inner matrix dimensions must agree.
>>
>> Error in ==> beamformer_dics at 314
>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>         leadfield
>>
>> Error in ==> ft_sourceanalysis at 595
>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>       squeeze(Cf(i,:,:)), optarg{:});
>>
>> Error in ==> newCode at 214
>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>
>>
>>
>>
>> Any help would be appreciated.
>>
>>
>> Regards;
>>
>>
>> Mushfa Yousuf
>>
>> Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From chaowang0704 at gmail.com  Tue May  7 13:35:20 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 14:35:20 +0300
Subject: [FieldTrip] Some Questions on the resample design
Message-ID: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>

I
 have been using field-trip. Recently, I tried to use it for statistic
test by non-parametric method, e.g. bootstrap and permutation. As usual,
the two method involve resample original data with or without replacement.
I carefully inspected the code in the function *resampledesign* but I was
quite confused by the method in the bootstrap section:

254resample = zeros(cfg.numrandomization, Nrepl);
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From chaowang0704 at gmail.com  Tue May  7 14:08:57 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Tue, 7 May 2013 15:08:57 +0300
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
Message-ID: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>

I'm sorry to make a mistake just now. The previous message sent didn't
fullfill my meaning.

I carefully inspected the code in the function *resampledesign* but I was
quite confused by the codes in the bootstrap section (For paired design,
the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
and design(2,N+1:2*N)=2 and N is for example the subject number; and
cfg.uvar=2):
91     Nvar  = size(design,1);   % number of factors or regressors
92     Nrepl = size(design,2);   % number of replications
...
...
248   units = design(cfg.uvar,:);
249   for k = 1:length(unique(units))
250     sel = find(units==k);
251     indx(:,k) = sel;
252     Nrep(k)   = length(sel);
253   end
254   resample = zeros(cfg.numrandomization, Nrepl);
...
...
274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
275   for i=1:cfg.numrandomization*10
276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
277   end

278   tmp = unique(tmp, 'rows');
279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
size(tmp,1), cfg.numrandomization*10);
...
...
292   for i=1:cfg.numrandomization
293      for k=1:size(indx,1)
294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
295      end
296   end

My question was on the code in 276 line. These code was to generate a
number of rand numbers (about cfg.numrandomization lines) in the range of 1
to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
If the function '*sort*' is used, then every row of matrix tmp is the same,
which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line to
the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
result is by no means what we want, I think. What we do want is several
rows numbers with same range but with distinct orders. Only in this way,
can we guarantee that each resample is not the same.



On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:

> I
> have been using field-trip. Recently, I tried to use it for statistic test
> by non-parametric method, e.g. bootstrap and permutation. As usual, the two
> method involve resample original data with or without replacement. I
> carefully inspected the code in the function *resampledesign* but I was
> quite confused by the method in the bootstrap section:
>
> 254resample = zeros(cfg.numrandomization, Nrepl);
>
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From zriouil.imane at gmail.com  Tue May  7 14:48:24 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 7 May 2013 14:48:24 +0200
Subject: [FieldTrip] convert .plx to .nex ?
Message-ID: <CABu=cReD7OPEna8o=40exmxV=QQvcWNxmbyj9w=mWzaJRPD2dg@mail.gmail.com>

Hi

i have a problem to read data with extension .plx and i want to convert
this to .nex. it's possible or no?

please respond me
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From johanna.zumer at donders.ru.nl  Tue May  7 14:53:40 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Tue, 7 May 2013 14:53:40 +0200
Subject: [FieldTrip] Some Questions on the resample design
In-Reply-To: <CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
References: <CAGvTfVn3DYd6s6eQjmtx4BgYUYX2GEbe31914cugyVaUu7ZHWg@mail.gmail.com>
	<CAGvTfVnUE121vLwLxrrfe1Fc+qvwqcHsfokDiYXXenR2JAH68g@mail.gmail.com>
Message-ID: <CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA@mail.gmail.com>

Dear Chao,

I'm not familiar with this piece of code, but I had a quick look.  Line
276, with the 'sort' command, is testing for the number of unique 'rows'
(line 278).  It then uses this information to modify the value of
cfg.numrandomization (line 283 which you have not displayed), which is
reduced if not enough unique information to do the requested number of
randomizations.   Then (I think) the actual randomization should be
occuring in subsequent lines of code (292-296).    Note also that this part
of code is only reached if max(design(cfg.uvar,:)) < 20.

Does that help?    Maybe someone else with more experience in this section
of code can comment as well?

Or if you still find that it indeed is not randomizing, you can file a bug
here (http://bugzilla.fcdonders.nl/), ideally with a small test script.

Cheers,
Johanna




2013/5/7 Chao Wang <chaowang0704 at gmail.com>

> I'm sorry to make a mistake just now. The previous message sent didn't
> fullfill my meaning.
>
> I carefully inspected the code in the function *resampledesign* but I was
> quite confused by the codes in the bootstrap section (For paired design,
> the design matrix should be like this, design(1,:)=[1:N 1:N], design(2,1:N)=1
> and design(2,N+1:2*N)=2 and N is for example the subject number; and
> cfg.uvar=2):
> 91     Nvar  = size(design,1);   % number of factors or regressors
> 92     Nrepl = size(design,2);   % number of replications
> ...
> ...
> 248   units = design(cfg.uvar,:);
> 249   for k = 1:length(unique(units))
> 250     sel = find(units==k);
> 251     indx(:,k) = sel;
> 252     Nrep(k)   = length(sel);
> 253   end
> 254   resample = zeros(cfg.numrandomization, Nrepl);
> ...
> ...
> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');
> 279   fprintf('found %d unique rows in bootstrap matrix of %d bootstraps',
> size(tmp,1), cfg.numrandomization*10);
> ...
> ...
> 292   for i=1:cfg.numrandomization
> 293      for k=1:size(indx,1)
> 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> 295      end
> 296   end
>
> My question was on the code in 276 line. These code was to generate a
> number of rand numbers (about cfg.numrandomization lines) in the range of 1
> to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> design and Nrep is the number of repetition (Nrep(:)=2 for paired design).
> If the function '*sort*' is used, then every row of matrix tmp is the
> same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278 line
> to the result: temp=1:Nrepl/Nrep(1) (because of the function unique). This
> result is by no means what we want, I think. What we do want is several
> rows numbers with same range but with distinct orders. Only in this way,
> can we guarantee that each resample is not the same.
>
>
>
> On Tue, May 7, 2013 at 2:35 PM, Chao Wang <chaowang0704 at gmail.com> wrote:
>
>> I
>> have been using field-trip. Recently, I tried to use it for statistic
>> test by non-parametric method, e.g. bootstrap and permutation. As usual,
>> the two method involve resample original data with or without replacement.
>> I carefully inspected the code in the function *resampledesign* but I
>> was quite confused by the method in the bootstrap section:
>>
>> 254resample = zeros(cfg.numrandomization, Nrepl);
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From antony.passaro at gmail.com  Wed May  8 23:17:21 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Wed, 8 May 2013 17:17:21 -0400
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
Message-ID: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>

 Hi Fieldtrippers,

I am trying to perform a group-level comparison of 2 conditions across 10
subjects based on the DTF connectivity. For the time being, we are looking
at the DTF for a subset of frequencies (alpha) and choosing the avgoverfreq
option which gives us a 4096 x 1 matrix since we are looking at 64 x 64
channels. Using ft_freqstatistics, I noticed that it will throw an error
explaining that there is not yet an implementation for data with channelcmb
for a cluster analysis so I took it upon myself to identify channel pairs
which should be considered neighbors and build a new neighbor structure
prior to running ft_freqstatistics. To do that, I took the basic neighbor
structure for 64 channels and then created a new neighbor structure of 4096
channel pairs based on the code below:

for i=1:4096
    label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
end

labelcmb = dtf.labelcmb;

chans=64;

%Identify the channel pairs which are neighbors with the target channel
NBtarget = {};
for ch=1:chans^2
    NBtarget(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,1},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat(x,['_' labelcmb{ch,2}]),{neighbours(
1,target).neighblabel},'UniformOutput',0);
    NBtarget(ch).neighblabel = tempnb{:};
end

%Identify the channel pairs which are neighbors with the reference channel
NBref = {};
for ch=1:chans^2
    NBref(ch).label = label{ch};
    target = find(cellfun(@(x) strcmp(labelcmb{ch,2},x),{neighbours(:).label})
==1) ;
    tempnb = cellfun(@(x) strcat([labelcmb{ch,1}
'_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
    NBref(ch).neighblabel = tempnb{:};
end


%Append both sets of neighbors (ref and target)
NBboth= {};
for ch=1:chans^2
    NBboth(ch).label = label{ch};
    NBboth(ch).neighblabel = [NBref(ch).neighblabel;
NBtarget(ch).neighblabel];
end


This seems to work and the clustering method proceeds without error. My
question is the following: is this the proper way to utilize the clustering
method using ft_freqstatistics on connectivity data or am I missing
something?

Thanks,
-Tony
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From chaowang0704 at gmail.com  Thu May  9 10:51:37 2013
From: chaowang0704 at gmail.com (Chao Wang)
Date: Thu, 9 May 2013 11:51:37 +0300
Subject: [FieldTrip] Some Questions on the resample design (Johanna
	Zumer)
Message-ID: <CAGvTfVmzpDNoJ7FKbeeKHCzBPunx0J1+=b5yJKqxfs6qN9hHRw@mail.gmail.com>

Dear

Johanna,

Thank you! I understand your meaning and that's right
that
this part of code is only reached if

max(design(cfg.uvar,:)) < 20, but what I do not understand is that for what
reason,
the '20' is set to test the
max(design(cfg.uvar,:)). And besides, by using 'sort', each row of tmp will
be the same, in ascending order, which will lead the 278 line using
'unique' to have tmp only one row. That is size(tmp,1)=1; this will
lead to cfg.numrandomization=1
in 284 line.

> 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> 275   for i=1:cfg.numrandomization*10
> 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> 277   end
>
> 278   tmp = unique(tmp, 'rows');

Best regards!

Chao

Message: 4

> Date: Tue, 7 May 2013 14:53:40 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Some Questions on the resample design
> Message-ID:
>         <
> CAL4kA6d-WLuip_tUvBRbQr2JiYQ9vr0rb_FnOe18aK8tqEmadA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Chao,
>
> I'm not familiar with this piece of code, but I had a quick look.  Line
> 276, with the 'sort' command, is testing for the number of unique 'rows'
> (line 278).  It then uses this information to modify the value of
> cfg.numrandomization (line 283 which you have not displayed), which is
> reduced if not enough unique information to do the requested number of
> randomizations.   Then (I think) the actual randomization should be
> occuring in subsequent lines of code (292-296).    Note also that
> 
> this part
> of code is only reached if
> 
> max(design(cfg.uvar,:)) < 20.
>
> Does that help?    Maybe someone else with more experience in this section
> of code can comment as well?
>
> Or if you still find that it indeed is not randomizing, you can file a bug
> here (http://bugzilla.fcdonders.nl/), ideally with a small test script.
>
> Cheers,
> 
> Johanna
>
>
>
>
> 2013/5/7 Chao Wang <chaowang0704 at gmail.com>
>
> > I'm sorry to make a mistake just now. The previous message sent didn't
> > fullfill my meaning.
> >
> > I carefully inspected the code in the function *resampledesign* but I was
> > quite confused by the codes in the bootstrap section (For paired design,
> > the design matrix should be like this, design(1,:)=[1:N 1:N],
> design(2,1:N)=1
> > and design(2,N+1:2*N)=2 and N is for example the subject number; and
> > cfg.uvar=2):
> > 91     Nvar  = size(design,1);   % number of factors or regressors
> > 92     Nrepl = size(design,2);   % number of replications
> > ...
> > ...
> > 248   units = design(cfg.uvar,:);
> > 249   for k = 1:length(unique(units))
> > 250     sel = find(units==k);
> > 251     indx(:,k) = sel;
> > 252     Nrep(k)   = length(sel);
> > 253   end
> > 254   resample = zeros(cfg.numrandomization, Nrepl);
> > ...
> > ...
> > 274   tmp = zeros(cfg.numrandomization*10, Nrepl/Nrep(1));
> > 275   for i=1:cfg.numrandomization*10
> > 276      tmp(i,:) = *sort*(randsample(1:Nrepl/Nrep(1), Nrepl/Nrep(1)));
> > 277   end
> >
> > 278   tmp = unique(tmp, 'rows');
> > 279   fprintf('found %d unique rows in bootstrap matrix of %d
> bootstraps',
> > size(tmp,1), cfg.numrandomization*10);
> > ...
> > ...
> > 292   for i=1:cfg.numrandomization
> > 293      for k=1:size(indx,1)
> > 294        resample(i,indx(k,:)) = indx(k,tmp(i,:));
> > 295      end
> > 296   end
> >
> > My question was on the code in 276 line. These code was to generate a
> > number of rand numbers (about cfg.numrandomization lines) in the range
> of 1
> > to Nrepl/Nrep(1), in which Nrepl is the number of replications in the
> > design and Nrep is the number of repetition (Nrep(:)=2 for paired
> design).
> > If the function '*sort*' is used, then every row of matrix tmp is the
> > same, which will be 1,2,..., Nrepl/Nrep(1). And this will lead the 278
> line
> > to the result: temp=1:Nrepl/Nrep(1) (because of the function unique).
> This
> > result is by no means what we want, I think. What we do want is several
> > rows numbers with same range but with distinct orders. Only in this way,
> > can we guarantee that each resample is not the same.
>
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From marianapbranco1 at gmail.com  Fri May 10 10:08:41 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Fri, 10 May 2013 10:08:41 +0200
Subject: [FieldTrip] Real-time processing
References: <9B1A8EA6-CCDE-4CED-83FD-C5D2F21607F5@student.tudelft.nl>
Message-ID: <31275A3B-B8D6-4C46-8B30-5EF745AD13BA@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From mengtongxiao at gmail.com  Fri May 10 11:39:29 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Fri, 10 May 2013 17:39:29 +0800
Subject: [FieldTrip] cooradinate
Message-ID: <CADiddyVv3S8CvCQY-RPFo4GTj1Su68U5WWdjmy2L9MwsCi1Emg@mail.gmail.com>

Dear all，

I got some ROIs from MNE. But  in MNE it use brain template that is *MNI152 .
*
I want use fieldtrip compute the spatial filter for ROIs.
For this reason ,I want got the position in sourcemodel from template in
fieldtrip.
I see the fieldtrip seem to use *MNI305  ,*isn,t it?
If fieldtrip use *MNI305 ,*  this problem is making me question whether a
transformation  is really necessary ?
The both "MNI" space cooradation * x ,y,z axis *represent right,anterior,
superior.(+x=right,+y=anterior,+z=superior)?(MNI cooradation from
http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach)
I find infieldtrip (http://fieldtrip.fcdonders.nl/tutorial/connectivity)
sourcemodel is that *x ,y,z axis *represent anterior, right,superior?
If a transformation  is really necessary ,how should I do?

Then I am puzzed what do *x ,y,z axis *represent in stanard_1020.elc

Thanks for your help,
best,
xiao
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From mengtongxiao at gmail.com  Mon May 13 03:30:06 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Mon, 13 May 2013 09:30:06 +0800
Subject: [FieldTrip] grid-template
Message-ID: <CADiddyVrmgpO+fX+SoyY7cWHBXfc=4Tch9js+fcTV4V9QRfj_w@mail.gmail.com>

Dear all,

I want to konw what is  the MNI-template  that  constructed 3D-grids in the
fieldtrip (Template sourcemodels ) ?
is it MNI305 ,clin27 ,MNI125 or something else?

thanks,
xiao
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From jm.horschig at donders.ru.nl  Mon May 13 11:13:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 11:13:14 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
Message-ID: <5190AEAA.3020301@donders.ru.nl>

Dear Mushfa,

I think you have to compute two leadfield matrices, one for EEG (elec) 
and one for MEG (grad), and then concatenate these (and make sure that 
the order of sensors won't get mixed up anywhere, because  
sourceanalysis just expects the leadfield matrix to be ordered like your 
data. If that's not the case, you either encounter the previous error 
you described or (if the number of channels matches, but order is mixed 
up) it will just return wrong source estimated activity.

Best,
Jörn

On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
> Hello;
>
> Yes you were right. I have defined the wrong sensors i.e 'grad' 
> instead of 'elec' while calculating the Leadfield.
>
> Actually I am trying to calculate Combined source reconstruction from 
> both EEG and MEG sensors.
>
> Do you have any idea, how to define both elec and grad definition  
> while calculating first forward then inverse solution.
>
> Because in a fieldtrip either you can defined elec or grad at one time.
>
>
> Regards;
>
>
> Mushfa Yousuf
>
> Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer 
> <johanna.zumer at gmail.com <mailto:johanna.zumer at gmail.com>> wrote:
>
>     Hi Mushfa,
>
>     My guess is that the channels that have you used to compute
>     .csdspctrm are not the same as the channels in cfg.elec.    If you
>     set cfg.channel = freqPost.label, does that solve it?
>
>     Cheers,
>     Johanna
>
>
>     2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com
>     <mailto:mushfa.yousuf at googlemail.com>>
>
>         Hello Fieldtrippers,
>
>         I am doing source reconstruction using EEG channels on a
>         fieldtrip.
>
>         I have computed Forward solution i.e head model using
>          'Openmeeg' and lead field successfully.
>
>         For the inverse solution using 'dics' method, I wrote the
>         following syntax
>
>
>
>
>
>          cfg              = [];
>          cfg.method       = 'dics';
>          cfg.frequency    = 130;
>          cfg.elec         = dataFIC12.hdr.elec;
>          cfg.grid         = grid;
>          cfg.vol          = vol;
>
>          sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>         and I have received the following error:
>
>
>         ??? Error using ==> mtimes
>         Inner matrix dimensions must agree.
>
>         Error in ==> beamformer_dics at 314
>                 filt = pinv(lf' * invCf * lf) * lf' * invCf;          %
>                 Gross eqn. 3, use PINV/SVD to cover rank deficient
>                 leadfield
>
>         Error in ==> ft_sourceanalysis at 595
>               dip(i) = beamformer_dics(grid, sens, vol, [],
>         squeeze(Cf(i,:,:)), optarg{:});
>
>         Error in ==> newCode at 214
>         sourcePost = ft_sourceanalysis(cfg, freqPost);
>
>
>
>
>         Any help would be appreciated.
>
>
>         Regards;
>
>
>         Mushfa Yousuf
>
>         Neurozentrum,
>         Universitätsklinikum Schleswig-Holstein,
>         Campus Kiel (UKSH), Deutschland
>
>
>         _______________________________________________
>         fieldtrip mailing list
>         fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From naran.kutt at gmail.com  Mon May 13 11:48:17 2013
From: naran.kutt at gmail.com (Narayanan Kutty)
Date: Mon, 13 May 2013 05:48:17 -0400
Subject: [FieldTrip] Mutual Information
Message-ID: <CAGgtWvU9tSr=6XGAt__T=mQUWQx-7h34oLjS_kgMekRkJYzdVQ@mail.gmail.com>

Hello All,

Are there any functions within fieldtrip to calculate mutual information
between channels at the sensor level. I remember that eeglab used to have a
plugin for that. Couldn't find anything in fieldtrip.

Thank you,
Naran.
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From jm.horschig at donders.ru.nl  Mon May 13 14:14:44 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 13 May 2013 14:14:44 +0200
Subject: [FieldTrip] Clustering channel dimension of DTF Connectivity
In-Reply-To: <CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
References: <CAB8wAYSR6m4Zz8N_RSdEOsukGuZ84yynr-62SLrbc=A4ozf9CQ@mail.gmail.com>
	<CAB8wAYQXFAY51_aK+5jRP58xC=9F6zik_qmpLKH-2fZJv=hovw@mail.gmail.com>
Message-ID: <5190D934.5020407@donders.ru.nl>

Dear Tony,

I had a quick look at your code, and I think it is fine. However, I 
would define neighbours purely based on the target sensor, not on the 
reference, e.g. when computing cortico-muscular coherence on channel 
level, you  are interested in spatial clusters near the cortex and not 
in cluster on the arm where the reference sensor is.
Also check out this:

data = ft_checkdata(data, 'cmbrepresentation', 'full');

This will turn chancmb (Nx1) into chan X chan (RxS, where R*S = N).

Best,
Jörn

On 5/8/2013 11:17 PM, Antony Passaro wrote:
> Hi Fieldtrippers,
> I am trying to perform a group-level comparison of 2 conditions across 
> 10 subjects based on the DTF connectivity. For the time being, we are 
> looking at the DTF for a subset of frequencies (alpha) and choosing 
> the avgoverfreq option which gives us a 4096 x 1 matrix since we are 
> looking at 64 x 64 channels. Using ft_freqstatistics, I noticed that 
> it will throw an error explaining that there is not yet an 
> implementation for data with channelcmb for a cluster analysis so I 
> took it upon myself to identify channel pairs which should be 
> considered neighbors and build a new neighbor structure prior to 
> running ft_freqstatistics. To do that, I took the basic neighbor 
> structure for 64 channels and then created a new neighbor structure of 
> 4096 channel pairs based on the code below:
> for i=1:4096
> label{i,1} = [dtf.labelcmb{i,1},'_',dtf.labelcmb{i,2}];
> end
> labelcmb = dtf.labelcmb;
>
> chans=64;
> %Identify the channel pairs which are neighbors with the target channel
> NBtarget = {};
> for ch=1:chans^2
> NBtarget(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,1},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat(x,['_' 
> labelcmb{ch,2}]),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBtarget(ch).neighblabel = tempnb{:};
> end
>
> %Identify the channel pairs which are neighbors with the reference channel
> NBref = {};
> for ch=1:chans^2
> NBref(ch).label = label{ch};
> target = find(cellfun(@(x) 
> strcmp(labelcmb{ch,2},x),{neighbours(:).label}) ==1) ;
> tempnb = cellfun(@(x) strcat([labelcmb{ch,1} 
> '_'],x),{neighbours(1,target).neighblabel},'UniformOutput',0);
> NBref(ch).neighblabel = tempnb{:};
> end
>
>
> %Append both sets of neighbors (ref and target)
> NBboth= {};
> for ch=1:chans^2
> NBboth(ch).label = label{ch};
> NBboth(ch).neighblabel = [NBref(ch).neighblabel; 
> NBtarget(ch).neighblabel];
> end
> This seems to work and the clustering method proceeds without error. 
> My question is the following: is this the proper way to utilize the 
> clustering method using ft_freqstatistics on connectivity data or am I 
> missing something?
> Thanks,
> -Tony
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From sanbelluzo at gmail.com  Mon May 13 21:13:08 2013
From: sanbelluzo at gmail.com (Santiago Belluzo)
Date: Mon, 13 May 2013 16:13:08 -0300
Subject: [FieldTrip] Emotiv + FieldTrip + Matlab
In-Reply-To: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
References: <CAKkp94zaVKehkHPmTT3bq4cg0w4dfx5eYodBW7J0Rz1bt1GqHQ@mail.gmail.com>
Message-ID: <CAKkp94yg=a2VrUUSN2dxGBLTQD4E_6JOJ=VSXKrNLBVjBv8h3w@mail.gmail.com>

Hi, i´m trying to use emotiv2ft in a windows machine and Matlab return this
message

"Waiting for the device to become ready - press [Escape] to quit
EDK: User added, will now start acquisition.
Streaming 16 out of 22 channels
Could not connect to buffer server at localhost:1972."


In http://fieldtrip.fcdonders.nl/development/realtime/emotiv?s[]=emotiv said
that  "If port 1972 cannot be accessed on a Windows machine it may help to
first initialize the port from matlab, e.g., via ft_realtime_fileproxy".
But i´m not sure how to do it....
 Someone can help me?.

Santiago.


2013/3/4 Santiago Belluzo <sanbelluzo at gmail.com>

> *Hi, I'm new to FieldTrip and I'm interested in using it to capture **realtime data from the Emotiv headset using the function emotiv2ft.I`ve tried some examples like signalviewer andpowerviewer with random signal from signalproxy to check that the FieldTripBuffer works fine. Then i`ve tried to use emotiv2ft and have problems.  *
>
> *I'm not sure about how to call to this interface from within **Matlab.*
>
> *I`ve read some messages from the mailinglist with similar problem but in there is not clear for me how they solve it. *
>
> *I´ll be waiting for any help!.*
>
> *Thanks.*
>
> --
> Santiago
>



-- 
Santiago Belluzo
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From chenxiaogang1986 at 163.com  Tue May 14 03:37:29 2013
From: chenxiaogang1986 at 163.com (Xiaogang Chen)
Date: Tue, 14 May 2013 09:37:29 +0800 (CST)
Subject: [FieldTrip] ft_topoplotCC of vector
Message-ID: <5ef5e6c2.25f7.13ea0af63fd.Coremail.chenxiaogang1986@163.com>

Hi all,

 

I am trying to plot some results that are not the output from a ft function, using a ft_topoplotCC function. However, I don’t know how to use it. Would you send me some simple examples? Thanks very much.

 

Best,

 

Xiaogang Chen 
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From yoel.sher at mail.huji.ac.il  Tue May 14 18:09:37 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Tue, 14 May 2013 19:09:37 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
Message-ID: <519261C1.3020002@mail.huji.ac.il>

Dear FieldTrippers,

I would like to know if there is an option to extract the Topographic 
map (Such as the scalp in ft_topoplotER) to a matrix. I've searched 
around the functions in fieldtrip and couldn't find any..

Many Thanks,
Yoel


From eelke.spaak at donders.ru.nl  Tue May 14 19:25:40 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 14 May 2013 19:25:40 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <519261C1.3020002@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
Message-ID: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>

Dear Yoel,

I'm not sure if I understand what you mean exactly, but do you simply
want the values plotted by ft_topoplotER in case of plotting the
results of ft_timelockanalysis? In that case, you can look at the
tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
rather trivial, so I think you must mean something else.

Best,
Eelke

On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear FieldTrippers,
>
> I would like to know if there is an option to extract the Topographic map
> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
> functions in fieldtrip and couldn't find any..
>
> Many Thanks,
> Yoel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From yoel.sher at mail.huji.ac.il  Wed May 15 12:08:20 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:08:20 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
Message-ID: <51935E94.7090605@mail.huji.ac.il>

Dear Eelke,

First, thanks for you fast replay. Second, let me clarify my question. 
I'm looking for other result than the average ERP/ERF. I'm looking for a 
matrix that output the EEG value per each location (not just the 
electrodes) on the scalp. Of course that every location other than the 
electrode is an interpolated value. The plot of ft_topoplotER shows that 
matrix (but does not output, as far as I know).

Regards,
Yoel

On 05/14/2013 08:25 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> I'm not sure if I understand what you mean exactly, but do you simply
> want the values plotted by ft_topoplotER in case of plotting the
> results of ft_timelockanalysis? In that case, you can look at the
> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
> rather trivial, so I think you must mean something else.
>
> Best,
> Eelke
>
> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear FieldTrippers,
>>
>> I would like to know if there is an option to extract the Topographic map
>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around the
>> functions in fieldtrip and couldn't find any..
>>
>> Many Thanks,
>> Yoel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From eelke.spaak at donders.ru.nl  Wed May 15 12:22:21 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 15 May 2013 12:22:21 +0200
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <51935E94.7090605@mail.huji.ac.il>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
Message-ID: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>

Dear Yoel,

Ah, I understand now; you want the interpolated matrix. This is not
possible with standard FieldTrip code.

However, it should not be very difficult to get this. I would
recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
Then, when the code breaks at that point, you can type in the command
window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
you have the x and y coordinates and the data (z) in variables in your
base workspace.

Getting this matrix programmatically in a script should also be
possible, but that would require custom hacks of ft_plot_topo (e.g.
you could put this assignin call in your local copy of the function,
or add Xi,Yi,Zi as output arguments, etc.)

Good luck,
best,

Eelke

On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
> Dear Eelke,
>
> First, thanks for you fast replay. Second, let me clarify my question. I'm
> looking for other result than the average ERP/ERF. I'm looking for a matrix
> that output the EEG value per each location (not just the electrodes) on the
> scalp. Of course that every location other than the electrode is an
> interpolated value. The plot of ft_topoplotER shows that matrix (but does
> not output, as far as I know).
>
> Regards,
> Yoel
>
>
> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>
>> Dear Yoel,
>>
>> I'm not sure if I understand what you mean exactly, but do you simply
>> want the values plotted by ft_topoplotER in case of plotting the
>> results of ft_timelockanalysis? In that case, you can look at the
>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>> rather trivial, so I think you must mean something else.
>>
>> Best,
>> Eelke
>>
>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>
>>> Dear FieldTrippers,
>>>
>>> I would like to know if there is an option to extract the Topographic map
>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>> the
>>> functions in fieldtrip and couldn't find any..
>>>
>>> Many Thanks,
>>> Yoel
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>


From yoel.sher at mail.huji.ac.il  Wed May 15 12:47:06 2013
From: yoel.sher at mail.huji.ac.il (Yoel Sher)
Date: Wed, 15 May 2013 13:47:06 +0300
Subject: [FieldTrip] EEG -> Topographic Matrix
In-Reply-To: <CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
References: <519261C1.3020002@mail.huji.ac.il>
	<CABPNLUrzeJnGMOvN4Md52B_2jVzMbUufg6=1=rsTx4O4_vE+pg@mail.gmail.com>
	<51935E94.7090605@mail.huji.ac.il>
	<CABPNLUpLc5SL1uhmsEjuqOqG62g8CmgU7CY9VLsfz0cn38kjfA@mail.gmail.com>
Message-ID: <519367AA.60204@mail.huji.ac.il>

Dear Eelke,

Many thanks, I'll try it out.

Best,
- Yoel

On 05/15/2013 01:22 PM, Eelke Spaak wrote:
> Dear Yoel,
>
> Ah, I understand now; you want the interpolated matrix. This is not
> possible with standard FieldTrip code.
>
> However, it should not be very difficult to get this. I would
> recommend to set a breakpoint in plotting/ft_plot_topo.m, at line 220.
> Then, when the code breaks at that point, you can type in the command
> window assignin('base','Xi',Xi) and the same for Yi and Zi, that way
> you have the x and y coordinates and the data (z) in variables in your
> base workspace.
>
> Getting this matrix programmatically in a script should also be
> possible, but that would require custom hacks of ft_plot_topo (e.g.
> you could put this assignin call in your local copy of the function,
> or add Xi,Yi,Zi as output arguments, etc.)
>
> Good luck,
> best,
>
> Eelke
>
> On 15 May 2013 12:08, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>> Dear Eelke,
>>
>> First, thanks for you fast replay. Second, let me clarify my question. I'm
>> looking for other result than the average ERP/ERF. I'm looking for a matrix
>> that output the EEG value per each location (not just the electrodes) on the
>> scalp. Of course that every location other than the electrode is an
>> interpolated value. The plot of ft_topoplotER shows that matrix (but does
>> not output, as far as I know).
>>
>> Regards,
>> Yoel
>>
>>
>> On 05/14/2013 08:25 PM, Eelke Spaak wrote:
>>> Dear Yoel,
>>>
>>> I'm not sure if I understand what you mean exactly, but do you simply
>>> want the values plotted by ft_topoplotER in case of plotting the
>>> results of ft_timelockanalysis? In that case, you can look at the
>>> tl.avg field (if tl = ft_timelockanalysis(cfg, data)). But that seems
>>> rather trivial, so I think you must mean something else.
>>>
>>> Best,
>>> Eelke
>>>
>>> On 14 May 2013 18:09, Yoel Sher <yoel.sher at mail.huji.ac.il> wrote:
>>>> Dear FieldTrippers,
>>>>
>>>> I would like to know if there is an option to extract the Topographic map
>>>> (Such as the scalp in ft_topoplotER) to a matrix. I've searched around
>>>> the
>>>> functions in fieldtrip and couldn't find any..
>>>>
>>>> Many Thanks,
>>>> Yoel
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From ggonesc at upo.es  Wed May 15 19:37:11 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 15 May 2013 19:37:11 +0200
Subject: [FieldTrip] PLV and ImC computation
Message-ID: <8d77945c28ba0f58.5193e3e7@upo.es>

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From mbj0310 at gmail.com  Thu May 16 08:28:13 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 15:28:13 +0900
Subject: [FieldTrip] About preprocessing and define trial
Message-ID: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>


Dear all,

Hello, my name is BJ Min from Korea.

I am just a beginner in the Fieldtrip.
Anyway, with the help of tutorials, I could make grand average ERP of my data finally. 

However, my question is about the order of preprocessing. According to the tutorials, and examples, it looks the ft_definetrial step is the first, then ft_preprocessing step is followed.  But, is there any method to flip these two steps? What I want to do is preprocessing (filtering, notch filtering) first then to use ft_definetrial sequentially.

Best regards


BeomJun Min, M.D.

Ph. D. student, Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST) 
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
500-712, Republic of Korea (South) 
Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr

-------------- next part --------------
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From eelke.spaak at donders.ru.nl  Thu May 16 08:52:02 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 08:52:02 +0200
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
Message-ID: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>

Dear BeomJun,

What you describe is definitely possible. If you specify:

cfg = [];
cfg.dataset = 'dataset';
data = ft_preprocessing(cfg);

you will get one very big 'trial' in the data structure, representing
just all your data. In the step above, you can also specify filter
options.

After this step, you can segment your data into trials by using
ft_redefinetrial (rather than ft_definetrial). However, you still need
a trl matrix containing the trial definition. The easiest way to
obtain this is to still call ft_definetrial as you used to do:

cfg = [];
cfg.dataset = 'dataset';
cfg.trialdef.....
% all the trial definition options go here
cfgout = ft_definetrial(cfg);

and then just save the output trl matrix:

trl = cfgout.trl;

now you can call ft_redefinetrial:

cfg = [];
cfg.trl = trl;
data = ft_redefinetrial(cfg, data);

and your data will be segmented.

Hope this helps,
Best,

Eelke


On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I am just a beginner in the Fieldtrip.
> Anyway, with the help of tutorials, I could make grand average ERP of my
> data finally.
>
> However, my question is about the order of preprocessing. According to the
> tutorials, and examples, it looks the ft_definetrial step is the first, then
> ft_preprocessing step is followed.  But, is there any method to flip these
> two steps? What I want to do is preprocessing (filtering, notch filtering)
> first then to use ft_definetrial sequentially.
>
> Best regards
>
>
> BeomJun Min, M.D.
>
> Ph. D. student, Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From mbj0310 at gmail.com  Thu May 16 10:06:51 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 16 May 2013 17:06:51 +0900
Subject: [FieldTrip] About preprocessing and define trial
In-Reply-To: <CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
References: <9F7D3012-ADFE-40C4-AC5F-AA3F320348AD@gmail.com>
	<CABPNLUqJ1kGLUr90wsch6=vkg5niJBcrsFH6jgDMrDweCjb02Q@mail.gmail.com>
Message-ID: <CA+v9jvJ0bo1UFp+_qSezeO8B4LpyQ+RDiSr=2pKLWK6-8pRf4w@mail.gmail.com>

Dear Eelke Spaak

Thank you very much.
It works perfect!

Best regards.


2013/5/16 Eelke Spaak <eelke.spaak at donders.ru.nl>

> Dear BeomJun,
>
> What you describe is definitely possible. If you specify:
>
> cfg = [];
> cfg.dataset = 'dataset';
> data = ft_preprocessing(cfg);
>
> you will get one very big 'trial' in the data structure, representing
> just all your data. In the step above, you can also specify filter
> options.
>
> After this step, you can segment your data into trials by using
> ft_redefinetrial (rather than ft_definetrial). However, you still need
> a trl matrix containing the trial definition. The easiest way to
> obtain this is to still call ft_definetrial as you used to do:
>
> cfg = [];
> cfg.dataset = 'dataset';
> cfg.trialdef.....
> % all the trial definition options go here
> cfgout = ft_definetrial(cfg);
>
> and then just save the output trl matrix:
>
> trl = cfgout.trl;
>
> now you can call ft_redefinetrial:
>
> cfg = [];
> cfg.trl = trl;
> data = ft_redefinetrial(cfg, data);
>
> and your data will be segmented.
>
> Hope this helps,
> Best,
>
> Eelke
>
>
> On 16 May 2013 08:28, Beom Jun Min <mbj0310 at gmail.com> wrote:
> >
> > Dear all,
> >
> > Hello, my name is BJ Min from Korea.
> >
> > I am just a beginner in the Fieldtrip.
> > Anyway, with the help of tutorials, I could make grand average ERP of my
> > data finally.
> >
> > However, my question is about the order of preprocessing. According to
> the
> > tutorials, and examples, it looks the ft_definetrial step is the first,
> then
> > ft_preprocessing step is followed.  But, is there any method to flip
> these
> > two steps? What I want to do is preprocessing (filtering, notch
> filtering)
> > first then to use ft_definetrial sequentially.
> >
> > Best regards
> >
> >
> > BeomJun Min, M.D.
> >
> > Ph. D. student, Department of Medical System Engineering (DMSE)
> > Gwangju Institute of Science and Technology (GIST)
> > 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> > 500-712, Republic of Korea (South)
> > Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> > E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From eelke.spaak at donders.ru.nl  Thu May 16 10:07:47 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 10:07:47 +0200
Subject: [FieldTrip] Second-level one-sample t test with clustering
Message-ID: <CABPNLUqSFsDCGBZCMQa2ZzQ5TDxLjH2ynmCy5jYzkQMNGJddTA@mail.gmail.com>

Dear fellow FieldTrippers,

At the moment, I want to do second-level source statistics on my data
(but the question is the same for sensor statistics). I have computed
two-sample t-scores for each subject, between the trials in conditions
A and B.

Now, the appropriate per-voxel test to do across subjects would be a
one-sample t-test. This is rather easy to do, but I would like to use
cluster permutations to correct for multiple comparisons. My idea is
to generate fake data of all zeroes, the same size as my t-score
descriptive data per subject, and then do a paired-samples t test
between the real data and these zeroes (using ft_statfun_depsamplesT).
The voxel-level t statistic of data vs 0 should be the same as a
one-sample test of course. However, I am not sure the permutations of
the data would give me a valid distribution of the cluster statistic.

The test for the real data would be (comparing column 1 to column 2):
dataA 0
dataB 0
dataC 0
dataD 0

whereas a permutation might look like so:
0 dataA
dataB 0
dataC 0
0 dataD

Intuitively, I think this makes sense, as the t score of 0 vs data
will be the negative of t(data vs 0), I should get an appropriate
randomization distribution. But I'm not completely sure of this.

So, my question: does anyone see a problem with my approach? Or is
this a valid way of cluster-correcting a one-sample T test? If not,
what would be the right way to proceed?

Many thanks,
best,
Eelke


From e.maris at psych.ru.nl  Thu May 16 16:31:15 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 16:31:15 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
Message-ID: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>

Hi Eelke,

This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.

Eric


http://www.nphyscog.com/contact
----- fieldtrip-request at science.ru.nl schreef:
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
> 
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


From eelke.spaak at donders.ru.nl  Thu May 16 16:43:32 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 16 May 2013 16:43:32 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>

Hi Eric,

Thanks, that's what I expected. However, that approach does not take
into account the different between-trial variances in the different
subjects. What would you recommend to take those into account?

Best,
Eelke

On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> Hi Eelke,
>
> This not valid. At the second level, you must use the condition means (per subject) as the observations about which you have a hypothesis and which therefore have to be permuted.
>
> Eric
>
>
> http://www.nphyscog.com/contact
> ----- fieldtrip-request at science.ru.nl schreef:
>> Send fieldtrip mailing list submissions to
>> fieldtrip at science.ru.nl
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> or, via email, send a message with subject or body 'help' to
>> fieldtrip-request at science.ru.nl
>>
>> You can reach the person managing the list at
>> fieldtrip-owner at science.ru.nl
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of fieldtrip digest..."
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From e.maris at psych.ru.nl  Thu May 16 17:28:36 2013
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 16 May 2013 17:28:36 +0200 (CEST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
In-Reply-To: <CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
Message-ID: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>

Hi Eelke,

It all depends on the null hypothesis that you want to test. It's better
to discuss this with you in person or at some meeting with other
colleagues (for non-Donders Discussion List readers, Eelke and I work at
the same institute), because at the end it is a matter of deciding on what
is an interesting null hypothesis (both for you and the reviewers of your
paper).

I remember a discussion with a colleague about the same issue (using
first-level t-statistics at the second level), and he was quite unhappy
when I questioned this approach (by asking whether this is really the null
hypothesis he was interested in). At the end, it turned out that he also
had tried the standard approach (using only condition means) but this did
not result in a significant p-value.

Best,

Eric


> -----Original Message-----
> From: eelke.spaak at gmail.com [mailto:eelke.spaak at gmail.com] On Behalf Of
> Eelke Spaak
> Sent: donderdag 16 mei 2013 16:44
> To: Eric Maris; FieldTrip discussion list
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 20
> 
> Hi Eric,
> 
> Thanks, that's what I expected. However, that approach does not take
> into account the different between-trial variances in the different
> subjects. What would you recommend to take those into account?
> 
> Best,
> Eelke
> 
> On 16 May 2013 16:31, Eric Maris <e.maris at psych.ru.nl> wrote:
> > Hi Eelke,
> >
> > This not valid. At the second level, you must use the condition means
> (per subject) as the observations about which you have a hypothesis and
> which therefore have to be permuted.
> >
> > Eric
> >
> >
> > http://www.nphyscog.com/contact
> > ----- fieldtrip-request at science.ru.nl schreef:
> >> Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> or, via email, send a message with subject or body 'help' to
> >> fieldtrip-request at science.ru.nl
> >>
> >> You can reach the person managing the list at
> >> fieldtrip-owner at science.ru.nl
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of fieldtrip digest..."
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From tim.curran at Colorado.EDU  Fri May 17 14:36:54 2013
From: tim.curran at Colorado.EDU (Tim Curran)
Date: Fri, 17 May 2013 06:36:54 -0600
Subject: [FieldTrip] Postdoctoral Position, Curran Lab,
	University of Colorado Boulder
In-Reply-To: <022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
References: <mailman.0.1368698418.10.fieldtrip@science.ru.nl>
	<245706559.668339.1368714675557.JavaMail.root@draco.zimbra.ru.nl>
	<CABPNLUqB5RE8Ceay8SO-MaoS+y2JfRBYqKyfNt2dVYTZgJyr=g@mail.gmail.com>
	<022601ce524a$0c47c250$24d746f0$@maris@psych.ru.nl>
Message-ID: <AEF2F5AF-5A3C-4FA3-B17D-1429D57A46FC@colorado.edu>

Postdoctoral Position
Curran Lab, University of Colorado Boulder
Postdoctoral research position available in the lab of Tim Curran at the Department of Psychology & Neuroscience, University of Colorado Boulder to work on NIH-funded ERP studies of memory and perceptual expertise.  Desirable qualifications include research experience related to memory, perceptual expertise, ERP/EEG, and/or related domains.  Anticipated start date is summer or fall of 2013.  The University of Colorado is an Equal Opportunity/Affirmative Action employer. For further information contact, tim.curran at colorado.edu<mailto:tim.curran at colorado.edu>.  Applicants must submit a CV, a statement of research experience/interests, and a cover letter including email addresses for at least three referees to contact for recommendation letters if needed. Applications will be accepted electronically at https://www.jobsatcu.com/postings/63602
http://psych.colorado.edu/~tcurran/




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From ggonesc at upo.es  Fri May 17 17:45:40 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Fri, 17 May 2013 17:45:40 +0200
Subject: [FieldTrip] problem in connectivityanalysis
Message-ID: <9f89709b303dae2.51966cc4@upo.es>

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From jessetinker at gmail.com  Fri May 17 21:36:12 2013
From: jessetinker at gmail.com (Jesse Tinker)
Date: Fri, 17 May 2013 12:36:12 -0700
Subject: [FieldTrip] Segmentation Memory Issue
Message-ID: <CACKMsgNPvYLv33cxDr0fM-SJ3QR_8y1aY+93fBmGqMOT+Lo58Q@mail.gmail.com>

Hello Fieldtrippers!

This is my first post ever and I just want to say thank you to everyone for
promoting such a vibrant and supportive intellectual community.

I have an issue which seems so simple but I am somewhat stymied by: using
fieldtrip to accomplish the coregistration. The main points of my code are:

mri = ft_read_mri( );

mri = ft_volumerealign(cfg, mri);           % Mark fiducials

mrireslice = ft_volumereslice(cfg,mri);  %To apply the resultant
transformation matrix

segmentedmri  = ft_volumesegment(cfg, mrireslice);



First, if I skip the reslice step, everything works fine. However, if I do
the reslice and then try to segment, spm_preproc tries to create a 1.8 Tb
array. Although it bravely tries, my 24 Gb of RAM inevitably fails. The
analogous array for the unsliced mri is 2Mb.

I found this confusing as the quantity of information in the resliced image
is the exact same. I traced through all the coding and the computation that
fails is based on the transformation matrix of the MRI which, of course,
changes with the reslicing. I am happy to provide details of that but won't
at the moment.

My question, has anyone else encountered this or developed a workaround?

Very much appreciated,

Jesse
British Columbia Mental Health and Research Institute
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From mengtongxiao at gmail.com  Sat May 18 16:06:20 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sat, 18 May 2013 22:06:20 +0800
Subject: [FieldTrip] a .mat file about meg data do preprocessing
Message-ID: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>

Dear all,
I have a .mat file about meg data(102*98800，channel*time,channel is
'MEG0111','MEG0121'.....'M*1' );
Then I use eeglab read it,got .set file;I want use ft_timelockanalysis then
*cfg = [];
cfg.dataset     = 'megalpha.set';
cfg.grad=grad;
data_org        = ft_preprocessing(cfg)*
>grad =
     chanori: [102x3 double]
     chanpos: [102x3 double]
    chantype: {102x1 cell}
    chanunit: {102x1 cell}
     coilori: [510x3 double]
     coilpos: [510x3 double]
       label: {102x1 cell}
         tra: [102x510 double]
        unit: 'cm'
Warning: creating default channel names
> In fileio\private\read_eeglabheader at 53
  In ft_read_header at 572
  In ft_preprocessing at 343
processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005'
'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012'
'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019'
'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026'
'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033'
'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040'
'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047'
'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054'
'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061'
'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068'
'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075'
'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082'
'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089'
'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096'
'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
reading and preprocessing
reading and preprocessing trial 1 from 1
data_org =
           hdr: [1x1 struct]
         label: {102x1 cell}
          time: {[1x98800 double]}
         trial: {[102x98800 double]}
       fsample: 1037
    sampleinfo: [1 98800]
           cfg: [1x1 struct]

*cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'M*1';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);*
timelock =
       avg: [0x98800 double]
       var: [0x98800 double]
      time: [1x98800 double]
       dof: [0x98800 double]
     label: {0x1 cell}
    dimord: 'chan_time'
       cov: []
       cfg: [1x1 struct]

there is no error displyed in command window but the timlock is empty,why?

thanks for you help,
best,
xiao
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From eeguser at hotmail.com  Sat May 18 18:21:48 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 19:21:48 +0300
Subject: [FieldTrip] computing threshold for PLV
Message-ID: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>

Dear FT Experts,



I have calculated PLV for a set of EEG data from 5 different patients. 
Now I want to convert the PLV matrix of each patient into a binary 
matrix. For this I need a threshold PLV value below which I can assume 
the phase locking is zero.

My question is, how do I compute this threshold. I know hard 
thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), 
but I guess it is not a very good option.



Can somebody suggest a better and robust (statistical) way of determining the threshold ?  		 	   		  
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From sherrykhan78 at gmail.com  Sat May 18 18:37:28 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 12:37:28 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>

You can randomly shift in time the epochs, to compute null-distribution,
and then threshold at some  p-value say p < 0.01, you can even correct
for multiple comparison in space and time using  this principle.



On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com>wrote:

> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Sat May 18 19:25:50 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 18 May 2013 19:25:50 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<CALEzDDVvPy2agtUb7K0Yp8qSOXD3ubDdMi68Xpy0YFgcYUhsRw@mail.gmail.com>
Message-ID: <4EDB7A1D-4484-454B-A9CE-5AE826E2AE98@donders.ru.nl>

Dear all,

Note that shuffling the epochs with respect to one another (where for one of the channels in the pair the epoch order stays fixed) usually yields a too liberal null-distribution. The reason is that the shuffling also destroys all structure in the data that is due to electromagnetic field spread. So, even if an observed pattern of PLV is caused by a single underlying neural generator, shuffling the epochs most likely makes this pattern 'significant'. However, it still does not reflect physiological interaction between sources.

Best,
Jan-Mathijs


On May 18, 2013, at 6:37 PM, Sheraz Khan wrote:

> You can randomly shift in time the epochs, to compute null-distribution, and then threshold at some  p-value say p < 0.01, you can even correct for multiple comparison in space and time using  this principle.
> 
> 
> 
> On Sat, May 18, 2013 at 12:21 PM, Subramaniam Iyer <eeguser at hotmail.com> wrote:
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From smoratti at psi.ucm.es  Sat May 18 20:11:11 2013
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Sat, 18 May 2013 20:11:11 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
Message-ID: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,

Stephan



________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From eeguser at hotmail.com  Sat May 18 21:42:05 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sat, 18 May 2013 22:42:05 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
Message-ID: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>




Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es
Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,
You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
Hope that helps,
Stephan



________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain
and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? _______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  
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From sherrykhan78 at gmail.com  Sun May 19 01:55:07 2013
From: sherrykhan78 at gmail.com (Sheraz Khan)
Date: Sat, 18 May 2013 19:55:07 -0400
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
Message-ID: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>

Most of the previois discussion targeted toward event related plv for
continous data may be look at Hipp 2012 Nature Neuroscience orthogonal
correlation paper
On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:

>  Dear FT Experts
>
> Thank you for your inputs. I should add here that I have continuous EEG
> data (so effectively single trial). The way I am computing PLV is by
> dividing my data into windows of 2 seconds each and computing PLV for each
> window and then I finally average the PLV values of all the windows.
>
> So when we talk of shuffling trials, in my case should i consider each of
> 2 second window as a trial ? Sorry if this sounds stupid as I am new to
> this kind of analysis.
>
> ------------------------------
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
>
> Dear Sheraz,
>
> You might consult the following article: Lachaux, J. P. et al. 1999.
> Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208.
> In principle you have to create surrogate data that represent the null
> hypothesis that there is no phase locking between your electrodes, sources,
> etc. Then you create hundreds or thousands of surrogate data sets and
> calculate each time you PLV. That way you create a distribution of your PLV
> values under the Null hypothesis. Then you check in what percentile your
> observed PLV lies (e. g. if its beyond the 95% percentile you would reject
> the Null hypothesis).
>
> Hope that helps,
>
> Stephan
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
>
> Dear FT Experts,
>
> I have calculated PLV for a set of EEG data from 5 different patients. Now
> I want to convert the PLV matrix of each patient into a binary matrix. For
> this I need a threshold PLV value below which I can assume the phase
> locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding
> is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is
> not a very good option.
>
> Can somebody suggest a better and robust (statistical) way of determining
> the threshold ?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________ fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mengtongxiao at gmail.com  Sun May 19 09:32:37 2013
From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=)
Date: Sun, 19 May 2013 15:32:37 +0800
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ@mail.gmail.com>

Dear all，
when I use ft_timelockanalysis like follow,there are some mistake.

cfg                   = [];
cfg.covariance        = 'yes';
cfg.channel           = 'all';
cfg.vartrllength      = 2;
cfg.covariancewindow  = 'all';
timelock              = ft_timelockanalysis(cfg, data_org);
the input is raw data with 102 channels and 1 trials
averaging trials
averaging trial 1 of 1

the call to "ft_timelockanalysis" took 5 seconds
??? Error using ==> mxSerialize
Error during serialization of (null)

Error in ==> ft_postamble_provenance at 76
  cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
  cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
  'UniformOutput', false), 'UniformOutput', false);

Error in ==> ft_postamble at 55
  evalin('caller', ['ft_postamble_' cmd]);
Error in ==> ft_timelockanalysis at 401
ft_postamble provenance timelock

Thank you so much for your help!!
xiao
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From eeguser at hotmail.com  Sun May 19 09:54:21 2013
From: eeguser at hotmail.com (Subramaniam Iyer)
Date: Sun, 19 May 2013 10:54:21 +0300
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>,
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>,
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>,
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <BLU176-W121107702786A05888CC94B9AE0@phx.gbl>

So, does it mean that PLV method does not make much sense for continuous data ? To be more specific, I am trying to investigate synchrony from epileptic EEG recordings.

Date: Sat, 18 May 2013 19:55:07 -0400
From: sherrykhan78 at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper

On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:







Dear FT Experts
Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.

So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.

From: smoratti at psi.ucm.es

Date: Sat, 18 May 2013 20:11:11 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] computing threshold for PLV

Dear Sheraz,

You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).

Hope that helps,
Stephan




________________________________________________________Stephan Moratti, PhD

see also: http://web.me.com/smoratti/


Universidad Complutense de MadridFacultad de PsicologíaDepartamento de Psicología Básica ICampus de Somosaguas28223 Pozuelo de Alarcón (Madrid)Spain

and
Center for Biomedical TechnologyLaboratory for Cognitive and Computational NeuroscienceParque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982



El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:

Dear FT Experts,

I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.

My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.

Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From politzerahless at gmail.com  Sun May 19 14:27:37 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 19 May 2013 07:27:37 -0500
Subject: [FieldTrip] help about ft_timelockanalysis
Message-ID: <CAJT2k_8-ndM9giikDhgz4qem475i-bf76MkE=_BSX1MOAuy+nQ@mail.gmail.com>

Hello Xiao,

I don't know if this is what is causing the error, but I did notice that
your dataset apparently only has one trial. Usually ft_timelockanalysis()
would take a dataset consisting of multiple trials and average them; you
may need to run ft_preprocessing() to divide your dataset into trials.

Best,
Steve



>
> Message: 1
> Date: Sun, 19 May 2013 15:32:37 +0800
> From: ?? <mengtongxiao at gmail.com>
> To: fieldtrip <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] help about ft_timelockanalysis
> Message-ID:
>         <
CADiddyWhMO7vgM2ZjV8xABCVe8WS4d2eXNwvY92hcj2oA0piFQ at mail.gmail.com>
> Content-Type: text/plain; charset="gb2312"
>
> Dear all?
> when I use ft_timelockanalysis like follow,there are some mistake.
>
> cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'all';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);
> the input is raw data with 102 channels and 1 trials
> averaging trials
> averaging trial 1 of 1
>
> the call to "ft_timelockanalysis" took 5 seconds
> ??? Error using ==> mxSerialize
> Error during serialization of (null)
>
> Error in ==> ft_postamble_provenance at 76
>   cfg.callinfo.outputhash = cellfun(@CalcMD5, cellfun(@mxSerialize,
>   cellfun(@eval, ft_default.postamble, 'UniformOutput', false),
>   'UniformOutput', false), 'UniformOutput', false);
>
> Error in ==> ft_postamble at 55
>   evalin('caller', ['ft_postamble_' cmd]);
> Error in ==> ft_timelockanalysis at 401
> ft_postamble provenance timelock
>
> Thank you so much for your help!!
> xiao
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From stephanie.ries at berkeley.edu  Mon May 20 06:32:49 2013
From: stephanie.ries at berkeley.edu (Stephanie Kathleen Ries-cornou)
Date: Sun, 19 May 2013 21:32:49 -0700
Subject: [FieldTrip] dipole modeling using field trip
Message-ID: <CAHckMuRtCLu8LGLxXX57ktWhx3DbNK2m5P4Oy9R5047GPuChFA@mail.gmail.com>

Hi,

I would like to know if it possible to reject horizontal eye movements from
scalp EEG signal using equivalent dipole modeling in Fieldtrip. I have
tried doing this using ICA but it was not possible to identify a component
reflecting saccades for all subjects. Has anyone ever done this? If yes,
any suggestion would be great!

I am trying to learn about source reconstruction using two dipoles thinking
this might be a good start and have started going through the tutorial. I
got the following error messages:

>> data = ft_dipolesimulation(cfg);
using headmodel specified in the configuration
using gradiometers specified in the configuration
computing simulated data
Error using  .*
Matrix dimensions must agree.

Error in ft_dipolesimulation (line 203)
    simulated.trial{trial}  = simulated.trial{trial} + lf(:,i:3:end) * ...

This was fixed when I removed the "..." but then I got this message:

Error using ft_fetch_vol (line 76)
no headmodel specified

Error in prepare_headmodel (line 51)
vol = ft_fetch_vol(cfg, data);

Error in ft_dipolesimulation (line 106)
[vol, sens, cfg] = prepare_headmodel(cfg, []);

The "vol" parameter is defined, so I do not know where the error is coming
from.

Best,

Stephanie


Stephanie Ries, PhD
Knight Lab - Helen Wills Neuroscience Institute
University of California at Berkeley
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From ggonesc at upo.es  Mon May 20 09:28:55 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Mon, 20 May 2013 09:28:55 +0200
Subject: [FieldTrip] problem with PLV and ImC computing
Message-ID: <1115d37d2b1643b.5199ecd7@upo.es>

I'm re-sending this, becasue searching at the fieldtrip archives, I've notice that my message was scrubbed...


Dear Fieltrip experts,

I  have my continuous data imported to fieldtrip with matlab, I'm looking  for performing connectivity analysis between pairs of sensors, I have  succed as:
data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels and 2000 samples
data.label {59x1};
data.time {1xNepochs};

then, calculate only the FFT of all sensors as:
cfg=[];
cfg.output='fourier';
cfg.method='mtmfft';
cfg.taper='hanning';
cfg.foilim=[8.5 9.5];
cfg.tapsmofrq=0;
cfg.trials='all';
cfg.keeptrials='yes';
cfg.channel='all';
fourier=ft_freqanalysis(cfg, data)
as output I get:
dimord = 'rpttap_chan_freq'
freq= [1x9]
fourierspctrm=[7x59x9 double]

Then compute the imaginary part of coherency as:
cfg=[];
cfg.method ='cohe';
cfg.complex='imag';
cfg.channelcbm={'all' 'all'};
coher = ft_connectivityanalysis (cfg, fourier)
as output get: 
dimord='chan_chan_freq';
cohspctrm=[59x59x9 double];
dof=7;

I have two main questions:

A)  As you see, this makes an average over the epochs of each channel, and  not over the samples (which in this case are the 9 frequencies of the  FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for each epoch (repetition) on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt, Is this possible?



B)  Another question I have is: for the Imaginary part of Coherence is not  necessary to compute the cross-spectrum with 'powandcsd', only the FFT,  but for the PLV, PPC or WPLI is that way too?



Many thanks in advanced,
Gabriel.
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From jan.schoffelen at donders.ru.nl  Tue May 21 08:24:48 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 21 May 2013 08:24:48 +0200
Subject: [FieldTrip] computing threshold for PLV
In-Reply-To: <CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
References: <BLU176-W366D48A475DDC9801925AEB9AD0@phx.gbl>
	<AE383F11-D866-413D-B91E-40F29FB0C7B2@psi.ucm.es>
	<BLU176-W44E63A8EA57DC39AB8DF9FB9AD0@phx.gbl>
	<CALEzDDXx_qkN4W6hOBXndTc0uVWXee1gWHW8syhnRdT-gu0xDw@mail.gmail.com>
Message-ID: <EF65D844-0661-44BA-8369-78933B7102A8@donders.ru.nl>

Hi all,

PLV is in principle a perfectly valid method to investigate synchrony, also in continuous data. Jörg (Hipp)'s paper introduces a connectivity metric that is insensitive to the effects of electromagnetic field spread, but it is a measure whose relationship to synchrony is hard to interpret; it quantifies amplitude envelope correlations after explicit removal of the instantaneous mixing, and does not quantify the consistency of phase relationships, as does PLV. If you are after interpreting the connectivity in terms of synchrony, you could look into using the imaginary part of coherency, or the weighted phase lag index, although neither of these methods are easy in their interpretation, either.

Best,
Jan-Mathijs

On May 19, 2013, at 1:55 AM, Sheraz Khan wrote:

> Most of the previois discussion targeted toward event related plv for continous data may be look at Hipp 2012 Nature Neuroscience orthogonal correlation paper
> 
> On May 18, 2013 3:42 PM, "Subramaniam Iyer" <eeguser at hotmail.com> wrote:
> Dear FT Experts
> 
> Thank you for your inputs. I should add here that I have continuous EEG data (so effectively single trial). The way I am computing PLV is by dividing my data into windows of 2 seconds each and computing PLV for each window and then I finally average the PLV values of all the windows.
> 
> So when we talk of shuffling trials, in my case should i consider each of 2 second window as a trial ? Sorry if this sounds stupid as I am new to this kind of analysis.
> 
> From: smoratti at psi.ucm.es
> Date: Sat, 18 May 2013 20:11:11 +0200
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] computing threshold for PLV
> 
> Dear Sheraz,
> 
> You might consult the following article: Lachaux, J. P. et al. 1999. Measuring Phase Synchrony in Brain Signal. Human Brain Mapping 8: 194-208. In principle you have to create surrogate data that represent the null hypothesis that there is no phase locking between your electrodes, sources, etc. Then you create hundreds or thousands of surrogate data sets and calculate each time you PLV. That way you create a distribution of your PLV values under the Null hypothesis. Then you check in what percentile your observed PLV lies (e. g. if its beyond the 95% percentile you would reject the Null hypothesis).
> 
> Hope that helps,
> 
> Stephan
> 
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> El 18/05/2013, a las 18:21, Subramaniam Iyer escribió:
> 
> Dear FT Experts,
> 
> I have calculated PLV for a set of EEG data from 5 different patients. Now I want to convert the PLV matrix of each patient into a binary matrix. For this I need a threshold PLV value below which I can assume the phase locking is zero.
> My question is, how do I compute this threshold. I know hard thresholding is one option ( for ex setting 0.1 or 0.2 as threshold), but I guess it is not a very good option.
> 
> Can somebody suggest a better and robust (statistical) way of determining the threshold ? 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From jm.horschig at donders.ru.nl  Tue May 21 08:31:22 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:31:22 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <9f89709b303dae2.51966cc4@upo.es>
References: <9f89709b303dae2.51966cc4@upo.es>
Message-ID: <519B14BA.9030908@donders.ru.nl>

Dear Gabriel,

> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?

No. You should think of coherence more as a measure for the consistency 
of the phase relation between channels across trials, so coherence is 
just not defined per trial,neither would it make sense to compute 
coherence for a single trial.

> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
I see some terminology issues here. Let me try to explain in a simple 
(aka least-mathematical I can think of) way:

For all these connectivity measures, we need the phase information from 
the Fourier transform (FFT) to compute the cross-spectral density matrix 
(CSD). The CSD can be regarded as the equivalent in the frequency domain 
to the covariance matrix in the time domain, thus it is a measures how a 
certain channels activity is co-modulated with another channels activity 
(for a particular frequency) - makes pretty much sense to make use of 
this when computing connectivity, right? :)
As you might know, a Fourier transform returns complex numbers, where 
the imaginary part of this number contains phase information. When 
calling ft_freqanalysis, you can decide if it shall only return the 
(squared) real part of the frequency spectrum (cfg.output='pow'), or 
instead the full CSD (cfg.output = 'powandcsd'). Alternatively, you can 
also let ft_freqanalysis return the raw Fourier coefficients 
(cfg.output='fourier'). From the Fourier coefficients, however, you can 
easily obtain the CSD or the power spectrum basically by multiplication 
the Fourier matrix with itself (transposed). All of these measures 
quantify the phase relation between channels across trials, and as phase 
information is coded in the imaginary part of the fourier output, thus 
for connectivityanalysis you need the CSD which can be obtained either 
by 'powandcsd' or by 'fourier'.

I hope that somehow clarifies your questions.

Best,
Jörn

On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> Dear Fieltrip experts,
>
> I have my continuous data imported to fieldtrip with matlab, I'm 
> looking for performing connectivity analysis between pairs of sensors, 
> I have succed as:
> data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59 channels 
> and 2000 samples
> data.label {59x1};
> data.time {1xNepochs};
>
> then, calculate only the FFT of all sensors as:
> cfg=[];
> cfg.output='fourier';
> cfg.method='mtmfft';
> cfg.taper='hanning';
> cfg.foilim=[8.5 9.5];
> cfg.tapsmofrq=0;
> cfg.trials='all';
> cfg.keeptrials='yes';
> cfg.channel='all';
> fourier=ft_freqanalysis(cfg, data)
> as output I get:
> dimord = 'rpttap_chan_freq'
> freq= [1x9]
> fourierspctrm=[7x59x9 double]
>
> Then compute the imaginary part of coherency as:
> cfg=[];
> cfg.method ='cohe';
> cfg.complex='imag';
> cfg.channelcbm={'all' 'all'};
> coher = ft_connectivityanalysis (cfg, fourier)
> as output get:
> dimord='chan_chan_freq';
> cohspctrm=[59x59x9 double];
> dof=7;
>
> I have two main questions:
>
> A) As you see, this makes an average over the epochs of each channel, 
> and not over the samples (which in this case are the 9 frequencies of 
> the FFT), And I would like to have the opposite, this is, to get the 
> imaginary part of coherence for each epoch (repetition) on all my 
> channels and not for each frequency, something like: chan_chan_rpt or 
> chancbm_rpt, Is this possible?
>
>
>
> B) Another question I have is: for the Imaginary part of Coherence is 
> not necessary to compute the cross-spectrum with 'powandcsd', only the 
> FFT, but for the PLV, PPC or WPLI is that way too?
>
>
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From jm.horschig at donders.ru.nl  Tue May 21 08:39:14 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 21 May 2013 08:39:14 +0200
Subject: [FieldTrip] a .mat file about meg data do preprocessing
In-Reply-To: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
References: <CADiddyXqEo+2Fc12er6TLTq=3xZAXSR6fx7zyQiuda+ykqEXSg@mail.gmail.com>
Message-ID: <519B1692.3080101@donders.ru.nl>

Dear Xiao,

Somehow your channel names seem to not be recognized by FieldTrip, and 
then it reverts to default channel names (chan001, chan002, ...). You 
will see that data_org.label will have those channel labels. 
Subsequently, you define in the cfg for timelockanalysis channel names 
that are not in your data (your channels are called chanXXX, not MEGXXXX 
now), and FieldTrip thus does not perform the operation on any channel.
I don't know much about EEGLAB and how it is integrated with FieldTrip - 
there should be an eeglab2fieldtrip function though in 
fieldtrip/external/eeglab. Maybe you can try this, or maybe someone else 
here knows why your channel labels do not get copied over to FieldTrip 
correctly.

Good luck :)
Best,
Jörn

On 5/18/2013 4:06 PM, ?? wrote:
> Dear all,
> I have a .mat file about meg data(102*98800,channel*time,channel is 
> 'MEG0111','MEG0121'.....'M*1' );
> Then I use eeglab read it,got .set file;I want use ft_timelockanalysis 
> then
> /cfg = [];
> cfg.dataset     = 'megalpha.set';
> cfg.grad=grad;
> data_org        = ft_preprocessing(cfg)/
> >grad =
>      chanori: [102x3 double]
>      chanpos: [102x3 double]
>     chantype: {102x1 cell}
>     chanunit: {102x1 cell}
>      coilori: [510x3 double]
>      coilpos: [510x3 double]
>        label: {102x1 cell}
>          tra: [102x510 double]
>         unit: 'cm'
> Warning: creating default channel names
> > In fileio\private\read_eeglabheader at 53
>   In ft_read_header at 572
>   In ft_preprocessing at 343
> processing channel { 'chan001' 'chan002' 'chan003' 'chan004' 'chan005' 
> 'chan006' 'chan007' 'chan008' 'chan009' 'chan010' 'chan011' 'chan012' 
> 'chan013' 'chan014' 'chan015' 'chan016' 'chan017' 'chan018' 'chan019' 
> 'chan020' 'chan021' 'chan022' 'chan023' 'chan024' 'chan025' 'chan026' 
> 'chan027' 'chan028' 'chan029' 'chan030' 'chan031' 'chan032' 'chan033' 
> 'chan034' 'chan035' 'chan036' 'chan037' 'chan038' 'chan039' 'chan040' 
> 'chan041' 'chan042' 'chan043' 'chan044' 'chan045' 'chan046' 'chan047' 
> 'chan048' 'chan049' 'chan050' 'chan051' 'chan052' 'chan053' 'chan054' 
> 'chan055' 'chan056' 'chan057' 'chan058' 'chan059' 'chan060' 'chan061' 
> 'chan062' 'chan063' 'chan064' 'chan065' 'chan066' 'chan067' 'chan068' 
> 'chan069' 'chan070' 'chan071' 'chan072' 'chan073' 'chan074' 'chan075' 
> 'chan076' 'chan077' 'chan078' 'chan079' 'chan080' 'chan081' 'chan082' 
> 'chan083' 'chan084' 'chan085' 'chan086' 'chan087' 'chan088' 'chan089' 
> 'chan090' 'chan091' 'chan092' 'chan093' 'chan094' 'chan095' 'chan096' 
> 'chan097' 'chan098' 'chan099' 'chan100' 'chan101' 'chan102' }
> reading and preprocessing
> reading and preprocessing trial 1 from 1
> data_org =
>            hdr: [1x1 struct]
>          label: {102x1 cell}
>           time: {[1x98800 double]}
>          trial: {[102x98800 double]}
>        fsample: 1037
>     sampleinfo: [1 98800]
>            cfg: [1x1 struct]
> /cfg                   = [];
> cfg.covariance        = 'yes';
> cfg.channel           = 'M*1';
> cfg.vartrllength      = 2;
> cfg.covariancewindow  = 'all';
> timelock              = ft_timelockanalysis(cfg, data_org);/
> timelock =
>        avg: [0x98800 double]
>        var: [0x98800 double]
>       time: [1x98800 double]
>        dof: [0x98800 double]
>      label: {0x1 cell}
>     dimord: 'chan_time'
>        cov: []
>        cfg: [1x1 struct]
> there is no error displyed in command window but the timlock is empty,why?
> thanks for you help,
> best,
> xiao
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From zriouil.imane at gmail.com  Tue May 21 10:18:58 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Tue, 21 May 2013 10:18:58 +0200
Subject: [FieldTrip] ft_read_event
Message-ID: <CABu=cRdhOYn=oSy0cHADOvqgWnCR3ui5cLwy9FUkpVz7KGKK_A@mail.gmail.com>

Hello,

i have a problems in ft_read_event. if you help me please


I try to follow all instructions on the tutorial: 'Preprocessing and
analysis of spike and local field potential data'

>> spike=ft_read_spike(filename)

spike =

        label: {'Elec_1_Neuron_1'  'Elec_2_Neuron_1'  'Elec_3_Neuron_1'}
    timestamp: {[1x20246 int32]  [1x9126 int32]  [1x74291 int32]}
     waveform: {[0x20246 double]  [0x9126 double]  [0x74291 double]}
         unit: {[1x20246 double]  [1x9126 double]  [1x74291 double]}
          hdr: [1x1 struct]
       dimord: '{chan}_lead_time_spike'

>> header=ft_read_header(filename)

header =

                nChans: 94
                    Fs: 781.2500
              nSamples: 862310
               nTrials: 1
           nSamplesPre: 0
                 label: {94x1 cell}
        FirstTimeStamp: 70433310
    TimeStampPerSample: 32
                  orig: [1x1 struct]
              chantype: {94x1 cell}
              chanunit: {94x1 cell}

>>cfg=[];
cfg.dataset=filename;
cfg.trialfun='trialfun_stimon_samples';
cfg=ft_definetrial(cfg)

evaluating trialfunction 'trialfun_stimon_samples'

??? Error using ==> fseek
Not enough input arguments.

Error in ==> read_nex_event at 49
status = fseek(fid,hdr.varheader(mrkvarnum).offset,'bof');

Error in ==> ft_read_event at 1528
    event = read_nex_event(filename);

Error in ==> trialfun_stimon_samples at 3
event = ft_read_event(cfg.dataset);

Error in ==> ft_definetrial at 157
    trl   = feval(cfg.trialfun, cfg);
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From ggonesc at upo.es  Tue May 21 17:52:21 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Tue, 21 May 2013 17:52:21 +0200
Subject: [FieldTrip] problem in connectivityanalysis
In-Reply-To: <519B14BA.9030908@donders.ru.nl>
References: <9f89709b303dae2.51966cc4@upo.es> <519B14BA.9030908@donders.ru.nl>
Message-ID: <1348f6433edc26f9.519bb455@upo.es>

Thank you so much for your answer Jörn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from  -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
 [0.9323  0.3679  0.8629  1.6436  0.6404  1.8782  0.1139] 
val(:,:,1,2)
 [0.8509-0.1555i  0.2507-0.1066i  0.8173-0.0290i  1.4328-0.2427i  0.5457-0.0500i  1.6505-0.0161i  0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
 [1  1  1  1  1  1  1] 
val(:,:,1,2)
 [0.9694-0.2133i  0.7011-0.3564i  0.9951-0.0104i  0.9014-0.3481i  0.9781-0.0819i  0.9982-0.0046i  0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        Jörn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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From antony.passaro at gmail.com  Tue May 21 18:13:28 2013
From: antony.passaro at gmail.com (Antony Passaro)
Date: Tue, 21 May 2013 12:13:28 -0400
Subject: [FieldTrip] Subject-level Statistics on mvar connectivity measures
Message-ID: <CAB8wAYS-F9FiW72edUz_s84dSuobXXA6nEwZYwWEhW5bL=ggkg@mail.gmail.com>

Hi everyone,

I have had some success processing the subject-level differences between
two conditions for phase-based measures such as coherence and plv but I was
wondering what the approach would be for the directed or mvar-based
measures such as dtf, granger, or pdc? Since there are no trials to shuffle
as you normally would for the phase-based connectivity measures, what would
be the optimal statistical approach? I thought about shuffling the trials
and recomputing the mvar over and over again for each condition as a
simulation but this doesn't seem practical as it would be too
computationally intensive.

Thank you,
-Tony
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From 13681530640 at 139.com  Wed May 22 04:20:45 2013
From: 13681530640 at 139.com (WangJing)
Date: Wed, 22 May 2013 10:20:45 +0800 (CST)
Subject: [FieldTrip] question About head model
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>




Hi


I am a freshman about field trip.


I am trying to build the forward model. but my mri data is different from the data in the tutorial. So I don't know how to bulid the head model. I use the date which is from the paper "Open Database of Epileptic EEG with MRI and Postoperational Assessment of Foci—a Real World Verification for the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans with morphologic substrate of the epilepsy (mostly cortical dysplasias, dysplastic tumors etc.). In some cases there is also a scan with the gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T scanner. The data is stored in the Digital Imaging and Communications in Medicine (DICOM) format. The name of the scan’s folder indicates its weighting.The scans have the following resolutions: T1: 512 × 512 pixels, pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels, pixel spacing 0.9375 mm,slice thickness 2.5 mm.


In the tutorial,the mri data stored in only one file, while the data which I used have many files, I don't know how to process. who can help me,Thanks1





Thanks very much!


Best Reagards


Jing Wang















--------------------------------------------------------------------------------



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To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-21 23:59:18
Subject：fieldtrip Digest, Vol 30, Issue 29

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Today's Topics:

   1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)


----------------------------------------------------------------------

Message: 1
Date: Tue, 21 May 2013 17:52:21 +0200
From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] problem in connectivityanalysis
Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
Content-Type: text/plain; charset="iso-8859-1"

Thank you so much for your answer J?rn,

Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.

Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.


I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g: 
data.dimord = 'rpt_rpt_chan_chan_freq'
ans size(data.crsspctrm) = [1 7 59 59]; 
So, both are apparently the same, but the data inside this matrices is different,

for example, when calculating the ImC the first 7 columns for the first two rows are: 
val(:,:,1,1)
?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139] 
val(:,:,1,2)
?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]

while when calculating the PLV are:
val(:,:,1,1)
?[1? 1? 1? 1? 1? 1? 1] 
val(:,:,1,2)
?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]


I'm pretty sure I'm doing something wrong here, but I don't really have a clue, 

If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.




On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?


Many thanks in advanced,
Gabriel.




----- Mensaje original -----
De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
Fecha: Martes, 21 de Mayo de 2013, 9:03 am
Asunto: Re: [FieldTrip] problem in connectivityanalysis
A: FieldTrip discussion list <fieldtrip at science.ru.nl>


              

     
> Dear Gabriel,
       > 
       > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
                        > 
>        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
       > 
       > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
       > 
>        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'. 
       > 
>        I hope that somehow clarifies your questions.
       > 
>        Best,
>        J?rn
       > 
>        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
          > Dear Fieltrip experts,
         > 
>          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
>          data.label {59x1};
>          data.time {1xNepochs};
         > 
>          then, calculate only the FFT of all sensors as:
>          cfg=[];
>          cfg.output='fourier';
>          cfg.method='mtmfft';
>          cfg.taper='hanning';
>          cfg.foilim=[8.5 9.5];
>          cfg.tapsmofrq=0;
>          cfg.trials='all';
>          cfg.keeptrials='yes';
>          cfg.channel='all';
>          fourier=ft_freqanalysis(cfg, data)
>          as output I get:
>          dimord = 'rpttap_chan_freq'
>          freq= [1x9]
>          fourierspctrm=[7x59x9 double]
         > 
>          Then compute the imaginary part of coherency as:
           > cfg=[];
             > cfg.method ='cohe';
             > cfg.complex='imag';
               > cfg.channelcbm={'all'               'all'};
             > coher = ft_connectivityanalysis (cfg, fourier)
         > as output get: 
           > dimord='chan_chan_freq';
             > cohspctrm=[59x59x9 double];
             > dof=7;
           > 
         > I have two main questions:
         > 
         > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
                 > 
                 > 
                 > 
                 > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
                 > 
                 > 
                 > 
                 > 
>                  Many thanks in advanced,
                 > Gabriel.
                 > 
                      > 
              > 
       > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip          
     > 
     > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web: http://www.ru.nl/donders >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

<font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>


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------------------------------

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 30, Issue 29
*****************************************

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From johanna.zumer at donders.ru.nl  Wed May 22 09:30:17 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Wed, 22 May 2013 09:30:17 +0200
Subject: [FieldTrip] question About head model
In-Reply-To: <2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
References: <mailman.163.1369151958.1286.fieldtrip@science.ru.nl>
	<2b26519c1b85ee0-0001c.Richmail.00022806623245833658@139.com>
Message-ID: <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w@mail.gmail.com>

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci—a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan’s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 × 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 × 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-21 23:59:18
> Subject：fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
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>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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> fieldtrip mailing list
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> End of fieldtrip Digest, Vol 30, Issue 29
> *****************************************
>
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From mushfa.yousuf at googlemail.com  Wed May 22 12:13:56 2013
From: mushfa.yousuf at googlemail.com (Mushfa Yousuf)
Date: Wed, 22 May 2013 12:13:56 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <5190AEAA.3020301@donders.ru.nl>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
Message-ID: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>

Hello Jörn;

I have calculated an indiviual leadfield for both EEG and MEG. The
structure of EEg and MEG shows the following variable

grid_meg =

        xgrid: [1x20 double]
        ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
        zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
          dim: [20 17 16]
          pos: [5440x3 double]
         unit: 'cm'
       inside: [1x3177 double]
      outside: [1x2263 double]
          cfg: [1x1 struct]
    leadfield: {1x5440 cell}


grid_eeg =

        xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
        ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
        zgrid: [2 3 4 5 6 7 8 9 10 11]
          dim: [16 13 10]
          pos: [2080x3 double]
         unit: 'cm'
       inside: [1x1331 double]
      outside: [1x749 double]
          cfg: [1x1 struct]
    leadfield: {1x2080 cell}


Can you please give me a rough idea that how to concatenate the variables
from both structure ?


Thank you

Regards ;

Mushfa Yousuf


On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Mushfa,
>
> I think you have to compute two leadfield matrices, one for EEG (elec) and
> one for MEG (grad), and then concatenate these (and make sure that the
> order of sensors won't get mixed up anywhere, because  sourceanalysis just
> expects the leadfield matrix to be ordered like your data. If that's not
> the case, you either encounter the previous error you described or (if the
> number of channels matches, but order is mixed up) it will just return
> wrong source estimated activity.
>
> Best,
> Jörn
>
>
> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>
> Hello;
>
>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
> of 'elec' while calculating the Leadfield.
>
>  Actually I am trying to calculate Combined source reconstruction from
> both EEG and MEG sensors.
>
>  Do you have any idea, how to define both elec and grad definition  while
> calculating first forward then inverse solution.
>
>  Because in a fieldtrip either you can defined elec or grad at one time.
>
>
>  Regards;
>
>
>  Mushfa Yousuf
>
>  Neurozentrum,
> Universitätsklinikum Schleswig-Holstein,
> Campus Kiel (UKSH), Deutschland
>
>
> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>
>> Hi Mushfa,
>>
>>  My guess is that the channels that have you used to compute .csdspctrm
>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>> freqPost.label, does that solve it?
>>
>>  Cheers,
>> Johanna
>>
>>
>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>
>>>   Hello Fieldtrippers,
>>>
>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>
>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>> lead field successfully.
>>>
>>>  For the inverse solution using 'dics' method, I wrote the following
>>> syntax
>>>
>>>
>>>
>>>
>>>
>>>   cfg              = [];
>>>   cfg.method       = 'dics';
>>>  cfg.frequency    = 130;
>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>  cfg.grid         = grid;
>>>  cfg.vol          = vol;
>>>
>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>  and I have received the following error:
>>>
>>>
>>>  ??? Error using ==> mtimes
>>> Inner matrix dimensions must agree.
>>>
>>>  Error in ==> beamformer_dics at 314
>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>         leadfield
>>>
>>>  Error in ==> ft_sourceanalysis at 595
>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>
>>>  Error in ==> newCode at 214
>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>
>>>
>>>
>>>
>>>  Any help would be appreciated.
>>>
>>>
>>>  Regards;
>>>
>>>
>>>  Mushfa Yousuf
>>>
>>>  Neurozentrum,
>>> Universitätsklinikum Schleswig-Holstein,
>>> Campus Kiel (UKSH), Deutschland
>>>
>>>
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From ggonesc at upo.es  Wed May 22 19:36:08 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Wed, 22 May 2013 19:36:08 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <596f90904ed40d3b.519d1e28@upo.es>

Dear Fieldtrip experts,

I finally understood how fieltrip computes the plv, so, my last e-mail has no sense now. Given say this, I have one question:

I've followed the fieltrip implementation to compute the PLV, and found that it takes the CSD, and normalizes it for the amplitude of the replicates, this is to divide the csd by the absolute of the same csd, then makes an average of the normalized csd's, to finally take the absolute of the average-normalized-csd as the PLV.  I think it can be summarized to something like, PLV = |E( csd/abs(csd) )|

I do not see the similarity with the clasical formula that appears in the papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the cross-spectrum, and E|.| is the expected value; I cannot find the relationship between the implementation on fieltrip of the PLV and the formula on the papers.

Can anyone explain to me the relationship between the two approaches? or tell me the paper where it is explained?

Many thanks in advanced,
Gabriel

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From 13681530640 at 139.com  Thu May 23 03:38:08 2013
From: 13681530640 at 139.com (WangJing)
Date: Thu, 23 May 2013 09:38:08 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
Message-ID: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>


Dear Johanna,


 


    Thank you for your suggestion. 


    1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is t1_vibe_traGAD-5. which one is best?
    2.when I convert MRI from DICOM into CTF format,the vitamin E marker didn't be found. what can I do?


 


Best Regards,


Jing Wang














--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-22 15:33:13
Subject：fieldtrip Digest, Vol 30, Issue 31

Send fieldtrip mailing list submissions to
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To subscribe or unsubscribe via the World Wide Web, visit
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or, via email, send a message with subject or body 'help' to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of fieldtrip digest..."


Today's Topics:

   1. Re: question About head model (Johanna Zumer)


----------------------------------------------------------------------

Message: 1
Date: Wed, 22 May 2013 09:30:17 +0200
From: Johanna Zumer <johanna.zumer at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] question About head model
Message-ID:
<CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Jing,

It is best to use the T1 MRI rather than the other scans.   To open a DICOM
format file, you can try one of these options:

% read the DICOM files
mri = ft_read_mri('single_file_of_DICOM_series.IMA');
 % or use a graphical file selection[f, p] = uigetfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html>('*');
mri = ft_read_mri(fullfile
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html>(p,
f));


I copied the above from documentation on the FieldTrip wiki:
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format

Then you can save the 'mri' into a *.mat file for future use with FieldTrip.

Best regards,
Johanna


2013/5/22 WangJing <13681530640 at 139.com>

> Hi
> I am a freshman about field trip.
> I am trying to build the forward model. but my mri data is different from
> the data in the tutorial. So I don't know how to bulid the head model. I
> use the date which is from the paper "Open Database of Epileptic EEG with
> MRI and Postoperational Assessment of Foci?a Real World Verification for
> the EEG Inverse Solutions",http://eeg.pl/epi. MRI recordings containing a
> T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> dysplastic tumors etc.). In some cases there is also a scan with the
> gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> scanner. The data is stored in the Digital Imaging and Communications in
> Medicine (DICOM) format. The name of the scan?s folder indicates its
> weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> In the tutorial,the mri data stored in only one file, while the data which
> I used have many files, I don't know how to process. who can help me,Thanks1
>  Thanks very much!
> Best Reagards
> Jing Wang
>
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> To?fieldtrip<fieldtrip at science.ru.nl>
> Date?2013-05-21 23:59:18
> Subject?fieldtrip Digest, Vol 30, Issue 29
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
> fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 May 2013 17:52:21 +0200
> From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] problem in connectivityanalysis
> Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thank you so much for your answer J?rn,
>
>
> Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
>
>
> Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
>
>
>
> I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> data.dimord = 'rpt_rpt_chan_chan_freq'
> ans size(data.crsspctrm) = [1 7 59 59];
>
> So, both are apparently the same, but the data inside this matrices is different,
>
>
> for example, when calculating the ImC the first 7 columns for the first two rows are:
> val(:,:,1,1)
> ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> val(:,:,1,2)
>
> ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
>
> while when calculating the PLV are:
> val(:,:,1,1)
> ?[1? 1? 1? 1? 1? 1? 1]
> val(:,:,1,2)
>
> ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
>
>
>
> I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
>
>
> If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
>
>
>
>
>
> On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
>
>
> Many thanks in advanced,
> Gabriel.
>
>
>
>
> ----- Mensaje original -----
> De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> Asunto: Re: [FieldTrip] problem in connectivityanalysis
> A: FieldTrip discussion list <fieldtrip at science.ru.nl>
>
>
>
>
>
> > Dear Gabriel,
>        >
>
>        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
>                         >
>
> >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
>        >
>
>        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
>        >
>
> >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
>
> >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
>        >
> >        I hope that somehow clarifies your questions.
>        >
> >        Best,
> >        J?rn
>        >
> >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
>           > Dear Fieltrip experts,
>          >
>
> >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
>
> >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> >          data.label {59x1};
> >          data.time {1xNepochs};
>          >
> >          then, calculate only the FFT of all sensors as:
> >          cfg=[];
> >          cfg.output='fourier';
> >          cfg.method='mtmfft';
> >          cfg.taper='hanning';
> >          cfg.foilim=[8.5 9.5];
> >          cfg.tapsmofrq=0;
> >          cfg.trials='all';
> >          cfg.keeptrials='yes';
> >          cfg.channel='all';
> >          fourier=ft_freqanalysis(cfg, data)
> >          as output I get:
> >          dimord = 'rpttap_chan_freq'
> >          freq= [1x9]
> >          fourierspctrm=[7x59x9 double]
>          >
> >          Then compute the imaginary part of coherency as:
>            > cfg=[];
>              > cfg.method ='cohe';
>              > cfg.complex='imag';
>                > cfg.channelcbm={'all'               'all'};
>              > coher = ft_connectivityanalysis (cfg, fourier)
>          > as output get:
>            > dimord='chan_chan_freq';
>              > cohspctrm=[59x59x9 double];
>              > dof=7;
>            >
>          > I have two main questions:
>          >
>
>          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
>                  >
>                  >
>                  >
>
>                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
>                  >
>                  >
>                  >
>                  >
> >                  Many thanks in advanced,
>                  > Gabriel.
>                  >
>                       >
>               >
>
>        > _______________________________________________ > fieldtrip mailing list >
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>      >
>
>      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> http://www.ru.nl/donders
>  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
>
>
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From eelke.spaak at donders.ru.nl  Thu May 23 10:09:17 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Thu, 23 May 2013 10:09:17 +0200
Subject: [FieldTrip] connectivity problem
In-Reply-To: <596f90904ed40d3b.519d1e28@upo.es>
References: <596f90904ed40d3b.519d1e28@upo.es>
Message-ID: <CABPNLUpec0sp=o5TWDKcU-PgQqGa_ROVSQ73uWWJbkwMHtEotA@mail.gmail.com>

Dear Gabriel,

If I am not mistaken, the classical formula in Lachaux et al. (1999)
Human Brain Mapping is PLV = 1/N * | sum(exp(i * theta(t,n))) | . This
is almost the same as the formula you mention, except, importantly,
that theta is the phase difference between two signals, so the angle
of the CSD, and *not* the imaginary part.

Note furthermore that 1 * exp(i*angle(z)) is equal to z/abs(z) for any
complex z, and you see that the implementation computes the classical
formula.

Hope this helps,
Best,
Eelke

On 22 May 2013 19:36, Gabriel Gonzalez Escamilla <ggonesc at upo.es> wrote:
> Dear Fieldtrip experts,
>
> I finally understood how fieltrip computes the plv, so, my last e-mail has
> no sense now. Given say this, I have one question:
>
> I've followed the fieltrip implementation to compute the PLV, and found that
> it takes the CSD, and normalizes it for the amplitude of the replicates,
> this is to divide the csd by the absolute of the same csd, then makes an
> average of the normalized csd's, to finally take the absolute of the
> average-normalized-csd as the PLV.  I think it can be summarized to
> something like, PLV = |E( csd/abs(csd) )|
>
> I do not see the similarity with the clasical formula that appears in the
> papers PLV=| E{exp(i*I{X})} |, where I{X} is the imaginary of the
> cross-spectrum, and E|.| is the expected value; I cannot find the
> relationship between the implementation on fieltrip of the PLV and the
> formula on the papers.
>
> Can anyone explain to me the relationship between the two approaches? or
> tell me the paper where it is explained?
>
> Many thanks in advanced,
> Gabriel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jeremiemattout at yahoo.fr  Thu May 23 10:19:09 2013
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Thu, 23 May 2013 09:19:09 +0100 (BST)
Subject: [FieldTrip] DCM for fMRI and EEG/MEG course - Seattle June 2013
Message-ID: <1369297149.1995.YahooMailNeo@web133005.mail.ir2.yahoo.com>

Dear Colleagues, We are pleased to announce DCM for fMRI and MEG/EEG, an intermediate-level, 3-day workshop designed for investigators having familiarity with the fundamental principles of fMRI or MEG/EEG data acquisition and analysis.. It will be held at the University of Washington in Seattle, WA from JUN 21-23, 2013, immediately following the OHBM 2013 meeting. This course will bring together investigators interested in using quantitative biophysical models to identify brain connectivity and dynamics using the tools of imaging neuroscience, including fMRI, EEG/MEG, and LFP. Presentations will include:
overviews of brain connectivity methods and models
descriptions of specifics of DCM for fMRI, EEG/MEG and LFP data
explanations of Bayesian analysis at both single-subject and group levels
explorations of DCM experimental design and other advanced issues
Each afternoon will include a laboratory session, in which participants will gather in small groups to work with the faculty through the stages of analyzing data from example experiments. Further details can be found at: http://www.neurometrika.org/DCM2013 Kind Regards, Tom Zeffiro, Jean Daunizeau & Jeremie Mattout
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From marianapbranco1 at gmail.com  Thu May 23 10:25:45 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 10:25:45 +0200
Subject: [FieldTrip] Online preprocessing
Message-ID: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>

Hello,

I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. 
My questions are:
1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?

I am sorry for all the questions.
Regards,

Mariana Branco


From jm.horschig at donders.ru.nl  Thu May 23 11:37:59 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 11:37:59 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
Message-ID: <519DE377.1020805@donders.ru.nl>

Hi Mariana,

On 5/23/2013 10:25 AM, Mariana Branco wrote:
> Hello,
>
> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
> My questions are:
> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?

no, you should use ft_read_data directly. The way to go is to check the 
header of your buffer for new events using ft_read_event. Upon detection 
of a relevant trigger, you need to use the returned event sample to 
compute your beginning and endsample manually (this is what 
ft_definetrial, or more precisely, your trialfun, usually does).  Then 
you can use ft_read_data to read data from the buffer into memory. 
ft_read_data returns a datamatrix that can be used to create your 
data.trial field. Also, you need to manually create the rest of the 
data-structure.
> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
It is definitely possible, once you converted the matrix to a regular 
fieldtrip structure. However, since it is about speed in online 
processing, you can think about using low-level functions of FieldTrip 
directly. Note that for resampling, you can also set up the shared 
memory (eg. acq2ftx) such that is downsamples right from the start.

> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
Do not use Welch's method, use another function. I don't know about this 
particular example function, but I think you would greatly benefit from 
finding out where the error is yourself. Note that online streaming od 
data *is* complicated and requires *you* to have knowledge about this.
> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
It should be an example, yes. Usually, there should be, as explained 
above, some ft_read_event statement to read the trigger value(s). In 
that particular example, the trialfun is used rather than ft_read_data 
directly, but trialfun is basically a wrapper around ft_read_data. Also, 
in that example a bunch of trials is read in, not just one. The thing 
you need to do to adjust this is to filter out the event structure such 
that only in case of the trigger of interest some data processing is 
done (you can use ft_filter_event for this).

My best advise for you is to read all (most) example functions and 
adjust them so that they run in your lab. Then sketch a flow diagram how 
triggers/data will be sent and read, try to implement this yourself (by 
copy&pasting relevant parts out of the example functions). If you have 
specific questions, feel free to always ask, but as this stage (please 
excuse my bluntnessI think you do not really know what needs to be done. 
I could write a lot about this, but I think you will benefit more if you 
first try yourself (especially because I do not know how your lab is set 
up and how things needs to be adjusted). But, as just said, feel free to 
write again when you have other questions.

Good luck!
Best,
Jörn

>
> I am sorry for all the questions.

No problem, no  way to know everything :)

> Regards,
>
> Mariana Branco
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From marianapbranco1 at gmail.com  Thu May 23 11:57:27 2013
From: marianapbranco1 at gmail.com (Mariana Branco)
Date: Thu, 23 May 2013 11:57:27 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <519DE377.1020805@donders.ru.nl>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
Message-ID: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>

Hi Jörn,

Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.

Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. 
In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?

Thank you again for all the advices, I will definitely pose more question in the future.

Mariana Branco

On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:

> Hi Mariana,
> 
> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>> Hello,
>> 
>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>> My questions are:
>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
> 
> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
> 
>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
> 
> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
> 
> Good luck!
> Best,
> Jörn
> 
>> 
>> I am sorry for all the questions.
> 
> No problem, no  way to know everything :)
> 
>> Regards,
>> 
>> Mariana Branco
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
> 
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
> 
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
> 
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From jm.horschig at donders.ru.nl  Thu May 23 12:08:33 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Thu, 23 May 2013 12:08:33 +0200
Subject: [FieldTrip] Online preprocessing
In-Reply-To: <B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com>
	<519DE377.1020805@donders.ru.nl>
	<B6CB7287-B3BB-43F5-81CB-85BD260E9CD7@gmail.com>
Message-ID: <519DEAA1.5030402@donders.ru.nl>

Hi Mariana,

ft_preprocessing demeans by the whole time window, in your 0s to 5s. The 
baseline window you specify depends on the time axis itself, if it goes 
from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, 
then you need to define [-3 0]. Time is relative :)
Also, please check ft_timelockbaseline. But such a simple thing as 
subtracting a number from a matrix can also easily be done without 
relying on a fieldtrip function :)

Best,
Jörn

On 5/23/2013 11:57 AM, Mariana Branco wrote:
> Hi Jörn,
>
> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do.
>
> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of  approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial.
> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong?
>
> Thank you again for all the advices, I will definitely pose more question in the future.
>
> Mariana Branco
>
> On 23 May 2013, at 11:37, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
>
>> Hi Mariana,
>>
>> On 5/23/2013 10:25 AM, Mariana Branco wrote:
>>> Hello,
>>>
>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file.
>>> My questions are:
>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time?
>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does).  Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure.
>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure?
>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start.
>>
>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this?
>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this.
>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing?
>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this).
>>
>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions.
>>
>> Good luck!
>> Best,
>> Jörn
>>
>>> I am sorry for all the questions.
>> No problem, no  way to know everything :)
>>
>>> Regards,
>>>
>>> Mariana Branco
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands



From andmib at gmail.com  Thu May 23 16:29:07 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Thu, 23 May 2013 10:29:07 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
Message-ID: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>

Hello all,

I am new to FieldTrip, so this is a very basic question I was hoping
someone might know an answer to.

I am using ft_read_data to read the first EPI volume after dummy scans are
thrown out. I want to write this volume to a .nii file to my disk. For some
reason, I am unable to figure out the correct structure that ft_volumewrite
wants. Using the output from ft_read_data ('dat') does not seem to work.
Does anybody have any suggestions?

[ For a longer explanation of exactly what I am aiming to do, in case you
have any suggestions: I have ROI that is defined in Talairach space. This
is the ROI I would like to pull my real-time data from for each subject in
my study. To do this, I plan to register a talairach template brain to
individual subject-space, and then apply that transformation to my ROI so
that it is in subject space. I was going to simply write out the subject's
EPI to an .nii file, and then run SPM's co-registration step which allows
for a 'child dataset' to be set (my ROI), with the source file being the
template, and the reference being the individual ROI].

Thanks
Andrew
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From ggonesc at upo.es  Thu May 23 16:46:53 2013
From: ggonesc at upo.es (Gabriel Gonzalez Escamilla)
Date: Thu, 23 May 2013 16:46:53 +0200
Subject: [FieldTrip] connectivity problem
Message-ID: <cade69b25ef8089f.519e47fd@upo.es>

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From johanna.zumer at donders.ru.nl  Fri May 24 10:21:24 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Fri, 24 May 2013 10:21:24 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
Message-ID: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>

Dear Andrew,

To read EPI (MRI) data, you should use ft_read_mri instead.   Then
hopefully the format will match what ft_volumewrite wants.

Cheers,
Johanna


2013/5/23 Andrew Brooks <andmib at gmail.com>

> Hello all,
>
> I am new to FieldTrip, so this is a very basic question I was hoping
> someone might know an answer to.
>
> I am using ft_read_data to read the first EPI volume after dummy scans are
> thrown out. I want to write this volume to a .nii file to my disk. For some
> reason, I am unable to figure out the correct structure that ft_volumewrite
> wants. Using the output from ft_read_data ('dat') does not seem to work.
> Does anybody have any suggestions?
>
> [ For a longer explanation of exactly what I am aiming to do, in case you
> have any suggestions: I have ROI that is defined in Talairach space. This
> is the ROI I would like to pull my real-time data from for each subject in
> my study. To do this, I plan to register a talairach template brain to
> individual subject-space, and then apply that transformation to my ROI so
> that it is in subject space. I was going to simply write out the subject's
> EPI to an .nii file, and then run SPM's co-registration step which allows
> for a 'child dataset' to be set (my ROI), with the source file being the
> template, and the reference being the individual ROI].
>
> Thanks
> Andrew
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From andmib at gmail.com  Fri May 24 15:15:09 2013
From: andmib at gmail.com (Andrew Brooks)
Date: Fri, 24 May 2013 09:15:09 -0400
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
Message-ID: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>

Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
pull a single volume from the buffer using ft_read_data, and then write it
out to a nifti file using ft_volumewrite, but ft_read_data does not output
the volume in a structure that ft_volumewrite wants.


On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer
<johanna.zumer at donders.ru.nl>wrote:

> Dear Andrew,
>
> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
> hopefully the format will match what ft_volumewrite wants.
>
> Cheers,
> Johanna
>
>
> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>
>> Hello all,
>>
>> I am new to FieldTrip, so this is a very basic question I was hoping
>> someone might know an answer to.
>>
>> I am using ft_read_data to read the first EPI volume after dummy scans
>> are thrown out. I want to write this volume to a .nii file to my disk. For
>> some reason, I am unable to figure out the correct structure that
>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>> seem to work. Does anybody have any suggestions?
>>
>> [ For a longer explanation of exactly what I am aiming to do, in case you
>> have any suggestions: I have ROI that is defined in Talairach space. This
>> is the ROI I would like to pull my real-time data from for each subject in
>> my study. To do this, I plan to register a talairach template brain to
>> individual subject-space, and then apply that transformation to my ROI so
>> that it is in subject space. I was going to simply write out the subject's
>> EPI to an .nii file, and then run SPM's co-registration step which allows
>> for a 'child dataset' to be set (my ROI), with the source file being the
>> template, and the reference being the individual ROI].
>>
>> Thanks
>> Andrew
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From johanna.zumer at gmail.com  Fri May 24 16:29:00 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Fri, 24 May 2013 16:29:00 +0200
Subject: [FieldTrip] Format for ft_volumewrite?
In-Reply-To: <CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
References: <CALJPz69PXzGtM0gdKVXbO9XiTFmRc4yfNe+1koPQpQqieE_H-Q@mail.gmail.com>
	<CAL4kA6crn6Y2B_NjXW5AY5edtP2JDjp+dKf9a4PDSi3g9h_86A@mail.gmail.com>
	<CALJPz6_ceN=x6XTaQnU3ij3XTXWzG7BNUxXRVaqM9+qeLSXFxQ@mail.gmail.com>
Message-ID: <CAL4kA6eCbXBJAFL9q5COz_jqgqGqT2FN8wUP3n3kOqiyK7sh0w@mail.gmail.com>

I'm not familiar with the buffer, but if you can read in your data
successfully, then to convert it to the structure that ft_volumewrite
wants, you can get some information inside ft_datatype_volume for what are
required or optional fields.




2013/5/24 Andrew Brooks <andmib at gmail.com>

> Thanks Johanna. Ft_read_mri only pulls from a file, correct? I'm trying to
> pull a single volume from the buffer using ft_read_data, and then write it
> out to a nifti file using ft_volumewrite, but ft_read_data does not output
> the volume in a structure that ft_volumewrite wants.
>
>
> On Fri, May 24, 2013 at 4:21 AM, Johanna Zumer <
> johanna.zumer at donders.ru.nl> wrote:
>
>> Dear Andrew,
>>
>> To read EPI (MRI) data, you should use ft_read_mri instead.   Then
>> hopefully the format will match what ft_volumewrite wants.
>>
>> Cheers,
>> Johanna
>>
>>
>> 2013/5/23 Andrew Brooks <andmib at gmail.com>
>>
>>>  Hello all,
>>>
>>> I am new to FieldTrip, so this is a very basic question I was hoping
>>> someone might know an answer to.
>>>
>>> I am using ft_read_data to read the first EPI volume after dummy scans
>>> are thrown out. I want to write this volume to a .nii file to my disk. For
>>> some reason, I am unable to figure out the correct structure that
>>> ft_volumewrite wants. Using the output from ft_read_data ('dat') does not
>>> seem to work. Does anybody have any suggestions?
>>>
>>> [ For a longer explanation of exactly what I am aiming to do, in case
>>> you have any suggestions: I have ROI that is defined in Talairach space.
>>> This is the ROI I would like to pull my real-time data from for each
>>> subject in my study. To do this, I plan to register a talairach template
>>> brain to individual subject-space, and then apply that transformation to my
>>> ROI so that it is in subject space. I was going to simply write out the
>>> subject's EPI to an .nii file, and then run SPM's co-registration step
>>> which allows for a 'child dataset' to be set (my ROI), with the source file
>>> being the template, and the reference being the individual ROI].
>>>
>>> Thanks
>>> Andrew
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From politzerahless at gmail.com  Sat May 25 15:11:18 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 25 May 2013 08:11:18 -0500
Subject: [FieldTrip] Sourcespace and volume conductor misaligned
Message-ID: <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=fFk0ouR0wzA@mail.gmail.com>

Hello all,

I am going through the workflow at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
the volume conduction model using ft_prepare_headmodel(), I noticed that
although the volume conduction model and sourcespace have the same
orientation and overall size/shape (after I converted the volume conduction
model to cm, which wasn't in the tutorial but my original model came out in
mm), they don't quite line up, as you can see in this figure:

http://i.imgur.com/mGEtLOa.png

I did interactively re-align the data to CTF (twice--in step 2 of
"Preprocessing of the anatomical MRI" and in step 4 of "Source model")
using fiducials, and to Talairach (step 5 of "Preprocessing of the
anatomical data"), so I'm not sure how it ended up this way. The code I've
used at each step is basically the same as that in the tutorial.

Is there any way to line up my volume conduction model and sourcespace now,
without going back and re-running most of the workflow?

Best,
Steve

-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From johanna.zumer at donders.ru.nl  Sat May 25 20:54:59 2013
From: johanna.zumer at donders.ru.nl (Johanna Zumer)
Date: Sat, 25 May 2013 20:54:59 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
In-Reply-To: <2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
References: <mailman.205.1369207993.1286.fieldtrip@science.ru.nl>
	<2b26519d65c97b6-0000c.Richmail.00022826124215434628@139.com>
Message-ID: <CAL4kA6eTL_TwECF62W-OoWY=Y1mpBR6QoOLh+ug8AcXNbVxQ1A@mail.gmail.com>

Dear Jing,

1.  Every MRI scanner is different, so I'm not familiar with that naming
scheme, but it seems the 'GAD' at the end of the file name indicates that
was with the Gadolinium contrast agent, so I would suggest to not use that,
but instead use the first (plain) T1.

2. I'm not sure what to suggest.  I assume you can see the vitamin E marker
clearly when viewing the DICOM file?   Is the issue that some slices are
missing in the conversion, or that the contrast on the image is not the
same?  or right/left flipped?

Best,
Johanna


2013/5/23 WangJing <13681530640 at 139.com>

> Dear Johanna,
>
>     Thank you for your suggestion.
>     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> t1_vibe_traGAD-5. which one is best?
>     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> didn't be found. what can I do?
>
> Best Regards,
> Jing Wang
>
>
>
>
> ------------------------------
> ----The following is the content of the forwarded email----
> From：fieldtrip-request<fieldtrip-request at science.ru.nl>
> To：fieldtrip<fieldtrip at science.ru.nl>
> Date：2013-05-22 15:33:13
> Subject：fieldtrip Digest, Vol 30, Issue 31
>
> Send fieldtrip mailing list submissions to
> fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Re: question About head model (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 May 2013 09:30:17 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] question About head model
> Message-ID:
> <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> It is best to use the T1 MRI rather than the other scans.   To open a DICOM
> format file, you can try one of these options:
>
> % read the DICOM files
> mri = ft_read_mri('single_file_of_DICOM_series.IMA');
>  % or use a graphical file selection[f, p] = uigetfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> >('*');
> mri = ft_read_mri(fullfile
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> >(p,
> f));
>
>
> I copied the above from documentation on the FieldTrip wiki:
>
> http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
>
>
> Then you can save the 'mri' into a *.mat file for future use with FieldTrip.
>
> Best regards,
> Johanna
>
>
> 2013/5/22 WangJing <13681530640 at 139.com>
>
> > Hi
> > I am a freshman about field trip.
> > I am trying to build the forward model. but my mri data is different from
> > the data in the tutorial. So I don't know how to bulid the head model. I
> > use the date which is from the paper "Open Database of Epileptic EEG with
> > MRI and Postoperational Assessment of Foci?a Real World Verification for
> > the EEG Inverse Solutions",http://eeg.pl/epi
> . MRI recordings containing a
>
> > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain scans
> > with morphologic substrate of the epilepsy (mostly cortical dysplasias,
> > dysplastic tumors etc.). In some cases there is also a scan with the
>
> > gadolinium (GAD) contrast. The images were collected by Siemens Sonata 1.5T
> > scanner. The data is stored in the Digital Imaging and Communications in
> > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > weighting.The scans have the following resolutions: T1: 512 ? 512 pixels,
> > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
>
> > In the tutorial,the mri data stored in only one file, while the data which
>
> > I used have many files, I don't know how to process. who can help me,Thanks1
> >  Thanks very much!
> > Best Reagards
> > Jing Wang
> >
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-21 23:59:18
> > Subject?fieldtrip Digest, Vol 30, Issue 29
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Tue, 21 May 2013 17:52:21 +0200
> > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Thank you so much for your answer J?rn,
> >
> >
>
> > Now I got it, so, I will let the 'fourier' as input to ft_connectivityanalysis, because for some indices I will need the auto-spectrum, and if I fully undertood what you said, it will be the same, as they always take the phase information from the fourier transform. And fieltrip will automatically compute the csd if the input is the frequency data.
> >
> >
>
> > Nevertheless, it give me some error when I tried to use the output from 'powandcsd' of freqanalysis, always gives me a matrix dimensions error, and when I use the output 'fourier' from connectivityanalysis, it computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they are signed, so this is ok), the problem are the ImC ranging from -inf to inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier' the values are. Which for me is really weird.
> >
> >
> >
>
> > I have checked internally, and even when I always use the 'fourier' as input, when it internally calculates cross-spectrum for the ImC and PLV, the data.crsspctrm is different, e.g:
> > data.dimord = 'rpt_rpt_chan_chan_freq'
> > ans size(data.crsspctrm) = [1 7 59 59];
> >
>
> > So, both are apparently the same, but the data inside this matrices is different,
> >
> >
>
> > for example, when calculating the ImC the first 7 columns for the first two rows are:
> > val(:,:,1,1)
> > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > val(:,:,1,2)
> >
>
> > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> >
> > while when calculating the PLV are:
> > val(:,:,1,1)
> > ?[1? 1? 1? 1? 1? 1? 1]
> > val(:,:,1,2)
> >
>
> > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> >
> >
> >
>
> > I'm pretty sure I'm doing something wrong here, but I don't really have a clue,
> >
> >
>
> > If I use the fourier transform to calculate the 'csd' in ft_connectivity analysis and use this csd as input to all other ft_connectivityanalysis indices all of them are set to NaN or 1, not ranging between any numbers.
> >
> >
> >
> >
> >
>
> > On the other hand, I have seen searching on the net, that fieltrip is capable of create surrogate data, by shifting the phase information on every trial for only one electrode of each pair while using the original samples of each trials on the second channel, but I couldn't find on the manual how to do such a thing. Is there any way to compute this kind of surrogates for every sensor? or was it something that some one suggest to somebody?
> >
> >
> > Many thanks in advanced,
> > Gabriel.
> >
> >
> >
> >
> > ----- Mensaje original -----
> > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >
> >
> >
> >
> >
> > > Dear Gabriel,
> >        >
> >
>
> >        > A) As you             see, this makes an average over the epochs of each channel,             and not over the samples (which in this case are the 9             frequencies of the FFT), And I would like to have the opposite, this is, to get the imaginary part of coherence for                   each epoch (repetition) on all                   my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,                 Is this possible?
> >                         >
> >
>
> > >        No. You should think of coherence more as a measure for the       consistency of the phase relation between channels across trials,       so coherence is just not defined per trial,neither would it make       sense to compute coherence for a single trial.
> >        >
> >
>
> >        > B)                     Another question I have is: for the Imaginary part                     of Coherence is not necessary to compute the                     cross-spectrum with 'powandcsd', only the FFT, but                     for the PLV, PPC or WPLI is that way too?       I see some terminology issues here. Let me try to explain in a       simple (aka least-mathematical I can think of) way:
> >        >
> >
>
> > >        For all these connectivity measures, we need the phase information       from the Fourier transform (FFT) to compute the cross-spectral       density matrix (CSD). The CSD can be regarded as the equivalent in       the frequency domain to the covariance matrix in the time domain,       thus it is a measures how a certain channels activity is       co-modulated with another channels activity (for a particular       frequency) - makes pretty much sense to make use of this when       computing connectivity, right? :)
> >
>
> > >        As you might know, a Fourier transform returns complex numbers,       where the imaginary part of this number contains phase       information. When calling ft_freqanalysis, you can decide if it       shall only return the (squared) real part of the frequency       spectrum (cfg.output='pow'), or instead the full CSD (cfg.output =       'powandcsd'). Alternatively, you can also let ft_freqanalysis       return the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier coefficients, however, you can easily obtain the CSD       or the power spectrum basically by multiplication the Fourier       matrix with itself (transposed). All of these measures quantify       the phase relation between channels across trials, and as phase       information is coded in the imaginary part of the fourier output,       thus for connectivityanalysis you need the CSD which can be       obtained either by 'powandcsd' or by 'fourier'.
> >        >
> > >        I hope that somehow clarifies your questions.
> >        >
> > >        Best,
> > >        J?rn
> >        >
> > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> >           > Dear Fieltrip experts,
> >          >
> >
>
> > >          I have my continuous data imported to fieldtrip with matlab, I'm         looking for performing connectivity analysis between pairs of         sensors, I have succed as:
> >
>
> > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch with 59 channels and 2000 samples
> > >          data.label {59x1};
> > >          data.time {1xNepochs};
> >          >
> > >          then, calculate only the FFT of all sensors as:
> > >          cfg=[];
> > >          cfg.output='fourier';
> > >          cfg.method='mtmfft';
> > >          cfg.taper='hanning';
> > >          cfg.foilim=[8.5 9.5];
> > >          cfg.tapsmofrq=0;
> > >          cfg.trials='all';
> > >          cfg.keeptrials='yes';
> > >          cfg.channel='all';
> > >          fourier=ft_freqanalysis(cfg, data)
> > >          as output I get:
> > >          dimord = 'rpttap_chan_freq'
> > >          freq= [1x9]
> > >          fourierspctrm=[7x59x9 double]
> >          >
> > >          Then compute the imaginary part of coherency as:
> >            > cfg=[];
> >              > cfg.method ='cohe';
> >              > cfg.complex='imag';
> >                > cfg.channelcbm={'all'               'all'};
> >              > coher = ft_connectivityanalysis (cfg, fourier)
> >          > as output get:
> >            > dimord='chan_chan_freq';
> >              > cohspctrm=[59x59x9 double];
> >              > dof=7;
> >            >
> >          > I have two main questions:
> >          >
> >
>
> >          > A) As you see, this makes an average over the           epochs of each channel, and not over the samples (which in           this case are the 9 frequencies of the FFT), And I would like           to have the opposite, this is, to               get the imaginary                 part of coherence for each epoch (repetition)                 on all my channels and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,               Is this possible?
> >                  >
> >                  >
> >                  >
> >
>
> >                  > B) Another question I have is: for the                   Imaginary part of Coherence is not necessary to                   compute the cross-spectrum with 'powandcsd', only the                   FFT, but for the PLV, PPC or WPLI is that way too?
> >                  >
> >                  >
> >                  >
> >                  >
> > >                  Many thanks in advanced,
> >                  > Gabriel.
> >                  >
> >                       >
> >               >
> >
>
> >        > _______________________________________________ > fieldtrip mailing list >
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >      >
> >
>
> >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging > Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands >  > Contact: > E-Mail:
> > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > http://www.ru.nl/donders
>
> >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands     > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
>
> > <font size="3">--------------------------<br />PhD. student Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> >
> >
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> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 30, Issue 29
> > *****************************************
> >
> > _______________________________________________
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> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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>
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> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 30, Issue 31
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From 13681530640 at 139.com  Sun May 26 11:26:07 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
Subject: [FieldTrip] Question about Memory requirement Of Head model
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
Message-ID: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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From julian.keil at gmail.com  Sun May 26 12:23:34 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Sun, 26 May 2013 12:23:34 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
Message-ID: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>

Dear Jing Wang,

this might be due to you using a 32bit System.
As far as I know, 32bit Windows can only use ~3 GB of Memory. At least that's what I experienced using Win XP, maybe it's different for the server.
However, I'd advise you to switch to a 64bit System and try again.

Best,

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 26.05.2013 um 11:26 schrieb WangJing:

> Hello Everyone,
>      I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.
> for example 1:
> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]
> cfg = [];
> ft_sourceplot(cfg,mri);
>  
> the result is:
> ??? Out of memory. Type HELP MEMORY for your options.
> Error in ==> ft_sourceplot at 368
>   ana  = (ana-dmin)./(dmax-dmin);
>  
> example 2:
> clear all
> mri = ft_read_mri('IM-0001-0001.dcm');
> cfg = [];
> cfg.method = 'interactive';
> cfg.coordsys = 'ctf';
> mri_realigned = ft_volumerealign(cfg,mri);
> clear mri
> cfg=[];
> mrirs = ft_volumereslice(cfg,mri_realigned);
>  
> when run to the last code, I face the same problem.
>  
> Thank you!
> Best Regards!
> Jing Wang
>  
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From 13681530640 at 139.com  Sun May 26 17:01:10 2013
From: 13681530640 at 139.com (WangJing)
Date: Sun, 26 May 2013 23:01:10 +0800 (CST)
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 37
References: <mailman.9.1369562405.16243.fieldtrip@science.ru.nl>
Message-ID: <2b1851a22104e22-00005.Richmail.00025896525295133618@139.com>


Hello Everyone,


    I have resolved the problem when I ran it in computer with 64 bit OS,  thanks.


Best Regards,


Jing Wang





 













--------------------------------------------------------------------------------



----The following is the content of the forwarded email----
From：fieldtrip-request<fieldtrip-request at science.ru.nl>
To：fieldtrip<fieldtrip at science.ru.nl>
Date：2013-05-26 18:00:05
Subject：fieldtrip Digest, Vol 30, Issue 37

Send fieldtrip mailing list submissions to
fieldtrip at science.ru.nl

To subscribe or unsubscribe via the World Wide Web, visit
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of fieldtrip digest..."


Today's Topics:

   1. Question about Memory requirement Of Head model (WangJing)


----------------------------------------------------------------------

Message: 1
Date: Sun, 26 May 2013 17:26:07 +0800 (CST)
From: WangJing <13681530640 at 139.com>
To: fieldtrip <fieldtrip at science.ru.nl>
Subject: [FieldTrip] Question about Memory requirement Of Head model
Message-ID:
<2b1851a17ca79ab-00017.Richmail.00027836529255037638 at 139.com>
Content-Type: text/plain; charset="utf-8"


Hello Everyone,


     I want to know what's the requiement of fieldtrip to hardware and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is windows sever 2003, and the matlab is 2011a(32bit).I often encounter the problem of out of Memery.


for example 1:


> mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 512 144]


cfg = [];
ft_sourceplot(cfg,mri);


 


the result is:


??? Out of memory. Type HELP MEMORY for your options.


Error in ==> ft_sourceplot at 368
  ana  = (ana-dmin)./(dmax-dmin);


 


example 2:


clear all
mri = ft_read_mri('IM-0001-0001.dcm');


cfg = [];
cfg.method = 'interactive';
cfg.coordsys = 'ctf';
mri_realigned = ft_volumerealign(cfg,mri);
clear mri
cfg=[];
mrirs = ft_volumereslice(cfg,mri_realigned);


 


when run to the last code, I face the same problem.


 


Thank you!


Best Regards!


Jing Wang


 


 
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------------------------------

_______________________________________________
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fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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*****************************************

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From jm.horschig at donders.ru.nl  Mon May 27 11:54:00 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 27 May 2013 11:54:00 +0200
Subject: [FieldTrip] Question about Memory requirement Of Head model
In-Reply-To: <95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
References: <mailman.487.1369508182.1286.fieldtrip@science.ru.nl>
	<2b1851a17ca79ab-00017.Richmail.00027836529255037638@139.com>
	<95C94C42-6516-4536-AD5A-66FA5041E3F3@gmail.com>
Message-ID: <51A32D38.3060908@donders.ru.nl>

Hi all,

Julian is right, that's a limit of the 32bit system (the OS does not 
matter, just the number of bits). FieldTrip itself does not have any 
requirements other than Matlab does, however the size of your data 
matters. If you want to put data with more than 3gigs into memory, it's 
just not possible with a 32bit OS or Matlab (note that even if you have 
a 64bit OS but 32bit Matlab then the 3GB limit hold). So the only way 
for you to go is to clear variables from memory or reduce the size of 
the data you want to read it (or, go to 64bit). Maybe closing background 
tasks or other programs that are running will help as well.

Best,
Jörn

On 5/26/2013 12:23 PM, Julian Keil wrote:
> Dear Jing Wang,
>
> this might be due to you using a 32bit System.
> As far as I know, 32bit Windows can only use ~3 GB of Memory. At least 
> that's what I experienced using Win XP, maybe it's different for the 
> server.
> However, I'd advise you to switch to a 64bit System and try again.
>
> Best,
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 26.05.2013 um 11:26 schrieb WangJing:
>
>> Hello Everyone,
>>      I want to know what's the requiement of fieldtrip to hardware 
>> and software. My computer 's CPU is 3GHz, and RAM is 8GB. the OS is 
>> windows sever 2003, and the matlab is 2011a(32bit).I often encounter 
>> the problem of out of Memery.
>> for example 1:
>> > mri = ft_read_mri('IM-0001-0001.dcm');    % the dim of data is [512 
>> 512 144]
>> cfg = [];
>> ft_sourceplot(cfg,mri);
>> the result is:
>> ??? Out of memory. Type HELP MEMORY for your options.
>> Error in ==> ft_sourceplot at 368
>>   ana  = (ana-dmin)./(dmax-dmin);
>> example 2:
>> clear all
>> mri = ft_read_mri('IM-0001-0001.dcm');
>> cfg = [];
>> cfg.method = 'interactive';
>> cfg.coordsys = 'ctf';
>> mri_realigned = ft_volumerealign(cfg,mri);
>> clear mri
>> cfg=[];
>> mrirs = ft_volumereslice(cfg,mri_realigned);
>> when run to the last code, I face the same problem.
>> Thank you!
>> Best Regards!
>> Jing Wang
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From member at linkedin.com  Mon May 27 14:14:43 2013
From: member at linkedin.com (Stavros Dimitriadis)
Date: Mon, 27 May 2013 12:14:43 +0000 (UTC)
Subject: [FieldTrip] Invitation to connect on LinkedIn
Message-ID: <1730678420.35398857.1369656883124.JavaMail.app@ela4-app0128.prod>

LinkedIn
------------




    Stavros Dimitriadis requested to add you as a connection on LinkedIn:
  

------------------------------------------

Diego,

I'd like to add you to my professional network on LinkedIn.

- Stavros

Accept invitation from Stavros Dimitriadis
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View profile of Stavros Dimitriadis
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From johanna.zumer at gmail.com  Mon May 27 15:12:27 2013
From: johanna.zumer at gmail.com (Johanna Zumer)
Date: Mon, 27 May 2013 15:12:27 +0200
Subject: [FieldTrip] Source Reconstruction using Openmeeg method
In-Reply-To: <CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
References: <CAFy9vnJiWc9xPWEx+G9G0bYMTsKji8fLU7+K06=9-KEJ7LRfwQ@mail.gmail.com>
	<CAL4kA6dmFssL2yOM581d01pp6fvKxsCeefJLDBtCm8zzjVdUVg@mail.gmail.com>
	<CAFy9vnK21cmrFx86wLoa2WD12KXmm0HnLd-eojQu_rr7AhGzdg@mail.gmail.com>
	<5190AEAA.3020301@donders.ru.nl>
	<CAFy9vnKJzBTVyAZMiX7-uK7609nJV=HrVfJ7WbSnUu68S2V06Q@mail.gmail.com>
Message-ID: <CAL4kA6cbk1c8bBztUG6JD_5k1W6Ds8CY3zRqer4uVxy-Edtpsg@mail.gmail.com>

Hi Mushfa,

The values inside grid_*.leadfield are the ones that need to be
concatenated, per grid position.   So the first thing to do is figure out
which rows in grid_eeg.pos match up with which rows in grid_meg.pos, and
then only for those that match, concatenate so that the *.leadfield is of
size [(number of eeg channels + number of meg channels)  X 3].

It might be easier to first ensure that the grid used to create these
leadfields have the same 'inside' positions (inside the volume conductor).

Best,
Johanna



2013/5/22 Mushfa Yousuf <mushfa.yousuf at googlemail.com>

> Hello Jörn;
>
> I have calculated an indiviual leadfield for both EEG and MEG. The
> structure of EEg and MEG shows the following variable
>
> grid_meg =
>
>         xgrid: [1x20 double]
>         ygrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8]
>         zgrid: [-2 -1 0 1 2 3 4 5 6 7 8 9 10 11 12 13]
>           dim: [20 17 16]
>           pos: [5440x3 double]
>          unit: 'cm'
>        inside: [1x3177 double]
>       outside: [1x2263 double]
>           cfg: [1x1 struct]
>     leadfield: {1x5440 cell}
>
>
> grid_eeg =
>
>         xgrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9]
>         ygrid: [-6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6]
>         zgrid: [2 3 4 5 6 7 8 9 10 11]
>           dim: [16 13 10]
>           pos: [2080x3 double]
>          unit: 'cm'
>        inside: [1x1331 double]
>       outside: [1x749 double]
>           cfg: [1x1 struct]
>     leadfield: {1x2080 cell}
>
>
> Can you please give me a rough idea that how to concatenate the variables
> from both structure ?
>
>
> Thank you
>
> Regards ;
>
> Mushfa Yousuf
>
>
> On Mon, May 13, 2013 at 11:13 AM, "Jörn M. Horschig" <
> jm.horschig at donders.ru.nl> wrote:
>
>>  Dear Mushfa,
>>
>> I think you have to compute two leadfield matrices, one for EEG (elec)
>> and one for MEG (grad), and then concatenate these (and make sure that the
>> order of sensors won't get mixed up anywhere, because  sourceanalysis just
>> expects the leadfield matrix to be ordered like your data. If that's not
>> the case, you either encounter the previous error you described or (if the
>> number of channels matches, but order is mixed up) it will just return
>> wrong source estimated activity.
>>
>> Best,
>> Jörn
>>
>>
>> On 5/6/2013 2:47 PM, Mushfa Yousuf wrote:
>>
>> Hello;
>>
>>  Yes you were right. I have defined the wrong sensors i.e 'grad' instead
>> of 'elec' while calculating the Leadfield.
>>
>>  Actually I am trying to calculate Combined source reconstruction from
>> both EEG and MEG sensors.
>>
>>  Do you have any idea, how to define both elec and grad definition
>> while calculating first forward then inverse solution.
>>
>>  Because in a fieldtrip either you can defined elec or grad at one time.
>>
>>
>>  Regards;
>>
>>
>>  Mushfa Yousuf
>>
>>  Neurozentrum,
>> Universitätsklinikum Schleswig-Holstein,
>> Campus Kiel (UKSH), Deutschland
>>
>>
>> On Tue, Apr 30, 2013 at 6:23 PM, Johanna Zumer <johanna.zumer at gmail.com>wrote:
>>
>>> Hi Mushfa,
>>>
>>>  My guess is that the channels that have you used to compute .csdspctrm
>>> are not the same as the channels in cfg.elec.    If you set cfg.channel =
>>> freqPost.label, does that solve it?
>>>
>>>  Cheers,
>>> Johanna
>>>
>>>
>>> 2013/4/30 Mushfa Yousuf <mushfa.yousuf at googlemail.com>
>>>
>>>>   Hello Fieldtrippers,
>>>>
>>>>  I am doing source reconstruction using EEG channels on a fieldtrip.
>>>>
>>>>  I have computed Forward solution i.e head model using  'Openmeeg' and
>>>> lead field successfully.
>>>>
>>>>  For the inverse solution using 'dics' method, I wrote the following
>>>> syntax
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>   cfg              = [];
>>>>   cfg.method       = 'dics';
>>>>  cfg.frequency    = 130;
>>>>  cfg.elec         = dataFIC12.hdr.elec;
>>>>  cfg.grid         = grid;
>>>>  cfg.vol          = vol;
>>>>
>>>>   sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>  and I have received the following error:
>>>>
>>>>
>>>>  ??? Error using ==> mtimes
>>>> Inner matrix dimensions must agree.
>>>>
>>>>  Error in ==> beamformer_dics at 314
>>>>         filt = pinv(lf' * invCf * lf) * lf' * invCf;              %
>>>>         Gross eqn. 3, use PINV/SVD to cover rank deficient
>>>>         leadfield
>>>>
>>>>  Error in ==> ft_sourceanalysis at 595
>>>>       dip(i) = beamformer_dics(grid, sens, vol, [],
>>>>       squeeze(Cf(i,:,:)), optarg{:});
>>>>
>>>>  Error in ==> newCode at 214
>>>> sourcePost = ft_sourceanalysis(cfg, freqPost);
>>>>
>>>>
>>>>
>>>>
>>>>  Any help would be appreciated.
>>>>
>>>>
>>>>  Regards;
>>>>
>>>>
>>>>  Mushfa Yousuf
>>>>
>>>>  Neurozentrum,
>>>> Universitätsklinikum Schleswig-Holstein,
>>>> Campus Kiel (UKSH), Deutschland
>>>>
>>>>
>>>>  _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>> FieldTrip Development Team
>>
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Contact:
>> E-Mail: jm.horschig at donders.ru.nl
>> Tel:    +31-(0)24-36-68493
>> Web: http://www.ru.nl/donders
>>
>> Visiting address:
>> Trigon, room 2.30
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From mbj0310 at gmail.com  Wed May 29 11:47:14 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Wed, 29 May 2013 18:47:14 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some files
Message-ID: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>

Dear all,

Hello, my name is BJ Min from Korea.

I'm dealing with EEG data of many subjects.

When I run ft_preprocessing, the error message below shows with only some
files of my data. (not all files)

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577
??? Error using ==> ft_read_data at 149
cannot read data after the end of the file

Error in ==> ft_preprocessing at 577
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
begsample, 'endsample', endsample, 'chanindx', rawindx,
      'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
cfg.dataformat)

I think that there might be a kind of problem in data acquisition, and I
modified below scripts in the ft_read_data function with comment %.

% % test whether the requested data segment is not outside the file
% if any(begsample<1)
%   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
the file');
% elseif any(endsample>(hdr.nSamples*hdr.nTrials))
%   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the
file');
% end

After that, the ft_preprocessing worked well.

However, the files with the first problem showed additional warning message
while running ft_definetrial. (not error message)

Warning: Integer operands are required for colon operator when used as
index
> In fileio\private\loadcnt at 464
  In ft_read_header at 1450
  In ft_preprocessing at 398

Warning: rounding "endsample" to the nearest integer
> In ft_read_data at 100
  In ft_preprocessing at 577

Also, during ft_redefinetrial, following warning message occurs.(not error
message)

Warning: removing inconsistent sampleinfo
> In ft_datatype_raw at 97
  In ft_checkdata at 213
  In ft_redefinetrial at 104

Warning: the trial definition in the configuration is inconsistent with the
actual data
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 74
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

Warning: reconstructing sampleinfo by assuming that the trials are
consecutive segments of a continuous recording
> In utilities\private\warning_once at 116
  In utilities\private\fixsampleinfo at 79
  In ft_datatype_raw at 154
  In ft_checkdata at 213
  In ft_redefinetrial at 206

I wonder if these messages during ft_redefinetrial mean wrong defining
trials.
Should I continue these process like this, modifying the ft_preprocessing
function?
Or, is it better to exclude some erroneous files?

Best regards

-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Wed May 29 12:01:31 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Wed, 29 May 2013 12:01:31 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
Message-ID: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>

Dear BJ Min,

what type of data are you trying to read in?
I had similar problems when reading in .CNT data.
Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.

Good Luck

Julian

********************
Dr. Julian Keil

AG Multisensorische Integration
Psychiatrische Universitätsklinik
der Charité im St. Hedwig-Krankenhaus
Große Hamburger Straße 5-11, Raum E 307
10115 Berlin

Telefon: +49-30-2311-1879
Fax:        +49-30-2311-2209 
http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration

Am 29.05.2013 um 11:47 schrieb Beom Jun Min:

> Dear all,
> 
> Hello, my name is BJ Min from Korea.
> 
> I'm dealing with EEG data of many subjects. 
> 
> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
> 
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
> 
> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
> 
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
> % end
> 
> After that, the ft_preprocessing worked well.
> 
> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
> 
> Warning: Integer operands are required for colon operator when used as index 
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
> 
> Warning: rounding "endsample" to the nearest integer 
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> 
> Also, during ft_redefinetrial, following warning message occurs.(not error message)
> 
> Warning: removing inconsistent sampleinfo 
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
> 
> Warning: the trial definition in the configuration is inconsistent with the actual data 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
> 
> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
> Should I continue these process like this, modifying the ft_preprocessing function? 
> Or, is it better to exclude some erroneous files?
> 
> Best regards
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From mbj0310 at gmail.com  Thu May 30 10:15:31 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Thu, 30 May 2013 17:15:31 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
Message-ID: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>

Dear Julian Keil,

Thank you for your reply.
I agree with that your problem was similar with mine.
My data was acquired by Neuroscan also.
There might a problem associated with .CNT file in the newer version.

Could you tell me the number of the older version you used?

Best Regards



2013/5/29 Julian Keil <julian.keil at gmail.com>

> Dear BJ Min,
>
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the
> problem, but this was in 2011, so I cannot say if the problem with .CNT
> files has been solved.
>
> Good Luck
>
> Julian
>
> ********************
> *Dr. Julian Keil*
> *
> *
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>
> Dear all,
>
> Hello, my name is BJ Min from Korea.
>
> I'm dealing with EEG data of many subjects.
>
> When I run ft_preprocessing, the error message below shows with only some
> files of my data. (not all files)
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
> ??? Error using ==> ft_read_data at 149
> cannot read data after the end of the file
>
> Error in ==> ft_preprocessing at 577
>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx,
>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
> cfg.dataformat)
>
> I think that there might be a kind of problem in data acquisition, and I
> modified below scripts in the ft_read_data function with comment %.
>
> % % test whether the requested data segment is not outside the file
> % if any(begsample<1)
> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of
> the file');
> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
> the file');
> % end
>
> After that, the ft_preprocessing worked well.
>
> However, the files with the first problem showed additional warning
> message while running ft_definetrial. (not error message)
>
> Warning: Integer operands are required for colon operator when used as
> index
> > In fileio\private\loadcnt at 464
>   In ft_read_header at 1450
>   In ft_preprocessing at 398
>
> Warning: rounding "endsample" to the nearest integer
> > In ft_read_data at 100
>   In ft_preprocessing at 577
>
> Also, during ft_redefinetrial, following warning message occurs.(not error
> message)
>
> Warning: removing inconsistent sampleinfo
> > In ft_datatype_raw at 97
>   In ft_checkdata at 213
>   In ft_redefinetrial at 104
>
> Warning: the trial definition in the configuration is inconsistent with
> the actual data
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 74
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
> > In utilities\private\warning_once at 116
>   In utilities\private\fixsampleinfo at 79
>   In ft_datatype_raw at 154
>   In ft_checkdata at 213
>   In ft_redefinetrial at 206
>
> I wonder if these messages during ft_redefinetrial mean wrong defining
> trials.
> Should I continue these process like this, modifying the ft_preprocessing
> function?
> Or, is it better to exclude some erroneous files?
>
> Best regards
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From julian.keil at gmail.com  Thu May 30 11:45:09 2013
From: julian.keil at gmail.com (Julian Keil)
Date: Thu, 30 May 2013 11:45:09 +0200
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <80EC72EF-2296-47F5-97EC-197F91402C79@gmail.com>

Dear BJ Min,

I used the field trip version 20111101. I don't know if it's still available though.
To set the bitrate, you have to specify

	cfg.headerformat='ns_cnt32'; 
        cfg.dataformat='ns_cnt32'; 
        cfg.eventformat='ns_cnt32';

in ft_preprocessing

One way to check this (and also if you set your bitrate correctly), is to see if you can find easily detectable ERPs, like the visual or auditory N1 in your data. If you can't see this component, then your settings are wrong, even if data has been read into Matlab.

Good Luck,

Julian

Am 30.05.2013 um 10:15 schrieb Beom Jun Min:

> Dear Julian Keil,
> 
> Thank you for your reply. 
> I agree with that your problem was similar with mine. 
> My data was acquired by Neuroscan also. 
> There might a problem associated with .CNT file in the newer version.
> 
> Could you tell me the number of the older version you used? 
> 
> Best Regards
> 
> 
> 
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
> Dear BJ Min,
> 
> what type of data are you trying to read in?
> I had similar problems when reading in .CNT data.
> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
> For me, reading in data with an older version of FieldTrip solved the problem, but this was in 2011, so I cannot say if the problem with .CNT files has been solved.
> 
> Good Luck
> 
> Julian
> 
> ********************
> Dr. Julian Keil
> 
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
> 
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209 
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
> 
> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
> 
>> Dear all,
>> 
>> Hello, my name is BJ Min from Korea.
>> 
>> I'm dealing with EEG data of many subjects. 
>> 
>> When I run ft_preprocessing, the error message below shows with only some files of my data. (not all files)
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>> 
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) 
>> 
>> I think that there might be a kind of problem in data acquisition, and I modified below scripts in the ft_read_data function with comment %.
>> 
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of the file');
>> % end
>> 
>> After that, the ft_preprocessing worked well.
>> 
>> However, the files with the first problem showed additional warning message while running ft_definetrial. (not error message)
>> 
>> Warning: Integer operands are required for colon operator when used as index 
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>> 
>> Warning: rounding "endsample" to the nearest integer 
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> 
>> Also, during ft_redefinetrial, following warning message occurs.(not error message)
>> 
>> Warning: removing inconsistent sampleinfo 
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>> 
>> Warning: the trial definition in the configuration is inconsistent with the actual data 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>> 
>> I wonder if these messages during ft_redefinetrial mean wrong defining trials. 
>> Should I continue these process like this, modifying the ft_preprocessing function? 
>> Or, is it better to exclude some erroneous files?
>> 
>> Best regards
>> 
>> -- 
>> BeomJun Min, M.D.
>> 
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST) 
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
>> 500-712, Republic of Korea (South) 
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
> BeomJun Min, M.D.
> 
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST) 
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju 
> 500-712, Republic of Korea (South) 
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244 
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From dr.chungki.lee at gmail.com  Thu May 30 11:56:02 2013
From: dr.chungki.lee at gmail.com (Chungki Lee)
Date: Thu, 30 May 2013 18:56:02 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
Message-ID: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>

Hi Min

you'd better use ft_definetrial routine before  ft_preprocessing.

example)

    cfg                              = [];
    cfg.dataset                 = filename;  % string
    cfg.trialdef.eventtype  =  your define text; % string
    cfg.trialdef.eventvalue = your label value;  % integer
    cfg.trialdef.prestim    = before onset time (sec); % positive integer,
not negative integer
    cfg.trialdef.poststim   = after onset time (sec); % positve integer
    cfg                            = ft_definetrial(cfg);
    data                          = ft_preprocessing(cfg);

have fun ^^


2013/5/30 Beom Jun Min <mbj0310 at gmail.com>

> Dear Julian Keil,
>
> Thank you for your reply.
> I agree with that your problem was similar with mine.
> My data was acquired by Neuroscan also.
> There might a problem associated with .CNT file in the newer version.
>
> Could you tell me the number of the older version you used?
>
> Best Regards
>
>
>
> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>
>> Dear BJ Min,
>>
>> what type of data are you trying to read in?
>> I had similar problems when reading in .CNT data.
>> Also, with some systems you have to specify the bit rate (e.g. Neuroscan).
>> For me, reading in data with an older version of FieldTrip solved the
>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>> files has been solved.
>>
>> Good Luck
>>
>> Julian
>>
>>  ********************
>> *Dr. Julian Keil*
>> *
>> *
>> AG Multisensorische Integration
>> Psychiatrische Universitätsklinik
>> der Charité im St. Hedwig-Krankenhaus
>> Große Hamburger Straße 5-11, Raum E 307
>> 10115 Berlin
>>
>> Telefon: +49-30-2311-1879
>> Fax:        +49-30-2311-2209
>>
>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>
>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>
>> Dear all,
>>
>> Hello, my name is BJ Min from Korea.
>>
>> I'm dealing with EEG data of many subjects.
>>
>> When I run ft_preprocessing, the error message below shows with only some
>> files of my data. (not all files)
>>
>>  Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>> ??? Error using ==> ft_read_data at 149
>> cannot read data after the end of the file
>>
>> Error in ==> ft_preprocessing at 577
>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>> cfg.dataformat)
>>
>> I think that there might be a kind of problem in data acquisition, and I
>> modified below scripts in the ft_read_data function with comment %.
>>
>> % % test whether the requested data segment is not outside the file
>> % if any(begsample<1)
>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>> of the file');
>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>> the file');
>> % end
>>
>> After that, the ft_preprocessing worked well.
>>
>> However, the files with the first problem showed additional warning
>> message while running ft_definetrial. (not error message)
>>
>> Warning: Integer operands are required for colon operator when used as
>> index
>> > In fileio\private\loadcnt at 464
>>   In ft_read_header at 1450
>>   In ft_preprocessing at 398
>>
>> Warning: rounding "endsample" to the nearest integer
>> > In ft_read_data at 100
>>   In ft_preprocessing at 577
>>
>> Also, during ft_redefinetrial, following warning message occurs.(not
>> error message)
>>
>> Warning: removing inconsistent sampleinfo
>> > In ft_datatype_raw at 97
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 104
>>
>> Warning: the trial definition in the configuration is inconsistent with
>> the actual data
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 74
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> Warning: reconstructing sampleinfo by assuming that the trials are
>> consecutive segments of a continuous recording
>> > In utilities\private\warning_once at 116
>>   In utilities\private\fixsampleinfo at 79
>>   In ft_datatype_raw at 154
>>   In ft_checkdata at 213
>>   In ft_redefinetrial at 206
>>
>> I wonder if these messages during ft_redefinetrial mean wrong defining
>> trials.
>> Should I continue these process like this, modifying the ft_preprocessing
>> function?
>> Or, is it better to exclude some erroneous files?
>>
>> Best regards
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>  _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> BeomJun Min, M.D.
>
> Department of Medical System Engineering (DMSE)
> Gwangju Institute of Science and Technology (GIST)
> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
> 500-712, Republic of Korea (South)
> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
----------------------------------------------------------------
Chungki Lee, Ph.D.
Post-doc
Biomedical Research Institute
Korea Institute of Science and Technology
E-mail: chungki at kist.re.kr
Tel:+82-2-958-5636, C.P: +82-10-5223-7309
----------------------------------------------------------------
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From lkystra at hotmail.it  Thu May 30 12:39:16 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 12:39:16 +0200
Subject: [FieldTrip] distorsion of .edf file
Message-ID: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>

Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  
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From zriouil.imane at gmail.com  Thu May 30 15:43:59 2013
From: zriouil.imane at gmail.com (z.imane)
Date: Thu, 30 May 2013 15:43:59 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>
Message-ID: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>

> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the
> use of read_edf, have a distorsion. Matlab indicate a warning for the 348
> row of read_edf . Can someone give to me a help?
>
> Best regards,
> Lucia
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 


Zriouil Imane
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From lkystra at hotmail.it  Thu May 30 17:33:55 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Thu, 30 May 2013 17:33:55 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
Message-ID: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>

I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')



2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>




Dear all,
I'm analyzing EEG files in format .edf with matlab. 
Many files after the use of read_edf, have a distorsion. Matlab indicate
 a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia
 		 	   		   		 	   		  

_______________________________________________

fieldtrip mailing list

fieldtrip at donders.ru.nl

http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 

 
 
Zriouil Imane






_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu May 30 18:31:22 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 30 May 2013 18:31:22 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>
Message-ID: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>

Hi Lucia,

Perhaps you need to be a bit more specific. 
In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.
Otherwise all of us are shooting in the dark.
Best wishes,
Jan-Mathijs


On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:

> I try and... it's not a good solution.
> 
> Date: Thu, 30 May 2013 15:43:59 +0200
> From: zriouil.imane at gmail.com
> To: fieldtrip at science.ru.nl
> Subject: Re: [FieldTrip] distorsion of .edf file
> 
> I have the same problem.
> 
> if you want to read your data. it's possible to use ft_read_data(filename')
> 
> 
> 
> 2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
> Dear all,
> I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?
> 
> Best regards,
> Lucia
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> -- 
>  
>  
> Zriouil Imane
> 
> 
> 
> 
> _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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From ebrahimi_nia at yahoo.com  Thu May 30 19:14:52 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Thu, 30 May 2013 10:14:52 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
Message-ID: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>

Hi dear all,

I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.

**** Error using fread

Invalid precision.
Error in loreta2fieldtrip (line 85)
activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***

Can someone give me a help?


Best regards,
Fatemeh
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From inieuwenhuis at berkeley.edu  Thu May 30 19:30:41 2013
From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis)
Date: Thu, 30 May 2013 10:30:41 -0700
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
Message-ID: <51A78CC1.6030906@berkeley.edu>

Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug, see 
http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export the 
source data as a text file. You can read that text file in with 
loreta2fieldtrip.m. It's a bit of a patch, but it worked for me.

Hope this helps,
Ingrid

On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:
> Hi dear all,
>
> I am analyzing EEG data. I have computed sLORETA (.slor) from ERP 
> data. Now I want to read and convert LORETA source reconstruction into a
> MATLAB data structure using "loreta2fieldtrip" function, But I have 
> gotten the bellow error.
>
> **** Error using fread
> Invalid precision.
> Error in loreta2fieldtrip (line 85)
> activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
> Can someone give me a help?
>
> Best regards,
> Fatemeh
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305

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From frank.ye.mei at gmail.com  Thu May 30 21:33:53 2013
From: frank.ye.mei at gmail.com (Ye Mei)
Date: Thu, 30 May 2013 15:33:53 -0400
Subject: [FieldTrip] error when using ctf2grad
Message-ID: <51A7A9A1.6020401@gmail.com>

Hi All,

I have some problem using ctf2grad.

The program will set   grad.balance.current = 'G3AR';,
and then do                 getfield(grad.balance, grad.balance.current)
but
grad.balance =    G1BR: [1x1 struct]
                             G2BR: [1x1 struct]
                             G3BR: [1x1 struct]

and has no G3AR in it. So an error will pop up.

Can anyone help me with that?

Also, What do G1BR,   G2BR,  G3BR, G3AR stand for?


thanks,
Ye


From politzerahless at gmail.com  Fri May 31 05:53:45 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Thu, 30 May 2013 22:53:45 -0500
Subject: [FieldTrip] Question about minimum norm estimate pipeline
Message-ID: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>

Hello all,

I have not yet gotten a response to my question below, but in the meantime
I have another question about the minimum norm estimate
workflow--specifically, about the coordinate system for the skull-stripped
anatomy in the step described at
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk.
I'm confused by the following bit of code:

% ensure that the skull-stripped anatomy is expressed in the same
coordinate system as the anatomy
seg.transform = mri_tal.transform;

In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
re-aligning to Talairach in the previous step?) whereas seg.coordsys is
'ctf' (as a result of re-aligning to CTF several steps earlier). (But
mri_tal also has a field mri_tal.transformorig, which seg does not have.)
So should I really be using the same transform for both, as shown in the
tutorial?

Apologies if this question is pretty basic; I'm just trying to pinpoint
where the mis-alignment described in my message below occurred, so I want
to make sure I understand each step of the workflow correctly

Best,
Steve


> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/



On Sat, May 25, 2013 at 1:56 PM, <fieldtrip-request at science.ru.nl> wrote:
>
> Send fieldtrip mailing list submissions to
>         fieldtrip at science.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>         fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
>         fieldtrip-owner at science.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>    1. Sourcespace and volume conductor misaligned
>       (Stephen Politzer-Ahles)
>    2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 25 May 2013 08:11:18 -0500
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> Message-ID:
>         <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0=
fFk0ouR0wzA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am going through the workflow at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate. After making
> the volume conduction model using ft_prepare_headmodel(), I noticed that
> although the volume conduction model and sourcespace have the same
> orientation and overall size/shape (after I converted the volume
conduction
> model to cm, which wasn't in the tutorial but my original model came out
in
> mm), they don't quite line up, as you can see in this figure:
>
> http://i.imgur.com/mGEtLOa.png
>
> I did interactively re-align the data to CTF (twice--in step 2 of
> "Preprocessing of the anatomical MRI" and in step 4 of "Source model")
> using fiducials, and to Talairach (step 5 of "Preprocessing of the
> anatomical data"), so I'm not sure how it ended up this way. The code I've
> used at each step is basically the same as that in the tutorial.
>
> Is there any way to line up my volume conduction model and sourcespace
now,
> without going back and re-running most of the workflow?
>
> Best,
> Steve
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Sat, 25 May 2013 20:54:59 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> Message-ID:
>         <CAL4kA6eTL_TwECF62W-OoWY=
Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Jing,
>
> 1.  Every MRI scanner is different, so I'm not familiar with that naming
> scheme, but it seems the 'GAD' at the end of the file name indicates that
> was with the Gadolinium contrast agent, so I would suggest to not use
that,
> but instead use the first (plain) T1.
>
> 2. I'm not sure what to suggest.  I assume you can see the vitamin E
marker
> clearly when viewing the DICOM file?   Is the issue that some slices are
> missing in the conversion, or that the contrast on the image is not the
> same?  or right/left flipped?
>
> Best,
> Johanna
>
>
> 2013/5/23 WangJing <13681530640 at 139.com>
>
> > Dear Johanna,
> >
> >     Thank you for your suggestion.
> >     1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > t1_vibe_traGAD-5. which one is best?
> >     2.when I convert MRI from DICOM into CTF format,the vitamin E marker
> > didn't be found. what can I do?
> >
> > Best Regards,
> > Jing Wang
> >
> >
> >
> >
> > ------------------------------
> > ----The following is the content of the forwarded email----
> > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > To?fieldtrip<fieldtrip at science.ru.nl>
> > Date?2013-05-22 15:33:13
> > Subject?fieldtrip Digest, Vol 30, Issue 31
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Re: question About head model (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 22 May 2013 09:30:17 +0200
> > From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > Subject: Re: [FieldTrip] question About head model
> > Message-ID:
> > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=HsAS_X0-w at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > It is best to use the T1 MRI rather than the other scans.   To open a
DICOM
> > format file, you can try one of these options:
> >
> > % read the DICOM files
> > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> >  % or use a graphical file selection[f, p] = uigetfile
> > <
http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > >('*');
> > mri = ft_read_mri(fullfile
> > <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > >(p,
> > f));
> >
> >
> > I copied the above from documentation on the FieldTrip wiki:
> >
> >
http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> >
> >
> > Then you can save the 'mri' into a *.mat file for future use with
FieldTrip.
> >
> > Best regards,
> > Johanna
> >
> >
> > 2013/5/22 WangJing <13681530640 at 139.com>
> >
> > > Hi
> > > I am a freshman about field trip.
> > > I am trying to build the forward model. but my mri data is different
from
> > > the data in the tutorial. So I don't know how to bulid the head
model. I
> > > use the date which is from the paper "Open Database of Epileptic EEG
with
> > > MRI and Postoperational Assessment of Foci?a Real World Verification
for
> > > the EEG Inverse Solutions",http://eeg.pl/epi
> > . MRI recordings containing a
> >
> > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted brain
scans
> > > with morphologic substrate of the epilepsy (mostly cortical
dysplasias,
> > > dysplastic tumors etc.). In some cases there is also a scan with the
> >
> > > gadolinium (GAD) contrast. The images were collected by Siemens
Sonata 1.5T
> > > scanner. The data is stored in the Digital Imaging and Communications
in
> > > Medicine (DICOM) format. The name of the scan?s folder indicates its
> > > weighting.The scans have the following resolutions: T1: 512 ? 512
pixels,
> > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256 pixels,
> > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> >
> > > In the tutorial,the mri data stored in only one file, while the data
which
> >
> > > I used have many files, I don't know how to process. who can help
me,Thanks1
> > >  Thanks very much!
> > > Best Reagards
> > > Jing Wang
> > >
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request<fieldtrip-request at science.ru.nl>
> > > To?fieldtrip<fieldtrip at science.ru.nl>
> > > Date?2013-05-21 23:59:18
> > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Re: problem in connectivityanalysis (Gabriel Gonzalez Escamilla)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > From: Gabriel Gonzalez Escamilla <ggonesc at upo.es>
> > > To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > Message-ID: <1348f6433edc26f9.519bb455 at upo.es>
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Thank you so much for your answer J?rn,
> > >
> > >
> >
> > > Now I got it, so, I will let the 'fourier' as input to
ft_connectivityanalysis, because for some indices I will need the
auto-spectrum, and if I fully undertood what you said, it will be the same,
as they always take the phase information from the fourier transform. And
fieltrip will automatically compute the csd if the input is the frequency
data.
> > >
> > >
> >
> > > Nevertheless, it give me some error when I tried to use the output
from 'powandcsd' of freqanalysis, always gives me a matrix dimensions
error, and when I use the output 'fourier' from connectivityanalysis, it
computes almost all indices to ok, raging from? -1 to 1 (I'm saw that they
are signed, so this is ok), the problem are the ImC ranging from -inf to
inf, and the PLV values ranging from 0 to inf, but when I use the 'fourier'
the values are. Which for me is really weird.
> > >
> > >
> > >
> >
> > > I have checked internally, and even when I always use the 'fourier'
as input, when it internally calculates cross-spectrum for the ImC and PLV,
the data.crsspctrm is different, e.g:
> > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > ans size(data.crsspctrm) = [1 7 59 59];
> > >
> >
> > > So, both are apparently the same, but the data inside this matrices
is different,
> > >
> > >
> >
> > > for example, when calculating the ImC the first 7 columns for the
first two rows are:
> > > val(:,:,1,1)
> > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i? 1.4328-0.2427i?
0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > >
> > > while when calculating the PLV are:
> > > val(:,:,1,1)
> > > ?[1? 1? 1? 1? 1? 1? 1]
> > > val(:,:,1,2)
> > >
> >
> > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i? 0.9014-0.3481i?
0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > >
> > >
> > >
> >
> > > I'm pretty sure I'm doing something wrong here, but I don't really
have a clue,
> > >
> > >
> >
> > > If I use the fourier transform to calculate the 'csd' in
ft_connectivity analysis and use this csd as input to all other
ft_connectivityanalysis indices all of them are set to NaN or 1, not
ranging between any numbers.
> > >
> > >
> > >
> > >
> > >
> >
> > > On the other hand, I have seen searching on the net, that fieltrip is
capable of create surrogate data, by shifting the phase information on
every trial for only one electrode of each pair while using the original
samples of each trials on the second channel, but I couldn't find on the
manual how to do such a thing. Is there any way to compute this kind of
surrogates for every sensor? or was it something that some one suggest to
somebody?
> > >
> > >
> > > Many thanks in advanced,
> > > Gabriel.
> > >
> > >
> > >
> > >
> > > ----- Mensaje original -----
> > > De: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > A: FieldTrip discussion list <fieldtrip at science.ru.nl>
> > >
> > >
> > >
> > >
> > >
> > > > Dear Gabriel,
> > >        >
> > >
> >
> > >        > A) As you             see, this makes an average over the
epochs of each channel,             and not over the samples (which in this
case are the 9             frequencies of the FFT), And I would like to
have the opposite, this is, to get the imaginary part of coherence for
              each epoch (repetition) on all                   my channels
and not for each frequency, something like: chan_chan_rpt or chancbm_rpt,
              Is this possible?
> > >                         >
> > >
> >
> > > >        No. You should think of coherence more as a measure for the
      consistency of the phase relation between channels across trials,
  so coherence is just not defined per trial,neither would it make
sense to compute coherence for a single trial.
> > >        >
> > >
> >
> > >        > B)                     Another question I have is: for the
Imaginary part                     of Coherence is not necessary to compute
the                     cross-spectrum with 'powandcsd', only the FFT, but
                    for the PLV, PPC or WPLI is that way too?       I see
some terminology issues here. Let me try to explain in a       simple (aka
least-mathematical I can think of) way:
> > >        >
> > >
> >
> > > >        For all these connectivity measures, we need the phase
information       from the Fourier transform (FFT) to compute the
cross-spectral       density matrix (CSD). The CSD can be regarded as the
equivalent in       the frequency domain to the covariance matrix in the
time domain,       thus it is a measures how a certain channels activity is
      co-modulated with another channels activity (for a particular
frequency) - makes pretty much sense to make use of this when
computing connectivity, right? :)
> > >
> >
> > > >        As you might know, a Fourier transform returns complex
numbers,       where the imaginary part of this number contains phase
information. When calling ft_freqanalysis, you can decide if it       shall
only return the (squared) real part of the frequency       spectrum
(cfg.output='pow'), or instead the full CSD (cfg.output =
'powandcsd'). Alternatively, you can also let ft_freqanalysis       return
the raw Fourier coefficients (cfg.output='fourier'). From       the Fourier
coefficients, however, you can easily obtain the CSD       or the power
spectrum basically by multiplication the Fourier       matrix with itself
(transposed). All of these measures quantify       the phase relation
between channels across trials, and as phase       information is coded in
the imaginary part of the fourier output,       thus for
connectivityanalysis you need the CSD which can be       obtained either by
'powandcsd' or by 'fourier'.
> > >        >
> > > >        I hope that somehow clarifies your questions.
> > >        >
> > > >        Best,
> > > >        J?rn
> > >        >
> > > >        On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > >           > Dear Fieltrip experts,
> > >          >
> > >
> >
> > > >          I have my continuous data imported to fieldtrip with
matlab, I'm         looking for performing connectivity analysis between
pairs of         sensors, I have succed as:
> > >
> >
> > > >          data.trials {1xNepochs}; % Nepochs = 7,         each epoch
with 59 channels and 2000 samples
> > > >          data.label {59x1};
> > > >          data.time {1xNepochs};
> > >          >
> > > >          then, calculate only the FFT of all sensors as:
> > > >          cfg=[];
> > > >          cfg.output='fourier';
> > > >          cfg.method='mtmfft';
> > > >          cfg.taper='hanning';
> > > >          cfg.foilim=[8.5 9.5];
> > > >          cfg.tapsmofrq=0;
> > > >          cfg.trials='all';
> > > >          cfg.keeptrials='yes';
> > > >          cfg.channel='all';
> > > >          fourier=ft_freqanalysis(cfg, data)
> > > >          as output I get:
> > > >          dimord = 'rpttap_chan_freq'
> > > >          freq= [1x9]
> > > >          fourierspctrm=[7x59x9 double]
> > >          >
> > > >          Then compute the imaginary part of coherency as:
> > >            > cfg=[];
> > >              > cfg.method ='cohe';
> > >              > cfg.complex='imag';
> > >                > cfg.channelcbm={'all'               'all'};
> > >              > coher = ft_connectivityanalysis (cfg, fourier)
> > >          > as output get:
> > >            > dimord='chan_chan_freq';
> > >              > cohspctrm=[59x59x9 double];
> > >              > dof=7;
> > >            >
> > >          > I have two main questions:
> > >          >
> > >
> >
> > >          > A) As you see, this makes an average over the
epochs of each channel, and not over the samples (which in           this
case are the 9 frequencies of the FFT), And I would like           to have
the opposite, this is, to               get the imaginary
part of coherence for each epoch (repetition)                 on all my
channels and not for each frequency, something like: chan_chan_rpt or
chancbm_rpt,               Is this possible?
> > >                  >
> > >                  >
> > >                  >
> > >
> >
> > >                  > B) Another question I have is: for the
      Imaginary part of Coherence is not necessary to
compute the cross-spectrum with 'powandcsd', only the
FFT, but for the PLV, PPC or WPLI is that way too?
> > >                  >
> > >                  >
> > >                  >
> > >                  >
> > > >                  Many thanks in advanced,
> > >                  > Gabriel.
> > >                  >
> > >                       >
> > >               >
> > >
> >
> > >        > _______________________________________________ > fieldtrip
mailing list >
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >      >
> > >
> >
> > >      > --  > J?rn M. Horschig > PhD Student > Donders Institute for
Brain, Cognition and Behaviour  > Centre for Cognitive Neuroimaging >
Radboud University Nijmegen  > Neuronal Oscillations Group > FieldTrip
Development Team >  > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands
>  > Contact: > E-Mail:
> > > jm.horschig at donders.ru.nl > Tel:    +31-(0)24-36-68493 > Web:
> > > http://www.ru.nl/donders
> >
> > >  >  > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
NL-6525 EN Nijmegen > The Netherlands     >
_______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > >
> >
> > > <font size="3">--------------------------<br />PhD. student Gabriel
Gonz?lez-Escamilla<br />Laboratory of Functional Neuroscience<br
/>Department of Physiology, Anatomy, and Cell Biology<br />University Pablo
de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain
-<br /><br />Email:
> > > ggonesc at upo.es<br />http://www.upo.es/neuroaging/es/</font>
> > >
> > >
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> > > ------------------------------
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > > End of fieldtrip Digest, Vol 30, Issue 29
> > > *****************************************
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
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--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://people.ku.edu/~sjpa/
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From a.stolk at fcdonders.ru.nl  Fri May 31 08:11:23 2013
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
Subject: [FieldTrip] Question about minimum norm estimate pipeline
In-Reply-To: <CAJT2k_82dWWORv_OtvGiTReg4b=X5HkHs2HPbgJpJK9d-cS9gA@mail.gmail.com>
Message-ID: <1914237354.1292588.1369980683984.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Steve, A quick guess; did you correctly align your resliced mri to Talairach space by indicating the commissures ( http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm correct, a point in the same place, e.g. between the hemispheres? This should update the transformation matrix. Best regards, Arjen ----- Oorspronkelijk bericht -----
> Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Vrijdag 31 mei 2013 05:53:45
> Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> Hello all,
> I have not yet gotten a response to my question below, but in the
> meantime I have another question about the minimum norm estimate
> workflow--specifically, about the coordinate system for the
> skull-stripped anatomy in the step described at
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> . I'm confused by the following bit of code:
> % ensure that the skull-stripped anatomy is expressed in the same
> coordinate system as the anatomy
> seg.transform = mri_tal.transform;
> In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> re-aligning to Talairach in the previous step?) whereas seg.coordsys
> is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> (But mri_tal also has a field mri_tal.transformorig, which seg does
> not have.) So should I really be using the same transform for both, as
> shown in the tutorial?
> Apologies if this question is pretty basic; I'm just trying to
> pinpoint where the mis-alignment described in my message below
> occurred, so I want to make sure I understand each step of the
> workflow correctly
> Best,
> Steve
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> On Sat, May 25, 2013 at 1:56 PM, < fieldtrip-request at science.ru.nl >
> wrote:
> >
> > Send fieldtrip mailing list submissions to
> > fieldtrip at science.ru.nl
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > fieldtrip-request at science.ru.nl
> >
> > You can reach the person managing the list at
> > fieldtrip-owner at science.ru.nl
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Sourcespace and volume conductor misaligned
> > (Stephen Politzer-Ahles)
> > 2. Re: fieldtrip Digest, Vol 30, Issue 31 (Johanna Zumer)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sat, 25 May 2013 08:11:18 -0500
> > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > Message-ID:
> > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello all,
> >
> > I am going through the workflow at
> > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > making
> > the volume conduction model using ft_prepare_headmodel(), I noticed
> > that
> > although the volume conduction model and sourcespace have the same
> > orientation and overall size/shape (after I converted the volume
> > conduction
> > model to cm, which wasn't in the tutorial but my original model came
> > out in
> > mm), they don't quite line up, as you can see in this figure:
> >
> > http://i.imgur.com/mGEtLOa.png
> >
> > I did interactively re-align the data to CTF (twice--in step 2 of
> > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > model")
> > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > anatomical data"), so I'm not sure how it ended up this way. The
> > code I've
> > used at each step is basically the same as that in the tutorial.
> >
> > Is there any way to line up my volume conduction model and
> > sourcespace now,
> > without going back and re-running most of the workflow?
> >
> > Best,
> > Steve
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://people.ku.edu/~sjpa/
> > -------------- next part --------------
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> > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130525/561df14f/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Sat, 25 May 2013 20:54:59 +0200
> > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 30, Issue 31
> > Message-ID:
> > <CAL4kA6eTL_TwECF62W-OoWY= Y1mpBR6QoOLh+ug8AcXNbVxQ1A at mail.gmail.com
> > >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Jing,
> >
> > 1. Every MRI scanner is different, so I'm not familiar with that
> > naming
> > scheme, but it seems the 'GAD' at the end of the file name indicates
> > that
> > was with the Gadolinium contrast agent, so I would suggest to not
> > use that,
> > but instead use the first (plain) T1.
> >
> > 2. I'm not sure what to suggest. I assume you can see the vitamin E
> > marker
> > clearly when viewing the DICOM file? Is the issue that some slices
> > are
> > missing in the conversion, or that the contrast on the image is not
> > the
> > same? or right/left flipped?
> >
> > Best,
> > Johanna
> >
> >
> > 2013/5/23 WangJing < 13681530640 at 139.com >
> >
> > > Dear Johanna,
> > >
> > > Thank you for your suggestion.
> > > 1.I have two folder of T1 MRI, one is t1_vibe_tra_4,and another is
> > > t1_vibe_traGAD-5. which one is best?
> > > 2.when I convert MRI from DICOM into CTF format,the vitamin E
> > > marker
> > > didn't be found. what can I do?
> > >
> > > Best Regards,
> > > Jing Wang
> > >
> > >
> > >
> > >
> > > ------------------------------
> > > ----The following is the content of the forwarded email----
> > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > Date?2013-05-22 15:33:13
> > > Subject?fieldtrip Digest, Vol 30, Issue 31
> > >
> > > Send fieldtrip mailing list submissions to
> > > fieldtrip at science.ru.nl
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > or, via email, send a message with subject or body 'help' to
> > > fieldtrip-request at science.ru.nl
> > >
> > > You can reach the person managing the list at
> > > fieldtrip-owner at science.ru.nl
> > >
> > > When replying, please edit your Subject line so it is more
> > > specific
> > > than "Re: Contents of fieldtrip digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. Re: question About head model (Johanna Zumer)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Wed, 22 May 2013 09:30:17 +0200
> > > From: Johanna Zumer < johanna.zumer at donders.ru.nl >
> > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > Subject: Re: [FieldTrip] question About head model
> > > Message-ID:
> > > <CAL4kA6fyA18h3eFkBKu0V5+y4eA1rCZuaf8UGTZ1=
> > > HsAS_X0-w at mail.gmail.com >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Dear Jing,
> > >
> > > It is best to use the T1 MRI rather than the other scans. To open
> > > a DICOM
> > > format file, you can try one of these options:
> > >
> > > % read the DICOM files
> > > mri = ft_read_mri('single_file_of_DICOM_series.IMA');
> > > % or use a graphical file selection[f, p] = uigetfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/uigetfile.html
> > > >('*');
> > > mri = ft_read_mri(fullfile
> > > <
> > > http://www.mathworks.com/access/helpdesk/help/techdoc/ref/fullfile.html
> > > >(p,
> > > f));
> > >
> > >
> > > I copied the above from documentation on the FieldTrip wiki:
> > >
> > > http://fieldtrip.fcdonders.nl/faq/how_can_i_convert_an_anatomical_mri_from_dicom_into_ctf_format
> > >
> > >
> > > Then you can save the 'mri' into a *.mat file for future use with
> > > FieldTrip.
> > >
> > > Best regards,
> > > Johanna
> > >
> > >
> > > 2013/5/22 WangJing < 13681530640 at 139.com >
> > >
> > > > Hi
> > > > I am a freshman about field trip.
> > > > I am trying to build the forward model. but my mri data is
> > > > different from
> > > > the data in the tutorial. So I don't know how to bulid the head
> > > > model. I
> > > > use the date which is from the paper "Open Database of Epileptic
> > > > EEG with
> > > > MRI and Postoperational Assessment of Foci?a Real World
> > > > Verification for
> > > > the EEG Inverse Solutions", http://eeg.pl/epi
> > > . MRI recordings containing a
> > >
> > > > T1, T2 or fluid attenuated inversion recovery (FLAIR) weighted
> > > > brain scans
> > > > with morphologic substrate of the epilepsy (mostly cortical
> > > > dysplasias,
> > > > dysplastic tumors etc.). In some cases there is also a scan with
> > > > the
> > >
> > > > gadolinium (GAD) contrast. The images were collected by Siemens
> > > > Sonata 1.5T
> > > > scanner. The data is stored in the Digital Imaging and
> > > > Communications in
> > > > Medicine (DICOM) format. The name of the scan?s folder indicates
> > > > its
> > > > weighting.The scans have the following resolutions: T1: 512 ?
> > > > 512 pixels,
> > > > pixel spacing 0.4687 mm, slice thickness 1.2 mm, T2: 256 ? 256
> > > > pixels,
> > > > pixel spacing 0.9375 mm,slice thickness 2.5 mm.
> > >
> > > > In the tutorial,the mri data stored in only one file, while the
> > > > data which
> > >
> > > > I used have many files, I don't know how to process. who can
> > > > help me,Thanks1
> > > > Thanks very much!
> > > > Best Reagards
> > > > Jing Wang
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------------
> > > > ----The following is the content of the forwarded email----
> > > > From?fieldtrip-request< fieldtrip-request at science.ru.nl >
> > > > To?fieldtrip< fieldtrip at science.ru.nl >
> > > > Date?2013-05-21 23:59:18
> > > > Subject?fieldtrip Digest, Vol 30, Issue 29
> > > >
> > > > Send fieldtrip mailing list submissions to
> > > > fieldtrip at science.ru.nl
> > > >
> > > > To subscribe or unsubscribe via the World Wide Web, visit
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > or, via email, send a message with subject or body 'help' to
> > > > fieldtrip-request at science.ru.nl
> > > >
> > > > You can reach the person managing the list at
> > > > fieldtrip-owner at science.ru.nl
> > > >
> > > > When replying, please edit your Subject line so it is more
> > > > specific
> > > > than "Re: Contents of fieldtrip digest..."
> > > >
> > > >
> > > > Today's Topics:
> > > >
> > > > 1. Re: problem in connectivityanalysis (Gabriel Gonzalez
> > > > Escamilla)
> > > >
> > > >
> > > > ----------------------------------------------------------------------
> > > >
> > > > Message: 1
> > > > Date: Tue, 21 May 2013 17:52:21 +0200
> > > > From: Gabriel Gonzalez Escamilla < ggonesc at upo.es >
> > > > To: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > > Subject: Re: [FieldTrip] problem in connectivityanalysis
> > > > Message-ID: < 1348f6433edc26f9.519bb455 at upo.es >
> > > > Content-Type: text/plain; charset="iso-8859-1"
> > > >
> > > > Thank you so much for your answer J?rn,
> > > >
> > > >
> > >
> > > > Now I got it, so, I will let the 'fourier' as input to
> > > > ft_connectivityanalysis, because for some indices I will need
> > > > the auto-spectrum, and if I fully undertood what you said, it
> > > > will be the same, as they always take the phase information from
> > > > the fourier transform. And fieltrip will automatically compute
> > > > the csd if the input is the frequency data.
> > > >
> > > >
> > >
> > > > Nevertheless, it give me some error when I tried to use the
> > > > output from 'powandcsd' of freqanalysis, always gives me a
> > > > matrix dimensions error, and when I use the output 'fourier'
> > > > from connectivityanalysis, it computes almost all indices to ok,
> > > > raging from? -1 to 1 (I'm saw that they are signed, so this is
> > > > ok), the problem are the ImC ranging from -inf to inf, and the
> > > > PLV values ranging from 0 to inf, but when I use the 'fourier'
> > > > the values are. Which for me is really weird.
> > > >
> > > >
> > > >
> > >
> > > > I have checked internally, and even when I always use the
> > > > 'fourier' as input, when it internally calculates cross-spectrum
> > > > for the ImC and PLV, the data.crsspctrm is different, e.g:
> > > > data.dimord = 'rpt_rpt_chan_chan_freq'
> > > > ans size(data.crsspctrm) = [1 7 59 59];
> > > >
> > >
> > > > So, both are apparently the same, but the data inside this
> > > > matrices is different,
> > > >
> > > >
> > >
> > > > for example, when calculating the ImC the first 7 columns for
> > > > the first two rows are:
> > > > val(:,:,1,1)
> > > > ?[0.9323? 0.3679? 0.8629? 1.6436? 0.6404? 1.8782? 0.1139]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.8509-0.1555i? 0.2507-0.1066i? 0.8173-0.0290i?
> > > > 1.4328-0.2427i? 0.5457-0.0500i? 1.6505-0.0161i? 0.0993+0.0016i]
> > > >
> > > > while when calculating the PLV are:
> > > > val(:,:,1,1)
> > > > ?[1? 1? 1? 1? 1? 1? 1]
> > > > val(:,:,1,2)
> > > >
> > >
> > > > ?[0.9694-0.2133i? 0.7011-0.3564i? 0.9951-0.0104i?
> > > > 0.9014-0.3481i? 0.9781-0.0819i? 0.9982-0.0046i? 0.9507-0.0483i]
> > > >
> > > >
> > > >
> > >
> > > > I'm pretty sure I'm doing something wrong here, but I don't
> > > > really have a clue,
> > > >
> > > >
> > >
> > > > If I use the fourier transform to calculate the 'csd' in
> > > > ft_connectivity analysis and use this csd as input to all other
> > > > ft_connectivityanalysis indices all of them are set to NaN or 1,
> > > > not ranging between any numbers.
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > > > On the other hand, I have seen searching on the net, that
> > > > fieltrip is capable of create surrogate data, by shifting the
> > > > phase information on every trial for only one electrode of each
> > > > pair while using the original samples of each trials on the
> > > > second channel, but I couldn't find on the manual how to do such
> > > > a thing. Is there any way to compute this kind of surrogates for
> > > > every sensor? or was it something that some one suggest to
> > > > somebody?
> > > >
> > > >
> > > > Many thanks in advanced,
> > > > Gabriel.
> > > >
> > > >
> > > >
> > > >
> > > > ----- Mensaje original -----
> > > > De: "J?rn M. Horschig" < jm.horschig at donders.ru.nl >
> > > > Fecha: Martes, 21 de Mayo de 2013, 9:03 am
> > > > Asunto: Re: [FieldTrip] problem in connectivityanalysis
> > > > A: FieldTrip discussion list < fieldtrip at science.ru.nl >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > Dear Gabriel,
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > >
> > >
> > > > > No. You should think of coherence more as a measure for the
> > > > > consistency of the phase relation between channels across
> > > > > trials, so coherence is just not defined per trial,neither
> > > > > would it make sense to compute coherence for a single trial.
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too? I see some terminology issues here. Let me try
> > > > > to explain in a simple (aka least-mathematical I can think of)
> > > > > way:
> > > > >
> > > >
> > >
> > > > > For all these connectivity measures, we need the phase
> > > > > information from the Fourier transform (FFT) to compute the
> > > > > cross-spectral density matrix (CSD). The CSD can be regarded
> > > > > as the equivalent in the frequency domain to the covariance
> > > > > matrix in the time domain, thus it is a measures how a certain
> > > > > channels activity is co-modulated with another channels
> > > > > activity (for a particular frequency) - makes pretty much
> > > > > sense to make use of this when computing connectivity, right?
> > > > > :)
> > > >
> > >
> > > > > As you might know, a Fourier transform returns complex
> > > > > numbers, where the imaginary part of this number contains
> > > > > phase information. When calling ft_freqanalysis, you can
> > > > > decide if it shall only return the (squared) real part of the
> > > > > frequency spectrum (cfg.output='pow'), or instead the full CSD
> > > > > (cfg.output = 'powandcsd'). Alternatively, you can also let
> > > > > ft_freqanalysis return the raw Fourier coefficients
> > > > > (cfg.output='fourier'). From the Fourier coefficients,
> > > > > however, you can easily obtain the CSD or the power spectrum
> > > > > basically by multiplication the Fourier matrix with itself
> > > > > (transposed). All of these measures quantify the phase
> > > > > relation between channels across trials, and as phase
> > > > > information is coded in the imaginary part of the fourier
> > > > > output, thus for connectivityanalysis you need the CSD which
> > > > > can be obtained either by 'powandcsd' or by 'fourier'.
> > > > >
> > > > > I hope that somehow clarifies your questions.
> > > > >
> > > > > Best,
> > > > > J?rn
> > > > >
> > > > > On 5/17/2013 5:45 PM, Gabriel Gonzalez Escamilla wrote:
> > > > > Dear Fieltrip experts,
> > > > >
> > > >
> > >
> > > > > I have my continuous data imported to fieldtrip with matlab,
> > > > > I'm looking for performing connectivity analysis between pairs
> > > > > of sensors, I have succed as:
> > > >
> > >
> > > > > data.trials {1xNepochs}; % Nepochs = 7, each epoch with 59
> > > > > channels and 2000 samples
> > > > > data.label {59x1};
> > > > > data.time {1xNepochs};
> > > > >
> > > > > then, calculate only the FFT of all sensors as:
> > > > > cfg=[];
> > > > > cfg.output='fourier';
> > > > > cfg.method='mtmfft';
> > > > > cfg.taper='hanning';
> > > > > cfg.foilim=[8.5 9.5];
> > > > > cfg.tapsmofrq=0;
> > > > > cfg.trials='all';
> > > > > cfg.keeptrials='yes';
> > > > > cfg.channel='all';
> > > > > fourier=ft_freqanalysis(cfg, data)
> > > > > as output I get:
> > > > > dimord = 'rpttap_chan_freq'
> > > > > freq= [1x9]
> > > > > fourierspctrm=[7x59x9 double]
> > > > >
> > > > > Then compute the imaginary part of coherency as:
> > > > > cfg=[];
> > > > > cfg.method ='cohe';
> > > > > cfg.complex='imag';
> > > > > cfg.channelcbm={'all' 'all'};
> > > > > coher = ft_connectivityanalysis (cfg, fourier)
> > > > > as output get:
> > > > > dimord='chan_chan_freq';
> > > > > cohspctrm=[59x59x9 double];
> > > > > dof=7;
> > > > >
> > > > > I have two main questions:
> > > > >
> > > >
> > >
> > > > > A) As you see, this makes an average over the epochs of each
> > > > > channel, and not over the samples (which in this case are the
> > > > > 9 frequencies of the FFT), And I would like to have the
> > > > > opposite, this is, to get the imaginary part of coherence for
> > > > > each epoch (repetition) on all my channels and not for each
> > > > > frequency, something like: chan_chan_rpt or chancbm_rpt, Is
> > > > > this possible?
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > B) Another question I have is: for the Imaginary part of
> > > > > Coherence is not necessary to compute the cross-spectrum with
> > > > > 'powandcsd', only the FFT, but for the PLV, PPC or WPLI is
> > > > > that way too?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > Many thanks in advanced,
> > > > > Gabriel.
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > > > _______________________________________________ > fieldtrip
> > > > > mailing list >
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > > >
> > > >
> > >
> > > > > -- > J?rn M. Horschig > PhD Student > Donders Institute for
> > > > > Brain, Cognition and Behaviour > Centre for Cognitive
> > > > > Neuroimaging > Radboud University Nijmegen > Neuronal
> > > > > Oscillations Group > FieldTrip Development Team > > P.O. Box
> > > > > 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: >
> > > > > E-Mail:
> > > > jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:
> > > > http://www.ru.nl/donders
> > >
> > > > > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 >
> > > > > > NL-6525 EN Nijmegen > The Netherlands >
> > > > > > _______________________________________________
> > > > > fieldtrip mailing list
> > > > > fieldtrip at donders.ru.nl
> > > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
> > > >
> > >
> > > > <font size="3">--------------------------<br />PhD. student
> > > > Gabriel Gonz?lez-Escamilla<br />Laboratory of Functional
> > > > Neuroscience<br />Department of Physiology, Anatomy, and Cell
> > > > Biology<br />University Pablo de Olavide<br />Ctra. de Utrera,
> > > > Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email:
> > > > ggonesc at upo.es <br /> http://www.upo.es/neuroaging/es/ </font>
> > > >
> > > >
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> > > >
> > > > ------------------------------
> > > >
> > > > _______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > > >
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> > > > *****************************************
> > > >
> > > > _______________________________________________
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> > > > fieldtrip at donders.ru.nl
> > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> > > ------------------------------
> > >
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> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > > End of fieldtrip Digest, Vol 30, Issue 31
> > > *****************************************
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> >
> > ------------------------------
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > End of fieldtrip Digest, Vol 30, Issue 36
> > *****************************************
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://people.ku.edu/~sjpa/
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From yukaokazaki at gmail.com  Fri May 31 08:21:56 2013
From: yukaokazaki at gmail.com (Yuka Okazaki)
Date: Fri, 31 May 2013 15:21:56 +0900
Subject: [FieldTrip] single subject headmodel and mni-transformed grid
	doesn't fit
Message-ID: <CAKHP_vRT6Ad1nLLOoaUoA5UFTLK5x-yp5jm8+HtY9sD6FER4dQ@mail.gmail.com>

Dear all

I have a problem that single subject headmodel and the warped its grid to
template grid do not fit, as attached figure. I expected they are exactly
fit each other but it seems not.

I generated this figure by following steps. MEG system is yokogawa.
Any advices I should check will be very helpful and appreciated.

Yuka

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
load('~\fieldtrip\template\sourcemodel\standard_sourcemodel3d10mm.mat')
template_grid  = sourcemodel;

% Read mri data
mri2nifti('subject.mri', 'mri.nii');
mri_nifti = ft_read_mri('mri.nii');

% Define fiducial position in MRI coordinate
cfg = [];
cfg.method = 'interactive';
mri = ft_volumerealign(cfg, mri_nifti);

% segment the anatomical MRI
cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg, mri);

% construct volume conductor model (i.e. head model) for each subject
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
vol = ft_convert_units(vol, 'cm');

% create the subject specific grid, using the template grid that has just
been created
cfg = [];
cfg.grid.warpmni   = 'yes';
cfg.grid.template  =  template_grid; %sourcemodel%
cfg.grid.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri;
grid               = ft_prepare_sourcemodel(cfg);

% make a figure of the single subject headmodel, and grid positions
figure;
ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4;
ft_plot_mesh(grid.pos(grid.inside,:),'vertexcolor','r');[image: Inline
image 1]
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From politzerahless at gmail.com  Fri May 31 08:27:19 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Fri, 31 May 2013 01:27:19 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 30, Issue 45
In-Reply-To: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
References: <mailman.340.1369980705.1040.fieldtrip@science.ru.nl>
Message-ID: <CAJT2k_9EcqcEeuGM_F8O7u0047tct6P9ZP-pLf2xdJ61p1tNMA@mail.gmail.com>

Hi Arjen,

Thanks for your message; I did indeed re-align to Talairach after
reslicing, although I can't be sure it was "correct" (the page linked from
the tutorial, http://neuroimage.usc.edu/brainstorm/CoordinateSystems,
didn't give guidelines on how anterior/posteriorly to place the
interhemispheric point, so I just placed it near the top of the head on
about the same plane as the commisures). But it wasn't until the end of the
anatomical processing that I noticed the issue, so I'm wondering if there's
a way to re-align the source space and volume conduction model to each
other without going back to the beginning of the pipeline.

Best,
Steve


> Message: 1
> Date: Fri, 31 May 2013 08:11:23 +0200 (CEST)
> From: "Stolk, A." <a.stolk at fcdonders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question about minimum norm estimate pipeline
> Message-ID:
>         <
1914237354.1292588.1369980683984.JavaMail.root at sculptor.zimbra.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve, A quick guess; did you correctly align your resliced mri to
Talairach space by indicating the commissures (
http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures ) and, if I'm
correct, a point in the same place, e.g. between the hemispheres? This
should update the transformation matrix. Best regards, Arjen -----
Oorspronkelijk bericht -----
> > Van: "Stephen Politzer-Ahles" <politzerahless at gmail.com>
> > Aan: fieldtrip at science.ru.nl
> > Verzonden: Vrijdag 31 mei 2013 05:53:45
> > Onderwerp: [FieldTrip] Question about minimum norm estimate pipeline
> > Hello all,
> > I have not yet gotten a response to my question below, but in the
> > meantime I have another question about the minimum norm estimate
> > workflow--specifically, about the coordinate system for the
> > skull-stripped anatomy in the step described at
> >
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#preprocessing_of_the_anatomical_mrisave_to_disk
> > . I'm confused by the following bit of code:
> > % ensure that the skull-stripped anatomy is expressed in the same
> > coordinate system as the anatomy
> > seg.transform = mri_tal.transform;
> > In my data, mri_tal.coordsys is 'spm' (I presume this is the result of
> > re-aligning to Talairach in the previous step?) whereas seg.coordsys
> > is 'ctf' (as a result of re-aligning to CTF several steps earlier).
> > (But mri_tal also has a field mri_tal.transformorig, which seg does
> > not have.) So should I really be using the same transform for both, as
> > shown in the tutorial?
> > Apologies if this question is pretty basic; I'm just trying to
> > pinpoint where the mis-alignment described in my message below
> > occurred, so I want to make sure I understand each step of the
> > workflow correctly
> > Best,
> > Steve
> > > Message: 1
> > > Date: Sat, 25 May 2013 08:11:18 -0500
> > > From: Stephen Politzer-Ahles < politzerahless at gmail.com >
> > > To: fieldtrip at donders.ru.nl
> > > Subject: [FieldTrip] Sourcespace and volume conductor misaligned
> > > Message-ID:
> > > <CAJT2k_9-hd_sM=hp4P-CUu+=aduSOMyZV7XPG0= fFk0ouR0wzA at mail.gmail.com
> > > >
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hello all,
> > >
> > > I am going through the workflow at
> > > http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate . After
> > > making
> > > the volume conduction model using ft_prepare_headmodel(), I noticed
> > > that
> > > although the volume conduction model and sourcespace have the same
> > > orientation and overall size/shape (after I converted the volume
> > > conduction
> > > model to cm, which wasn't in the tutorial but my original model came
> > > out in
> > > mm), they don't quite line up, as you can see in this figure:
> > >
> > > http://i.imgur.com/mGEtLOa.png
> > >
> > > I did interactively re-align the data to CTF (twice--in step 2 of
> > > "Preprocessing of the anatomical MRI" and in step 4 of "Source
> > > model")
> > > using fiducials, and to Talairach (step 5 of "Preprocessing of the
> > > anatomical data"), so I'm not sure how it ended up this way. The
> > > code I've
> > > used at each step is basically the same as that in the tutorial.
> > >
> > > Is there any way to line up my volume conduction model and
> > > sourcespace now,
> > > without going back and re-running most of the workflow?
> > >
> > > Best,
> > > Steve
> > >
> > > --
> > > Stephen Politzer-Ahles
> > > University of Kansas
> > > Linguistics Department
> > > http://people.ku.edu/~sjpa/
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From stefan.debener at uni-oldenburg.de  Fri May 31 09:18:51 2013
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Fri, 31 May 2013 09:18:51 +0200
Subject: [FieldTrip] Open ostdoc position
Message-ID: <51A84EDB.6010408@uni-oldenburg.de>

The cluster of excellence Hearing4all: Models, Technology and Solutions 
for Diagnostics, Restoration and Support of Hearing at the Carl von 
Ossietzky Universität Oldenburg (in collaboration with Medizinische 
Hochschule Hannover and Leibniz Universität Hannover) is seeking to fill 
the position of a

*Postdoctoral Research Associate in the Field of Auditory 
Psychophysiology *

in the Department of Psychology, Faculty of Medicine and Health Sciences.

The position is available from 1 September 2013, for initially 2 years, 
with prospect for continuation for up to 2.5 more years. Payment is 
depending on previous experience (German TV-L E13, full time).

A paramount goal of the cluster of excellence Hearing4all 
(www.hearing4all.de) is to transform audiology into an "exact" science 
based on the interplay between experiment and theory as well as between 
basic science and clinical research. In the framework provided by the 
cluster the successful candidate is expected to contribute to the 
research goals of task group 2 "Audioneurotechnology and theragnostics" 
or task group 7 "Brain-computer interface for hearing devices", e.g., by:

- studying hearing disorder related maladaptive plasticity in the human 
auditory cortex with non-invasive techniques (EEG, MEG, NIRS);

- electrophysiological characterisation of auditory cortex adaption to 
hearing device use (hearing aids, cochlear implants);

- the role of auditory neurofeedback on speech comprehension;

- the role of multisensory processes in auditory rehabilitation.

Candidates are expected to have an academic university degree in the 
field of psychology, biology, neuroscience, or a related discipline and 
have shown their ability to perform excellent scientific work, usually 
demonstrated by the outstanding quality of their Doctorate/PhD research 
and a good publication record. We are seeking candidates with extensive 
knowledge in at least one of the following methods: advanced EEG 
recording and analysis; near-infrared spectroscopy. Excellent Matlab 
skills are mandatory and good knowledge of EEG analysis software suites 
(e.g., EEGLAB, Fieldtrip, BESA, LORETA) will be an asset. It is also 
necessary to have a background in experimental psychology, and knowledge 
of the German language is required. The Department of Psychology will 
offer an attractive scientific environment with access to research 
dedicated state-of-the-art approaches to human neurophysiological 
techniques (fMRI, NIRS, EEG, MEG, mobile EEG and mobile eye-tracking).

The University of Oldenburg strives to increase the proportion of women 
in science, so we especially encourage female candidates to apply. 
Handicapped applicants will be given preference if equally qualified.

Please send your application including a cover letter, CV, list of 
potential referees, links to recent publications, and copies of 
certificates for academic grades by email to Prof. Stefan Debener 
(Stefan.Debener at uni-oldenburg.de 
<mailto:Stefan.Debener at uni-oldenburg.de>). Feel free to contact Stefan 
Debener for further questions regarding the position. The application 
deadline is July 15, 2013.

-- 
Prof. Dr. Stefan Debener
Neuropsychology	Lab
Department of Psychology
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email: stefan.debener at uni-oldenburg.de

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From baharbahar395 at yahoo.com  Fri May 31 09:48:25 2013
From: baharbahar395 at yahoo.com (Bahar Bahar)
Date: Fri, 31 May 2013 15:48:25 +0800 (SGT)
Subject: [FieldTrip] format conversion
Message-ID: <1369986505.7865.YahooMailNeo@web192306.mail.sg3.yahoo.com>

Hi dear all,

I have a technical question about format converter module via sLORETA software (.slor file to .txt one). Can any one give me some information about the conversion procedure (and the meaning of the column and row of the output file)?

Thanks,
bahar
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From mbj0310 at gmail.com  Fri May 31 11:11:33 2013
From: mbj0310 at gmail.com (Beom Jun Min)
Date: Fri, 31 May 2013 18:11:33 +0900
Subject: [FieldTrip] ft_preprocessing error message during reading some
	files
In-Reply-To: <CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
References: <CA+v9jv+t+iq+SYSn7WEYZ-K_wrcjMUOnsyzJoQ0Hwb0NfChDCg@mail.gmail.com>
	<C350C327-5F51-4B27-BABB-F37254C91994@gmail.com>
	<CA+v9jv+rPO9k8MHf-czCRtfyCq0NMpOpi9UhJD7dfz=-NWO+9Q@mail.gmail.com>
	<CAO5LYip7mzOWY4BRcza=KsM=q8JKz6pnNUD5r09MPnQ+43zFNw@mail.gmail.com>
Message-ID: <CA+v9jvLXKGfwUE4TkGx9t703fQnrtJVi=0w6ZFGBYVLKAvseSw@mail.gmail.com>

Dear respondent,

Thank you for your advices.
I will try these methods.

Best regards




2013/5/30 Chungki Lee <dr.chungki.lee at gmail.com>

> Hi Min
>
> you'd better use ft_definetrial routine before  ft_preprocessing.
>
> example)
>
>     cfg                              = [];
>     cfg.dataset                 = filename;  % string
>     cfg.trialdef.eventtype  =  your define text; % string
>     cfg.trialdef.eventvalue = your label value;  % integer
>     cfg.trialdef.prestim    = before onset time (sec); % positive
> integer, not negative integer
>     cfg.trialdef.poststim   = after onset time (sec); % positve integer
>     cfg                            = ft_definetrial(cfg);
>     data                          = ft_preprocessing(cfg);
>
> have fun ^^
>
>
> 2013/5/30 Beom Jun Min <mbj0310 at gmail.com>
>
>> Dear Julian Keil,
>>
>> Thank you for your reply.
>> I agree with that your problem was similar with mine.
>> My data was acquired by Neuroscan also.
>> There might a problem associated with .CNT file in the newer version.
>>
>> Could you tell me the number of the older version you used?
>>
>> Best Regards
>>
>>
>>
>> 2013/5/29 Julian Keil <julian.keil at gmail.com>
>>
>>> Dear BJ Min,
>>>
>>> what type of data are you trying to read in?
>>> I had similar problems when reading in .CNT data.
>>> Also, with some systems you have to specify the bit rate (e.g.
>>> Neuroscan).
>>> For me, reading in data with an older version of FieldTrip solved the
>>> problem, but this was in 2011, so I cannot say if the problem with .CNT
>>> files has been solved.
>>>
>>> Good Luck
>>>
>>> Julian
>>>
>>>  ********************
>>> *Dr. Julian Keil*
>>> *
>>> *
>>> AG Multisensorische Integration
>>> Psychiatrische Universitätsklinik
>>> der Charité im St. Hedwig-Krankenhaus
>>> Große Hamburger Straße 5-11, Raum E 307
>>> 10115 Berlin
>>>
>>> Telefon: +49-30-2311-1879
>>> Fax:        +49-30-2311-2209
>>>
>>> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>>>
>>> Am 29.05.2013 um 11:47 schrieb Beom Jun Min:
>>>
>>> Dear all,
>>>
>>> Hello, my name is BJ Min from Korea.
>>>
>>> I'm dealing with EEG data of many subjects.
>>>
>>> When I run ft_preprocessing, the error message below shows with only
>>> some files of my data. (not all files)
>>>
>>>  Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>> ??? Error using ==> ft_read_data at 149
>>> cannot read data after the end of the file
>>>
>>> Error in ==> ft_preprocessing at 577
>>>       dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
>>> begsample, 'endsample', endsample, 'chanindx', rawindx,
>>>       'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat',
>>> cfg.dataformat)
>>>
>>> I think that there might be a kind of problem in data acquisition, and I
>>> modified below scripts in the ft_read_data function with comment %.
>>>
>>> % % test whether the requested data segment is not outside the file
>>> % if any(begsample<1)
>>> %   error('FILEIO:InvalidBegSample', 'cannot read data before the begin
>>> of the file');
>>> % elseif any(endsample>(hdr.nSamples*hdr.nTrials))
>>> %   error('FILEIO:InvalidEndSample', 'cannot read data after the end of
>>> the file');
>>> % end
>>>
>>> After that, the ft_preprocessing worked well.
>>>
>>> However, the files with the first problem showed additional warning
>>> message while running ft_definetrial. (not error message)
>>>
>>> Warning: Integer operands are required for colon operator when used as
>>> index
>>> > In fileio\private\loadcnt at 464
>>>   In ft_read_header at 1450
>>>   In ft_preprocessing at 398
>>>
>>> Warning: rounding "endsample" to the nearest integer
>>> > In ft_read_data at 100
>>>   In ft_preprocessing at 577
>>>
>>> Also, during ft_redefinetrial, following warning message occurs.(not
>>> error message)
>>>
>>> Warning: removing inconsistent sampleinfo
>>> > In ft_datatype_raw at 97
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 104
>>>
>>> Warning: the trial definition in the configuration is inconsistent with
>>> the actual data
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 74
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> Warning: reconstructing sampleinfo by assuming that the trials are
>>> consecutive segments of a continuous recording
>>> > In utilities\private\warning_once at 116
>>>   In utilities\private\fixsampleinfo at 79
>>>   In ft_datatype_raw at 154
>>>   In ft_checkdata at 213
>>>   In ft_redefinetrial at 206
>>>
>>> I wonder if these messages during ft_redefinetrial mean wrong defining
>>> trials.
>>> Should I continue these process like this, modifying the
>>> ft_preprocessing function?
>>> Or, is it better to exclude some erroneous files?
>>>
>>> Best regards
>>>
>>> --
>>> BeomJun Min, M.D.
>>>
>>> Department of Medical System Engineering (DMSE)
>>> Gwangju Institute of Science and Technology (GIST)
>>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>>> 500-712, Republic of Korea (South)
>>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>>  _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>> --
>> BeomJun Min, M.D.
>>
>> Department of Medical System Engineering (DMSE)
>> Gwangju Institute of Science and Technology (GIST)
>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>> 500-712, Republic of Korea (South)
>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>> E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> ----------------------------------------------------------------
> Chungki Lee, Ph.D.
> Post-doc
> Biomedical Research Institute
> Korea Institute of Science and Technology
> E-mail: chungki at kist.re.kr
> Tel:+82-2-958-5636, C.P: +82-10-5223-7309
> ----------------------------------------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
BeomJun Min, M.D.

Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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From thomas.wunderle at esi-frankfurt.de  Fri May 31 11:42:03 2013
From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas)
Date: Fri, 31 May 2013 09:42:03 +0000
Subject: [FieldTrip] channel combination problems
Message-ID: <27E5CAD9145EEC41BB9B34C01716A1983046156B@UM-EXCDAG-A01.um.gwdg.de>

Hi all,

I'm new in fieldtrip and I try to get the cfg.channelcmb to work, because I want to plot the connectivity between the channels of different laminar electrodes,
let's say the connectivity between channel 1:24 and 25:38

I tried the following:
cfg           = [];
cfg.method    = 'mtmfft';
cfg.taper     = 'dpss';
cfg.output    = 'fourier';
cfg.tapsmofrq = 1;
freq          = ft_freqanalysis(cfg, data)

The output is:
>> freq
freq =
            label: {3x1 cell}
           dimord: 'rpttap_chan_freq'
            freq: [1x101 double]
            fourierspctrm: [500x3x101 double]
            cumsumcnt: [500x1 double]
            cumtapcnt: [500x1 double]
             cfg: [1x1 struct]


I then run

cfg           = [];
cfg.method    = 'coh';
cfg.channelcmb = {freq.label{1} freq.label{2};freq.label{2} freq.label{1}};
coh= ft_connectivityanalysis(cfg, freq);

And the output here is:

>> coh
coh =
       labelcmb: {2x2 cell}
       dimord: 'chan_freq'
       cohspctrm: [2x101 double]
        freq: [1x101 double]
        dof: 500
        cfg: [1x1 struct]

As you can seen, the output of dimord is 'chan_freq' so in the subsequent call of ft_connectivityplot I get an error message:

cfg           = [];
cfg.parameter = 'cohspctrm';
ft_connectivityplot(cfg, coh);

??? Error using ==> ft_connectivityplot at 99
the data should have a dimord of chan_chan_freq or chancmb_freq


If I use in ft_freqanalysis the cfg.method = 'powandcsd', cfg.channelcmb seems to have no effect at all,
the coherence is computed for all possible pairs.

I also don't understand the difference between "cfg.channelcmb" and "cfg.labelcmb"

Can you help me in how I should correctly use the cannelcmb and labelcmb options?

Thanks for your help,
Thomas



-----
Dr. Thomas Wunderle
Ernst Strüngmann Institute (ESI) for Neuroscience<http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
in Cooperation with Max Planck Society <http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews>
Deutschordenstrasse 46
60528 Frankfurt am Main, Germany
www.esi-frankfurt.de<http://www.esi-frankfurt.de/>
thomas.wunderle at esi-frankfurt.de<mailto:thomas.wunderle at esi-frankfurt.de>
Tel:   +49 69 96769 519
Fax:   +49 69 96769 555

Sitz der Gesellschaft: Frankfurt am Main
Registergericht: Amtsgericht Frankfurt - HRB 84266
Geschäftsführer: Prof. Dr. Pascal Fries


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From sid.kouider at gmail.com  Fri May 31 11:56:19 2013
From: sid.kouider at gmail.com (Sid Kouider)
Date: Fri, 31 May 2013 11:56:19 +0200
Subject: [FieldTrip] postdoctoral position on EEG/BCI in Paris
Message-ID: <007701ce5de5$1b083620$5118a260$@gmail.com>

The Department of Cognitive Science at the Ecole Normale Supérieure (Paris)
invites applications for a postdoctoral position to work on Brain-Computer
Interfaces and Virtual Reality in the framework of the CEEDs European
project ( <http://ceeds-project.eu/> http://ceeds-project.eu/). 

 

The post-doc will mainly be in charge of :

1) setting a BCI loop between a virtual environment and an EEG system

2) optimize online detection of specific EEG patterns 

3) participate in the design and elaboration of research protocols.

 

The successful applicant will be affiliated to the Brain and Consciousness
team of Pr Sid Kouider (http://www.lscp.net/persons/sidk/). The Department
of Cognitive Science offers a rich research environment composed of a
multidisciplinary set of research units on philosophy, cognitive psychology,
cognitive neurosciences and computational neurosciences. Our research team,
at the interface of these disciplines, is working on the cognitive and
neural determinants of consciousness, with an emphasis on the distinction
between unconscious perception and perceptual awareness. Our lab is  located
in central Paris, within the historical Quartier Latin.

 

Candidates should have at least a PhD degree in a relevant domain and a
solid training in EEG, Brain-Computer interfaces and machine learning.
Experience with virtual reality is desirable but not a prerequisite.

 

The position will start on September 1st, 2013.

The appointment is for one year initially but can be extended later on.

The net salary will range between 2 100 and 2 500 euros/month depending on
qualifications.

 

Consideration of applicants will commence June 1st, 2013 and will continue
until the position is filled.

 

Knowledge of French is not required as the team is international and verbal
interactions are primarily in English. 

 

Please send a CV along with the names and contact information of two
references to Sid Kouider (sid.kouider at ens dot fr) and Cécile Girard
(cecilegirard20 @ gmail dot com)

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Pr Sid Kouider, CNRS research director

Ecole Normale Supérieure

LSCP, Pavillon Jardin,

29 rue d'Ulm, 75005 Paris, France

www.lscp.net/persons/sidk/

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

 

 

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From haiteng.jiang at gmail.com  Fri May 31 12:15:59 2013
From: haiteng.jiang at gmail.com (Haiteng Jiang)
Date: Fri, 31 May 2013 12:15:59 +0200
Subject: [FieldTrip] time-domain granger causality in Fieldtrip?
Message-ID: <CAHSK_TRQUv9aqda123QUWA9jfWpWaJzpBnWxF0QTO08xtM58pA@mail.gmail.com>

Hi all,
   is it possible to run time-domain granger causality in Fieldtrip?
                                                         Best,
                                                          Haiteng






-- 
Haiteng Jiang
PhD candidate
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen

Visiting address
Room 2.32
Donders Centre for Cognitive Neuroimaging
Kapittelweg 29
6525 EN  Nijmegen
the Netherlands

 Tel.: +31 (0)243668291
 Web:  https://sites.google.com/site/haitengjiang/
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From d.lozanosoldevilla at fcdonders.ru.nl  Fri May 31 15:49:03 2013
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Fri, 31 May 2013 15:49:03 +0200 (CEST)
Subject: [FieldTrip] error when using ctf2grad
In-Reply-To: <51A7A9A1.6020401@gmail.com>
Message-ID: <2006439449.1303047.1370008143778.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Ye, Are you using a recent fieldtrip version? The ctf2grad function has recently updated improving its robustness. I don't have any clue why G3AR but it basically means that your CTF system has a specific gradiometer balancing. By the way, which CTF system are you using: CTF64, CTF151, CTF275? In any case, I could have a look if you file a bug and send to me the *.res4 file and we'll figure out what's happening (but please try with a recent Fieldtrip version and tell me) Regarding your gradiometer question, I asked Robert and this is the answer we can provide (please correct me if I'm wrong here), the CTF system sensors consist in first-order axial gradiometer that measure the magnetic field gradient change in the radial direction (orthogonal to the scalp). The following is taken from the CTF documentation "MEG File Formats - release 5.2.1" appendix C. --- Higher-order gradiometer formation is a noise-cancellation technique exclusive to the CTF MEG System. It permits the MEG detectors to be sensitive to the weak signals of the brain, yet impervious to the much stronger sources from the environment. This process, which is carried out in real time, allows the system to be run without the expense of magnetic shielding, or in combination with a standard shielded room for enhanced noise reduction. In order to calculate the forward solution, the same procedure must be performed on any field data calculated from a simulated dipole. The procedure consists of calculating the field at each coil in the sensor as well as each coil in a set of reference channels. The field values at the reference channels are then multiplied by the appropriate weight and subtracted from the MEG sensor channels. --- The data set on disk contains in the header the parameters that are used to convert the data between the original (raw) representation and the higher-order gradiometer representation. This conversion can be done in real-time during acquisition, but can also be done (and undone) afterwards using CTF DataEditor, or using ft_denoise_synthetic.m function. The grad structure included in the FieldTrip representation (i.e. hdr.grad or data.grad) should be consistent with the data, hence it contains grad.balance.current grad.balance.G1BR grad.balance.G2BR grad.balance.G3BR and potentially other "balancing" schemes (your "G3AR " for instance). The grad.balance.current describes which balancing was applied to the data and to the specification of the sensor array (grad.tra) for the forward computation. In order to provide a more intuitive description, I've made a wiki FAQ to explain How does the CTF higher-order gradiometer work: http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work All the best, Diego ----- Original Message -----
> From: "Ye Mei" <frank.ye.mei at gmail.com> > To: fieldtrip at science.ru.nl > Sent: Thursday, 30 May, 2013 9:33:53 PM > Subject: [FieldTrip] error when using ctf2grad > Hi All, > > I have some problem using ctf2grad. > > The program will set grad.balance.current = 'G3AR';, > and then do getfield(grad.balance, grad.balance.current) > but > grad.balance = G1BR: [1x1 struct] > G2BR: [1x1 struct] > G3BR: [1x1 struct] > > and has no G3AR in it. So an error will pop up. > > Can anyone help me with that? > > Also, What do G1BR, G2BR, G3BR, G3AR stand for? > > > thanks, > Ye > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- PhD Student Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6525 EN Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/
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From lkystra at hotmail.it  Fri May 31 17:15:01 2013
From: lkystra at hotmail.it (lucia abbatantuoni)
Date: Fri, 31 May 2013 17:15:01 +0200
Subject: [FieldTrip] distorsion of .edf file
In-Reply-To: <4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
References: <DUB107-W29524CAF810BFEAC80CE6BD9910@phx.gbl>, ,
	<CABu=cRcBrhDG-wWRJqxzFZ5J=F_TSjfR-5KdhBfMLwuPy0yOXA@mail.gmail.com>,
	<DUB107-W17F6497CB13EEA2F38E270D9910@phx.gbl>,
	<4C650B52-1AFF-4CAE-9F28-D320B9E00C75@donders.ru.nl>
Message-ID: <DUB107-W21B51E9DC3913CBC8A1A05D9920@phx.gbl>

Hi Jan-Mathijs,
the specifies that you asked to me, are: 

fieldtrip version: 20130401
operating system: windows 7
matlab version : I use R2011a (64bits) or R2007b (32bits)

I
 want to read a portion of my EEG signal of 3600 sec * 500 Hz. When I used
 a previous version of fieldtrip (2011-12-14), the lenght of the window wasn't 3600*500 but less. 

" Warning: Integer operands are required for colon operator when used as index 
> In read_edf at 348 "

With fieldtrip 20130401 the length of the window is right, but, when I plot the signal, I can see its distorsion.
Thank you for your attention,
Lucia

From: jan.schoffelen at donders.ru.nl
Date: Thu, 30 May 2013 18:31:22 +0200
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

Hi Lucia,
Perhaps you need to be a bit more specific. In particular with respect to the fieldtrip version, matlab version, operating system, and warning message.Otherwise all of us are shooting in the dark.Best wishes,Jan-Mathijs

On May 30, 2013, at 5:33 PM, lucia abbatantuoni wrote:I try and... it's not a good solution.

Date: Thu, 30 May 2013 15:43:59 +0200
From: zriouil.imane at gmail.com
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] distorsion of .edf file

I have the same problem.

if you want to read your data. it's possible to use ft_read_data(filename')


2013/5/30 lucia abbatantuoni <lkystra at hotmail.it>
Dear all,
I'm analyzing EEG files in format .edf with matlab. Many files after the use of read_edf, have a distorsion. Matlab indicate a warning for the 348 row of read_edf . Can someone give to me a help?

Best regards,
Lucia

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
  Zriouil Imane



_______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
Max Planck Institute for Psycholinguistics,Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nlTelephone: +31-24-3614793
http://www.hettaligebrein.nl



_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From ebrahimi_nia at yahoo.com  Fri May 31 17:56:55 2013
From: ebrahimi_nia at yahoo.com (Fatemeh Ebrahimi nia)
Date: Fri, 31 May 2013 08:56:55 -0700 (PDT)
Subject: [FieldTrip] loreta2fieldtrip function error
In-Reply-To: <51A78CC1.6030906@berkeley.edu>
References: <1369934092.15336.YahooMailNeo@web122405.mail.ne1.yahoo.com>
	<51A78CC1.6030906@berkeley.edu>
Message-ID: <1370015815.5183.YahooMailNeo@web122402.mail.ne1.yahoo.com>

Dear respondent,

Thank you for your advices.
I have used the function that you have updated. It works out. Can you give me information about the output structure (What do the matrixes refer to?) or advise a reference to study about that please? 

Best,
Fatemeh



________________________________
 From: Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu>
To: fieldtrip at science.ru.nl 
Sent: Thursday, May 30, 2013 10:30 AM
Subject: Re: [FieldTrip] loreta2fieldtrip function error
 


Hi Fatemeh,

I had the same error recently when I did the same. I filed the bug,
    see http://bugzilla.fcdonders.nl/show_bug.cgi?id=2144

I did create a work around. In the LORETA program, you can export
    the source data as a text file. You can read that text file in with
    loreta2fieldtrip.m. It's a bit of a patch, but it worked for me. 

Hope this helps,
Ingrid


On 5/30/2013 10:14 AM, Fatemeh Ebrahimi nia wrote:

Hi dear all,
>
>
>I am analyzing EEG data. I have computed sLORETA (.slor) from ERP data. Now I want to read and convert LORETA source reconstruction into a
>MATLAB data structure using "loreta2fieldtrip" function, But I have gotten the bellow error.
>
>
>**** Error using fread
>
>Invalid precision.
>Error in loreta2fieldtrip (line 85)
>activity = fread(fid, [voxnumber Ntime], 'float = >single'); ***
>
>
>Can someone give me a help?
>
>
>
>Best regards,
>Fatemeh
>
>
>
>
>_______________________________________________
fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From robince at gmail.com  Fri May 31 18:14:15 2013
From: robince at gmail.com (Robin)
Date: Fri, 31 May 2013 17:14:15 +0100
Subject: [FieldTrip] some of the requested samples occur twice
Message-ID: <CALsWBNOxcuA=LCMONaGWObU4fdZ3+vskGGFcKdTZE4jGRoW47Q@mail.gmail.com>

I have a problem in preprocessing where I am getting this error:

"""
some of the requested samples occur twice in the data

Error in ft_artifact_zvalue (line 262)
      dat{trlop} = ft_fetch_data(data,        'header', hdr, 'begsample',
      trl(trlop,1)-fltpadding, 'endsample', trl(trlop,2)+fltpadding,
      'chanindx', sgnind, 'checkboundary', strcmp(cfg.continuous,'no
Error in ft_artifact_muscle (line 158)
    [tmpcfg, artifact] = ft_artifact_zvalue(tmpcfg, data);
"""

I think this is because I am manually adding some extra padding to the
trials so that the artifact filtering can use that padding (I am doing
the artifact filtering on data in memory which is output from
ft_denoise_pca). So in this case it is not a problem if consecutive
trials overlap a bit.

I would therefore like to disable this error and wondered what is the
best way to do it. I am a bit confused because ft_artifact_zvalue
calls ft_fetch data with a "checkboundary" option which looks like it
might be what I want (and set correctly), but ft_fetch_data doesn't
seem to use that option. Instead it has an allowoverlap option.

So for now I will manually add the allowoverlap option to the call in
ft_artifact_zvalue, but I wondered what checkboundary doesn't appear
in ft_fetch_data or if this might be a bug.

Cheers

Robin