From daria.laptinskaya at googlemail.com  Tue Dec  1 09:58:46 2015
From: daria.laptinskaya at googlemail.com (Daria Laptinskaya)
Date: Tue, 1 Dec 2015 09:58:46 +0100
Subject: [FieldTrip] SCD and coherence analysis
In-Reply-To: <52d6-565c1c80-25-55c3b400@102538225>
References: <52d6-565c1c80-25-55c3b400@102538225>
Message-ID: <CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ@mail.gmail.com>

Hi Barbara,

try this:
 sens=ft_read_sens('GSN-HydroCel-257.sfp');
 cfg=[];
 cfg.elec=sens;

Hope it helps :-)
Daria






2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:

> Dear Fieltripers,
>
> I would like to do coherence analysis. I did a SCD analysis on my data
> first ('finite' method), and want to run ft_mvaranalysis now. I get
> the error
>
> Error using ft_datatype_sens (line 186)
> inconsistent number of channels in sensor description
>
> As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> fieldtrip (my raw data set has 257 channels), but there are only 256
> channels left after the SCD analysis. Can this cause the problem?
>
> Has anyone had this problem before and can provide a solution? I only
> found one prior entry with this topic, but there was no final solution for
> it.
>
>
> Thanks and all the best,
> Barbara
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From barbara.schorr at uni-ulm.de  Tue Dec  1 15:18:31 2015
From: barbara.schorr at uni-ulm.de (Barbara Schorr)
Date: Tue, 01 Dec 2015 15:18:31 +0100
Subject: [FieldTrip] =?utf-8?q?SCD_and_coherence_analysis?=
In-Reply-To: <mailman.19.1448967602.14550.fieldtrip@science.ru.nl>
Message-ID: <38ba-565dac00-3-4dd4ed00@147935417>

Dear Daria,

I did exactly this. 
The problem occurs afterwards, when I want to run ft_mvaranalysis on the data that result from ft_scalpcurrentdensity.
In the fieldtrip document it states, that the output data of  ft_scalpcurrentdensity has the same format as the input data.
When I run ft_mvaranalysis on the original data, everything works fine, but with the SCD data I get this error that the number of channels in sensor description is inconsistent.

Has anyone else experienced this problem?

Best,
Barbara


Am Dienstag, 01. Dezember 2015 12:00 CET, fieldtrip-request at science.ru.nl schrieb: 
 
> 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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> 
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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: power suppression during DICS beamforming ?
>       (Mait? Crespo Garc?a)
>    2. Re: SCD and coherence analysis (Daria Laptinskaya)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 30 Nov 2015 15:31:20 +0000 (UTC)
> From: Mait? Crespo Garc?a <maity_winky at yahoo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] power suppression during DICS beamforming ?
> Message-ID:
> 	<1881724873.21184223.1448897480847.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Fr?d?ri,
> maybe you have the solution already.
> In case not, could you explain how did you get the last two plots? Are spectra computed after averaging across all virtual channel spectra or you are representing the spectrum of the source with maximal power?
> Best,Maite
> 
> 
> 
>     El Jueves 26 de noviembre de 2015 13:55, Fr?d?ric Roux <f.roux at bcbl.eu> escribi?:
>  
> 
>  Dear all,
> 
> I am observing a counter-intuitive result after applying the spatial filters obtained from DICS beamforming to my MEG data.
> 
> The plot in the attachment summarizes the issue: The raw data shows a clear peak of activity at 10 Hz, however, after applying the spatial filter to the MEG data the spectrum of the virtual channels shows that power in this frequency band is reduced. The same also happens when I apply a spatial filter in the gamma range for power at 70 Hz to the raw MEG signals.
> 
> Is this something that falls out of the beamformer math due to the fact how the algorithm suppresses power at all locations by minimizing the noise level, or is there something wrong with my code? I (maybe naively) assumed that the results should come out the opposite. On the other hand, when plotting the noise normalized maps (NAI) of both the alpha and gamma beamformers the sources look quite accurate. Should I normalize with the level of noise first before plotting the spectrum to see the expected results (ie an upregulation of power instead of a downregulation of power)?
>  
> The code that I use to generate the figures is:
> 
> % 1) compute CSD matrix
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.foilim = [10 10];
> cfg.tapsmofrq = 2;
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> 
> [csd] = ft_freqanalysis(cfg,meg_data);
> 
> 
> % 2) compute DICS filter
> cfg = [];
> cfg.method = 'dics';
> cfg.grad = meg_data.grad;
> cfg.headmodel = vol;
> cfg.frequency = csd.freq;
> 
> cfg.dics.realfiter = 'yes';
> cfg.dics.fixedori = 'yes';
> 
> [alpha_filter]= ft_sourceanalysis(cfg,csd);
> 
> % 3) compute the virtual channel data
> 
> VC = meg_data;
> VC.trial = cell(1,length(meg_data.trial));
> VC.label = cell(1,length(alpha_filter.avg.pow));
> 
> for i = 1:length(VC.trial)
> ? for j = 1:length(VC.label)
> 
> ? ? ? VC.trial{i}(j,:) = alpha_filter{j}*meg_data.trial{i};
> ? ? ? VC.label(j) = {['virtual_channel',num2str(j)]};
> ? end;
> end;
> 
> % 4) compute the spectrum of the virtual channel data
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> cfg.tapsmofrq = 1;
> cfg.foi = 0.1:100;
> 
> [pow] = ft_freqanalysis(cfg,VC);
> 
> 
> Any help or suggestions would be greatly appreciated.
> 
> Fred
> 
> --
> Fr?d?ric Roux
> Postdoctoral Scientist, Marie-Curie fellow
> BCBL. Basque Center on Cognition, Brain & Language.
> 
> f.roux at bcbl.eu
> Tel: +34 943 309 300 Ext 211
> Fax: +34 943 309 052
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> ---------------------------------------------------------------------------
> 
> ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
>   
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> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 1 Dec 2015 09:58:46 +0100
> From: Daria Laptinskaya <daria.laptinskaya at googlemail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] SCD and coherence analysis
> Message-ID:
> 	<CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Barbara,
> 
> try this:
>  sens=ft_read_sens('GSN-HydroCel-257.sfp');
>  cfg=[];
>  cfg.elec=sens;
> 
> Hope it helps :-)
> Daria
> 
> 
> 
> 
> 
> 
> 2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:
> 
> > Dear Fieltripers,
> >
> > I would like to do coherence analysis. I did a SCD analysis on my data
> > first ('finite' method), and want to run ft_mvaranalysis now. I get
> > the error
> >
> > Error using ft_datatype_sens (line 186)
> > inconsistent number of channels in sensor description
> >
> > As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> > fieldtrip (my raw data set has 257 channels), but there are only 256
> > channels left after the SCD analysis. Can this cause the problem?
> >
> > Has anyone had this problem before and can provide a solution? I only
> > found one prior entry with this topic, but there was no final solution for
> > it.
> >
> >
> > Thanks and all the best,
> > Barbara
> >
> >
> > _______________________________________________
> > 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 61, Issue 1
> ****************************************
 
 
 
 





From eriksenj at ohsu.edu  Wed Dec  2 03:04:56 2015
From: eriksenj at ohsu.edu (K Jeffrey Eriksen)
Date: Wed, 2 Dec 2015 02:04:56 +0000
Subject: [FieldTrip] accommodating air pockets in FEM head model
Message-ID: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>

Hi,

I am reading the FieldTrip documentation on creating an FEM model and see that the following tissue types are output from the segmentation process:

Gray
White
Csf
Skull
Scalp

Q1: Since I am using a 256 channel EGI system with electrodes over the lower part of the head and face, I absolutely need to be able to include air voxels as well. Anyone have any knowledge of such a possibility?

Q2: Beyond that I would also like to include other tissue types such as fat, muscle, and eyeball (vitrious). I suppose I could find other segmentation software to simply create a more varied segmentation and insert it in the processing pipeline, but would like to know if that would mess anything up.

Q3: Next, can the FEM handle anisotropic conductivities for white matter and skull?

Q4: has anyone out there actually used the FDM model?

Thanks,
-Jeff Eriksen

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From carsten.wolters at uni-muenster.de  Wed Dec  2 08:53:17 2015
From: carsten.wolters at uni-muenster.de (Carsten Wolters)
Date: Wed, 2 Dec 2015 08:53:17 +0100
Subject: [FieldTrip] accommodating air pockets in FEM head model
In-Reply-To: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
References: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
Message-ID: <565EA36D.5030005@uni-muenster.de>

Hi Jeff,

Q3:
yes, FEM can model anisotropy and white matter is anisotropic, but skull 
is a three-layered-structure
consisting of spongiosa and compacta, see
http://www.ncbi.nlm.nih.gov/pubmed/20690140

For Q4:
FEM allows geometry-adaptation, see
http://www.ncbi.nlm.nih.gov/pubmed/17694865
As far as I know, modeling using irregular meshes might get difficult to 
implement within an FDM framework.

For Q1 and Q2:
Mainly tissues between sources and electrodes are important to be 
modeled (so white matter anisotropy
is only important for deeper sources) and FSL and freesurfer can do a 
good job on segmentation.
Air-compartments can possibly best be modeled by hand-correction of the 
FSL output.
Please see
http://www.ncbi.nlm.nih.gov/pubmed/24671208
on how we solve forward modeling to be able to combine EEG and MEG.

More infos are available in the two following theses:
http://www.sci.utah.edu/~wolters/PaperWolters/2014/Lanfer_Dissertation_July2-2014.pdf
http://www.sci.utah.edu/~wolters/PaperWolters/2015/Umit_Aydin_Dissertation_2015.pdf


Best regards
      Carsten

Am 02.12.2015 um 03:04 schrieb K Jeffrey Eriksen:
>
> Hi,
>
> I am reading the FieldTrip documentation on creating an FEM model and 
> see that the following tissue types are output from the segmentation 
> process:
>
> Gray
>
> White
>
> Csf
>
> Skull
>
> Scalp
>
> Q1: Since I am using a 256 channel EGI system with electrodes over the 
> lower part of the head and face, I absolutely need to be able to 
> include air voxels as well. Anyone have any knowledge of such a 
> possibility?
>
> Q2: Beyond that I would also like to include other tissue types such 
> as fat, muscle, and eyeball (vitrious). I suppose I could find other 
> segmentation software to simply create a more varied segmentation and 
> insert it in the processing pipeline, but would like to know if that 
> would mess anything up.
>
> Q3: Next, can the FEM handle anisotropic conductivities for white 
> matter and skull?
>
> Q4: has anyone out there actually used the FDM model?
>
> Thanks,
>
> -Jeff Eriksen
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From RICHARDS at mailbox.sc.edu  Wed Dec  2 14:55:57 2015
From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN)
Date: Wed, 2 Dec 2015 13:55:57 +0000
Subject: [FieldTrip] Head segmentation
Message-ID: <A84D7FC4-B8F0-4D9D-8EF0-8190153B1580@mailbox.sc.edu>

Jeff

The resources from Carsten Wolters and the answers were right on.

We have a 128 channel system.

We add “nasal cavity” which includes nasal, throat, and sinuses in our FEM model.  We do a lot of the segmenting with FSL (bet, fast, betsur, SPMf) and custom programs, and then do manual editing to identify the air passages.  The separate segments are then put together with a custom program. The air cavities might be important for the 256-channel EGI system, where on the sides and front of the face the electrodes could have some dipolar sources and the places in between would affect the source estimation.  Anything below the skull, not air cavity, we give a conductivity of muscle, which is very close to scalp; again the electrodes below the skull are over something and I presume would need a realistic estimated head media and conductivity.

As I wrote earlier, we have been using FT for FEM recently; also have gotten good (similar to FEM) results with the Dipoli BEM model. I have one already-published supplemental information that briefly describes our FEM model, and one in-press supplemental information, both articles using the EMSE program.  I am working on our first publication using the FEM from FT.

Re “Mainly tissues between sources and electrodes are important to be modeled (so white matter anisotropy is only important for deeper sources)”.  This may be practically correct, but I have suspected (and EGI’s rationale for whole-head coverage) that to get a good measure of a dipolar source whose positive or negative pole land somewhere below the skull area, one needs a good model of the head over all the places where the current flow is manifested.  We have some prefrontal  sources with large negative potentials exhibiting on the frontal-central 10-10 electrodes, and which have a large positive scalp potential on the “Oz” electrodes.  However, it turns out these potentials show up on Iz and in the EGI electrodes below Iz (128 channel), so having a model for scalp and muscle over the neck might be important.  I don’t know what the effect is of leaving these out, but I have preferred to do the whole head segmentation in case these have some effect.

One last consideration.  Most BEM and FEM models on the FT site use the segmentation of the brain, skull, and scalp about at the level of the MNI head.  This does not include the electrodes below the horizon of the MNI head, and there is a lot of area below the MNI head that is covered by the EGI 128 and 256 channel systems.  This adds significantly to the volume of the voxels used for the FEM estimation.  For BEM models we cut the head off at about 10% below the level of the lowest EGI 128 channel electrodes, and generally have done so also for the FEM models we use in FT. The electrodes are located on the places below the MNI head, so one has to have a “head” model with positions below those typically used in the FT’s demo programs.  We do a whole head MRI down to the neck, and then use a custom program to get a MRI volume with a head that extends about 10% lower than the lowest EGI-128 electrodes.

John


***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<mailto:richards-john at sc.edu>
HTTP: jerlab.psych.sc.edu
***********************************************

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From francois.tadel at mcgill.ca  Wed Dec  2 22:03:33 2015
From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=)
Date: Wed, 2 Dec 2015 16:03:33 -0500
Subject: [FieldTrip] Error in ft_dipolefitting.m ?
Message-ID: <565F5CA5.9080409@mcgill.ca>

Hello,

When fitting single dipoles on multiple time points at once, I have an 
error line 578:
     source.dip.unit = headmodel.unit;
The syntax is incorrect that source.dip is an array with multiple 
dipoles. Should this be replaced with the following line ?
     [source.dip.unit] = deal(headmodel.unit);

Cheers,
Francois


From erin.white at sickkids.ca  Wed Dec  2 22:55:40 2015
From: erin.white at sickkids.ca (Erin White)
Date: Wed, 2 Dec 2015 21:55:40 +0000
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
 multiplotER and multiplotTFR images
In-Reply-To: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
References: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
Message-ID: <0D4EE8880DEE3047BEC905C0EC463F8C2769EBD7@SKMBXX03.sickkids.ca>

Hi Steve,
Thanks so much for your helpful comment!
I'll give this a try!

All the best

Erin

----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [stephen.politzer-ahles at ling-phil.ox.ac.uk]
Sent: November 27, 2015 7:28 AM
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] Adding tick marks to the X and Y axes in multiplotER and multiplotTFR images

Hi Erin,

I don't use the multiplot functions much, so my solution is clunky and there may be others on the list with a better way to do this. But just in case, here's how I do it:

Rather than using multiplot, I make each plot individually, and use the subplot() command to arrange multiple plots into a figure. Within each subplot, I just use some custom code to draw the ticks. For example:

tickspots = [-200:200:1000]; % one tick every 200 ms, from -200 to 1000 ms
tickheight = [-.5 .5]; % how high and low the ticks will go

for tickspots = tickspot % iterate through tick spots
plot( [tickspot tickspot], tickheight, 'k' ); % plot each tick as a black line
end;


Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab, Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/<https://urldefense.proofpoint.com/v2/url?u=http-3A__users.ox.ac.uk_-7Ecpgl0080_&d=BQMFaQ&c=Dvjge31PR3JZstzk2paJYiflTxRSxp35GBhsbHdd2Zw&r=I8lBTmv7Y9oqVGvTj_vgdd74EEIPprGsdbxcnXduG2k&m=lnKeei_k8PbT5JQEFb_AdyFHThYK07IvJphgqiA4pd8&s=yHg_UuAaKeXLiYDOWrOeEtt0pDtbBRlk3w7TC1hOKdw&e=>


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

Message: 2
Date: Thu, 26 Nov 2015 12:48:25 +0000
From: Erin White <erin.white at sickkids.ca<mailto:erin.white at sickkids.ca>>
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
        multiplotER and multiplotTFR images
Message-ID:
        <0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca<mailto:0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
I'm new at programming and was wondering if someone could help with something that I'm sure is simple.
I'd like to add tick marks to my multiplotER and multiplotTFR figures so that the timing and amplitude (for multiplotER) and timing and frequency (for multiplotTFR) scales are presented clearly. For example, I'd like a tick mark on my X axes every 200 ms, and on the y axes, every 2 mV for ER images and every 5 Hz for TFR images.

Could anyone suggest what I should add to my code to show this?

Thanks very much!

Erin












----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813<tel:%28647%29834-7813>

________________________________

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
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End of fieldtrip Digest, Vol 60, Issue 23
*****************************************

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From p.babaeeghazvini at vu.nl  Fri Dec  4 20:14:26 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Fri, 4 Dec 2015 19:14:26 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
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From ronny.ibrahim at mq.edu.au  Mon Dec  7 05:36:14 2015
From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim)
Date: Mon, 7 Dec 2015 15:36:14 +1100
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency
	data
Message-ID: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a
time-frequency datasets that I've acquired using the ft_freqanalysis
function. When I run ft_freqstatistics on the data it would give me stats
result which is based on comparing the absolute values of power spectrum
instead the relative change with respect to the baseline. I have tried to
perform to do my relative change power spectrum data manually but it seems
that when I run the ft_freqstatistics it produces an error of which I could
not figure out on why.

Here is my code:



C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6}
outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13}
outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};



C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6}
outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13}
outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};



%% Performing cluster statistics for the paradigm

cfg                  = [];

cfg.layout           = 'EEG_KR.lay';

lay                  = ft_prepare_layout(cfg);

% Needs to change this

cfg.latency          = [0 0.6]; %Need to look this up according to what

cfg.frequency        = [8 12];% Need to do it for different frequency bands
(theta, alpha, beta, gamma).

cfg.channel          = 'all';

cfg.avgovertime      = 'no';

cfg.avgoverfreq      = 'yes';

cfg.avgoverchan      = 'no';

cfg.statistic        = 'ft_statfun_indepsamplesT';

cfg.numrandomization = 1000;

cfg.correctm         = 'cluster';

cfg.method           = 'montecarlo';

cfg.computeprob    = 'yes';

cfg.computecritval = 'yes';

cfg.clusteralpha     = 0.05;

cfg.clusterstatistic = 'maxsum';

cfg.minnbchan        = 3;

cfg.tail             = 0;

cfg.clustertail      = 0;

cfg.alpha            = 0.05;

cfg_neighb.layout    = lay;

cfg_neighb.method    = 'triangulation';

cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);

cfg.ivar             = 1;

cfg.design = [ones(1,18) 2*ones(1,18)];

stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});



%% Plotting significant clusters



cfg                  = [];

cfg.alpha            = 0.05;

cfg.parameter        = 'stat';

cfg.layout           = lay;

ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output
structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny
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From j.herring at donders.ru.nl  Mon Dec  7 09:24:32 2015
From: j.herring at donders.ru.nl (Herring, J.D. (Jim))
Date: Mon, 7 Dec 2015 08:24:32 +0000
Subject: [FieldTrip] Clusterstatistics on relative change (%) time
 frequency	data
In-Reply-To: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
References: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
Message-ID: <3D00B7615FB58D46A0B49B9AD67A33EB279C7AFB@exprd01.hosting.ru.nl>

Dear Ronny,

What error do you get when running this code?

You can perform a (relative) baseline correction using ft_freqbaseline with cfg.baselinetype = ‘relative’ or ‘relchange’ and cfg.baseline = [your baseline window];. If your code works on absolute values it should also work on baseline-corrected values using ft_freqbaseline.

Best,

Jim

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Ronny Ibrahim
Sent: maandag 7 december 2015 5:36
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency data

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a time-frequency datasets that I've acquired using the ft_freqanalysis function. When I run ft_freqstatistics on the data it would give me stats result which is based on comparing the absolute values of power spectrum instead the relative change with respect to the baseline. I have tried to perform to do my relative change power spectrum data manually but it seems that when I run the ft_freqstatistics it produces an error of which I could not figure out on why.

Here is my code:

C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6} outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13} outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};

C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6} outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13} outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};

%% Performing cluster statistics for the paradigm
cfg                  = [];
cfg.layout           = 'EEG_KR.lay';
lay                  = ft_prepare_layout(cfg);
% Needs to change this
cfg.latency          = [0 0.6]; %Need to look this up according to what
cfg.frequency        = [8 12];% Need to do it for different frequency bands (theta, alpha, beta, gamma).
cfg.channel          = 'all';
cfg.avgovertime      = 'no';
cfg.avgoverfreq      = 'yes';
cfg.avgoverchan      = 'no';
cfg.statistic        = 'ft_statfun_indepsamplesT';
cfg.numrandomization = 1000;
cfg.correctm         = 'cluster';
cfg.method           = 'montecarlo';
cfg.computeprob    = 'yes';
cfg.computecritval = 'yes';
cfg.clusteralpha     = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan        = 3;
cfg.tail             = 0;
cfg.clustertail      = 0;
cfg.alpha            = 0.05;
cfg_neighb.layout    = lay;
cfg_neighb.method    = 'triangulation';
cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);
cfg.ivar             = 1;
cfg.design = [ones(1,18) 2*ones(1,18)];
stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});

%% Plotting significant clusters

cfg                  = [];
cfg.alpha            = 0.05;
cfg.parameter        = 'stat';
cfg.layout           = lay;
ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny

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From julian.keil at gmail.com  Mon Dec  7 09:30:25 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 09:30:25 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
Message-ID: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

> Hello
> 
> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> Not from the voxel indicating maximum power ([maxval,
>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
> 
> Regards,
> Parinaz.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From p.babaeeghazvini at vu.nl  Mon Dec  7 12:52:55 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 11:52:55 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From julian.keil at gmail.com  Mon Dec  7 17:57:10 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 17:57:10 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
Message-ID: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>

Hi Parinaz,

> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

> How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

> Hi Julian,
> 
> Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:
> 
> cfg = []
> 
> cfg.atlas = atlas;
> 
> cfg.roi = atlas.tissuelabel(1)
> 
> cfg.inputcoord = 'mni';
> 
> mas = ft_volumelookup(cfg,grid);
> 
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.xgrid      =
> 
> cfg.grid.ygrid      =
> 
> cfg.grid.zgrid      =
> 
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> 
> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.
> 
> an other question that I have is that: when I compute the maximum index from
>  [maxvalr, maxpowindxr] = max(srcetask.avg.pow)
> 
> How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)
> 
> Regards,
> Parinaz.
> 
> 
> 
> 
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
> Sent: Monday, December 07, 2015 9:30 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch
> 
> Hi Parinaz,
> 
> I'm not sure if I understood your question correctly.
> Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?
> 
> In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
> In the second case, it's a tad more complicated, but here's how I do it:
> 1. Compute the virtual channels for all grid points in the cortex
> 2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
> 3. Build a high-resolution 3D-Grid on the standard MRI
> 4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
> 5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.
> 
> I hope this helps, let me know otherwise.
> 
> Julian
> 
> Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:
> 
>> Hello
>> 
>> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = hdm;
>> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.keepfilter   = 'yes';
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> Not from the voxel indicating maximum power ([maxval,
>>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
>> 
>> Regards,
>> Parinaz.
>> _______________________________________________
>> 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 p.babaeeghazvini at vu.nl  Mon Dec  7 20:20:15 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 19:20:15 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>,
 <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C29CB@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your help now it is completely clear for me.

Parinaz.
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 5:57 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Julian Keil [julian.keil at gmail.com<mailto:julian.keil at gmail.com>]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
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

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From amickan1990 at gmail.com  Thu Dec 10 18:14:10 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Thu, 10 Dec 2015 18:14:10 +0100
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation test
Message-ID: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>

Dear all,

I'm just starting to work on a cluster-based permutation test script based
on the tutorial for within-subject designs on the fieldtrip website. I ran
into an issue when computing the [stat] matrix. I used the code as it was
on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages.
However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat
and stat.negclusterslabelmat matrices which should apparantly contain far
more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume
has to do with the fact that "neg" does not have the appropriate matrix
dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me
out.

Thanks in advance!

Best,
Anne
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From nick.peatfield at gmail.com  Thu Dec 10 20:13:10 2015
From: nick.peatfield at gmail.com (Nicholas A. Peatfield)
Date: Thu, 10 Dec 2015 11:13:10 -0800
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
In-Reply-To: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
Message-ID: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>

Hi Anne,

To get an answer/suggestion you should provide the part of your script
detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:

> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Nicholas Peatfield, PhD
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From jan.schoffelen at donders.ru.nl  Thu Dec 10 20:36:45 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 10 Dec 2015 19:36:45 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based
	permutation	test
In-Reply-To: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
 <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9@fcdonders.ru.nl>

Hi Anne,

I agree with Nick, some more information would be helpful. At this stage my wild guess (assuming that you did not constrain your ‘search space’, using cfg.channel and cfg.latency before calling ft_timelockstatistics) would be that there’s a major discrepancy in the descriptive dimensions of your data (i.e. the ‘labels’ and the time points) across the input arguments. FieldTrip does an explicit check on the labels and time points, it only proceeds to do calculations on the channels and time points that are present in each and every input argument. With respect to time points: this could even mean that numerical inaccuracies are the showstopper here. These inaccuracies could be easily introduced when e.g. downsampling.

Best,
Jan-Mathijs


On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:

Hi Anne,

To get an answer/suggestion you should provide the part of your script detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:amickan1990 at gmail.com>> wrote:
Dear all,

I'm just starting to work on a cluster-based permutation test script based on the tutorial for within-subject designs on the fieldtrip website. I ran into an issue when computing the [stat] matrix. I used the code as it was on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages. However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat and stat.negclusterslabelmat matrices which should apparantly contain far more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume has to do with the fact that "neg" does not have the appropriate matrix dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me out.

Thanks in advance!

Best,
Anne


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



--
Nicholas Peatfield, PhD

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

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From aishwaryaselvaraj1708 at gmail.com  Fri Dec 11 07:30:39 2015
From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj)
Date: Fri, 11 Dec 2015 12:00:39 +0530
Subject: [FieldTrip] filed trip
In-Reply-To: <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
Message-ID: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
wrote:

> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Regards,
Aishwarya Selvaraj
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From stan.vanpelt at donders.ru.nl  Fri Dec 11 09:09:14 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Fri, 11 Dec 2015 08:09:14 +0000
Subject: [FieldTrip] filed trip
In-Reply-To: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
 <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0@exprd03.hosting.ru.nl>

Dear Aishwarya,

The data structure should look something like this:

% 1. Load data
load EEGdata.mat

% 2. Make FieldTrip structure, manually
data.label={'Channel1Name’,’Channel2Name’,’Channel3Name’}; %your channel names
data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each trial: channelsxtimepoints data
data.fsample=500; %your recording sampling frequency
data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data sample (e.g: [0 0.02 0.04 0.06 etc])

Going through the Walktrough Tutorial will be the best starting point when you just started to use FieldTrip: http://www.fieldtriptoolbox.org/walkthrough
After that, you may go through the other Tutorial documentation or Example Matlab scripts.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
Sent: vrijdag 11 december 2015 7:31
To: FieldTrip discussion list
Subject: Re: [FieldTrip] filed trip

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com<mailto:mishra408 at gmail.com>> wrote:
Hi Aishwarya,

I faced the similar problem. You are supposed to change your data
(.mat format) in a data structure that is read by fieldtrip. For that
you need at least following information
1. Channel label and their location (If you don't have this file you
can use standard file available in Fieldtrip and you can include only
those electrode that you have been using in your experiment)
2. sampling rate of the data (that you would have done while recording the data)
3. time vector
4. no. of trials

You can create them in MATLAB and put them together in a structure
along with your recorded data. This worked for me.

--
Ashutosh Mishra
5th year Integrated BS-MS student
Department of Physical Sciences
Indian Institute of Science Education and Research, Kolkata
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--
Regards,
Aishwarya Selvaraj
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From juangpc at gmail.com  Fri Dec 11 11:43:05 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 11:43:05 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating sourcemodel
Message-ID: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for
source-reconstruction of MEG or EEG data <http://goog_2124598831>
​"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized
space
​" procedure , there is an example code. This code throws an error when I
execute it with a version of Fieldtrip I downloaded yesterday. I think I
have downloaded correctly all the required info (Subject01.zip).

​Code:

% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
the coordinate system
 % segment the template brain and construct a volume conduction model
(i.e. head model): % this is needed to describe the boundary that
define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
Convert the vol to cm, because the CTF convenction is to express
everything in cm.
 % construct the dipole grid in the template brain coordinates% the
negative inwardshift means an outward shift of the brain surface for
inside/outside detection
cfg = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
= 1;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
 = 'yes';
cfg.inwardshift = -1.5;
​​
cfg.headmodel   = template_headmodel;

The problem occurs when I execute ​this line:

​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position
information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required
"sensor position information" by executing this code just before
(considering the folder with the information downloaded for this subject is
located just there:

​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';

Then the rest of the sample code in the tutorial can be executed with no
issues.

template_grid   = ft_prepare_sourcemodel(cfg);
 % make a figure with the template head model and dipole gridfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
'none');alpha 0.5; camlight
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));


My questions:

​Is there a better solution for this problem? Maybe I can learn a little
bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one
is placing the downloaded subject's data, and it is platform dependent.
Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan
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From jan.schoffelen at donders.ru.nl  Fri Dec 11 11:54:54 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 10:54:54 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925@fcdonders.ru.nl>

Hi Juan,

We’ll look into this specific issue soon, it should work without specifying sensor positions. However, for now and in general I would recommend just using a pre-cooked template grid. These can be found in fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I will make this more explicit shortly.

Best,

Jan-Mathijs

On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From jan.schoffelen at donders.ru.nl  Fri Dec 11 13:19:39 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 12:19:39 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>

Hi Juan,

I could reproduce your issue, and have done 2 things:
- I updated the wiki to make it clear that it would be easier to use a pre-cooked grid.
- I adjusted ft_prepare_sourcemodel so that it also works when only providing the template_headmodel, as per the example code.
The new version of ft_prepare_sourcemodel will become available in tonight’s release on the ftp-server.

Best wishes, and thanks for noticing.
Jan-Mathijs


On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From juangpc at gmail.com  Fri Dec 11 13:55:57 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 13:55:57 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating
	sourcemodel
In-Reply-To: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
 <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
Message-ID: <CAPO7YLJFQ=qB0xVBBS8WEiD2PW4OzaOnZX=xVzn_rgxd-vm9HQ@mail.gmail.com>

Hi Jan-Mathijs,

Thanks for your quick response, H2H. I've actually learned about precooked
models with your answer. Many thanks.

In the same page, in the part "Make the individual subjects' grid", there
seems to be a unit-related problem. One can find this code

% read the single subject anatomical MRI
mri = ft_read_mri('Subject01.mri');
 % segment the anatomical MRI
cfg        = [];
cfg.output = 'brain';
seg        = ft_volumesegment(cfg, mri);
 % construct the volume conductor model (i.e. head model) for each
subject% this is optional, and for the purpose of this tutorial only
required for% plotting, later on
cfg        = [];
cfg.method = 'singleshell';
headmodel  = ft_prepare_headmodel(cfg, seg);
 % create the subject specific grid, using the template grid that has
just been created
cfg                = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.warpmni
  = 'yes';
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.template
 = template_grid;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.nonlinear
= 'yes'; % use non-linear normalization
cfg.mri            = mri;grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>
             = ft_prepare_sourcemodel(cfg);
 % make a figure of the single subject headmodel, and grid
positionsfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>;
hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on;
ft_plot_vol(headmodel, 'edgecolor', 'none', 'facealpha', 0.4);
ft_plot_mesh(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.pos(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.inside,:));

When executing it, there seems to be a problem with dimensions. "headmodel"
struct is in mm and "grid" struct is in cm. So unfortunately the resulting
figure ends up being something like
[image: Inline image 1]

I've tested to specify 'mm' units in the configuration struct before
calling ft_prepare_sourcemodel: cfg.grid.unit='mm';

Or by calling ft_convert_units right after ft_prepare_sourcemodel.

grid=ft_convert_units(grid,'mm');

Both solutions work fine, producing a figure very similar to the one in the
tutorial. I've included the first solution in the wiki.

I hope this is ok.

Best,



Juan

On Fri, Dec 11, 2015 at 1:19 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Juan,
>
> I could reproduce your issue, and have done 2 things:
> - I updated the wiki to make it clear that it would be easier to use a
> pre-cooked grid.
> - I adjusted ft_prepare_sourcemodel so that it also works when only
> providing the template_headmodel, as per the example code.
> The new version of ft_prepare_sourcemodel will become available in
> tonight’s release on the ftp-server.
>
> Best wishes, and thanks for noticing.
> Jan-Mathijs
>
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831/>
> ​ <http:/>"
> ​​
>
> ​ ​when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ​" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ​Code:
>
> % NOTE: the path to the template file is user-specific
> template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system
>  % segment the template brain and construct a volume conduction model (i.e. head model): % this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.
>  % construct the dipole grid in the template brain coordinates% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
> cfg = [];
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
> cfg.inwardshift = -1.5;
> ​​
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ​this line:
>
> ​
> ​
> ​
> ​
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ​
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ​
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ​Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because​ my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ​ I figure this can be interesting to other people.​
> ​
> ​
>
> Best,
>
>
> Juan
>
> _______________________________________________
> 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 frsantos at fpce.up.pt  Fri Dec 11 13:57:52 2015
From: frsantos at fpce.up.pt (Fernando Ferreira-Santos)
Date: Fri, 11 Dec 2015 12:57:52 +0000
Subject: [FieldTrip] 3rd International Conference of the ESCAN
Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFD7B96@SRVMBX01.fpceup.psi.up.pt>

Dear Colleagues,
The 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) is accepting submissions for symposia and oral/poster presentations. The conference will take place in that will take place in Porto, Portugal, between 23-26 of June, 2016, at the Porto Palácio Congress Hotel & Spa (http://www.hotelportopalacio.com/en/hotel-overview.html).

The submission deadline is the 8th of January, 2016. Please find all the details in the conference website: www.escan2016.eu<http://www.escan2016.eu>
We would appreciate it if you could pass this information along to other colleagues and students. Attached you may find a poster with the call for submissions.

We are looking forward to seeing you in Porto in 2016!
Fernando Babosa and Fernando Ferreira-Santos (University of Porto)
Chairs of the Local Organizing Committee


P.S.: Apologies if you get multiple postings of this announcement.

--
Laboratory of Neuropsychophysiology
Faculty of Psychology and Education Sciences
University of Porto
Rua Alfredo Allen, 4200-135 Porto (Portugal)
Tel.: +351 226079700
http://www.fpce.up.pt/labpsi/

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From marlene.boenstrup at googlemail.com  Fri Dec 11 21:30:46 2015
From: marlene.boenstrup at googlemail.com (=?UTF-8?Q?Marlene_B=C3=B6nstrup?=)
Date: Fri, 11 Dec 2015 21:30:46 +0100
Subject: [FieldTrip] ft_sourceinterpolate fails when cfg.moveinward and
 cfg.inwardshift was used to create sourcemodel
Message-ID: <CAG0LeNnQE60kuJZHh7jSOYpNLOurgtnn3gBODE0LkXB_NTuzAg@mail.gmail.com>

Dear fieldtrip-community,

I struggle at plotting source reconstruction results, and my routine even
fails when using the template structural data.
I think it is based on a shortcoming of the ft_sourceinterpolation
function. This is why I am optimistic to find help in this platform:
I prepare the leadfields based on the standard_sourcemodel3d6mm, the vol
called standard_bem.mat, the electrode positions defined in
standard_1005.elc.
Since some of the dipoles that are assigned as "inside" in the
sourcemodel3d6mm are actually sticking out of the inner bem boundary,
leading to distorted leadfields, I re-prepare the sourcemodel based on the
following specifications:

mri=ft_read_mri('single_subj_T1.nii');
mri.coordsys = 'spm';
mri = ft_volumereslice([], mri);
cfg=[];
cfg.mri  = mri;
cfg.elec=elec;
cfg.vol=vol;
cfg.grid.warpmni   = 'yes';
cfg.grid.template  = grid; % sourcemodel3d6mm
cfg.grid.nonlinear = 'no';
cfg.moveinward=5;
cfg.inwardshift=0;
grid    = ft_prepare_sourcemodel(cfg);

this comes out with a vector of positions in three dimensional space, all
of them being assigned to inside and none of them as outside.
The leadfields prepared based on this sourcemodel look very convincing and
the ft_sourceanalysis function also works.
But the problem is to interpolate this on the anatomical image:
Nested in the function ft_sourceinterpolate, the function ft_checkdata,
specifically the subfunction source2volume leads to a misconfiguration with
all the positions of the functional data being distributed in to a full 3D
volume. In the end the orthoplot of the brain is a big fully activated
cube.

I hope someone has a good idea how to deal with this issue in fieldtrip and
shares his/her expertise with us.

Many greetings,

Marlene
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From amickan1990 at gmail.com  Sat Dec 12 16:12:57 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Sat, 12 Dec 2015 16:12:57 +0100
Subject: [FieldTrip] fieldtrip Digest, Vol 61, Issue 7
In-Reply-To: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
References: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
Message-ID: <CANX43OLN8qog=xL7qjDpRp_yTPjKV1oQhgbT4Wuy5z0fDmqTiw@mail.gmail.com>

Dear Nick and Jan-Mathijs,

thanks for your emails. Here is the part of the code that details the cfg
inputs. I basically stuck to what was in the tutorial:

cfg = [];
cfg.channel = 'all';

% prepare neighbouring channels

cfg_neighb = [];
cfg_neighb.method = 'distance';
cfg.channel = 'all';
cfg_neighb.feedback = 'yes';
cfg_neighb.layout = 'easycapM3.mat';

neighbours = ft_prepare_neighbours(cfg_neighb, Correct{1});

% settings for statistics

cfg = [];
cfg.channel = {'EEG'};
cfg.latency = [0 1];

cfg.method = 'montecarlo';
cfg.statistic = 'depsamplesT';
cfg.correctm = 'cluster';
cfg.clusteralpha = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan = 2;
cfg.neighbours = neighbours;
cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = 0.5;
cfg.numrandomization = 500;

% prepare design
subj = 24;
design = zeros(2,2*subj);
for i = 1:subj
  design(1,i) = i;
end
for i = 1:subj
  design(1,subj+i) = i;
end
design(2,1:subj)        = 1;
design(2,subj+1:2*subj) = 2;

cfg.design = design;
cfg.uvar  = 1;
cfg.ivar  = 2;

Best,
Anne

On Fri, Dec 11, 2015 at 12:00 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. Stats matrix incomplete - cluster-based permutation test
>       (Anne Mickan)
>    2. Re: Stats matrix incomplete - cluster-based permutation   test
>       (Nicholas A. Peatfield)
>    3. Re: Stats matrix incomplete - cluster-based       permutation
>  test
>       (Schoffelen, J.M. (Jan Mathijs))
>    4. Re: filed trip (aishwarya selvaraj)
>    5. Re: filed trip (Pelt, S. van (Stan))
>    6. possible bug in tutorial code for creating sourcemodel (Juan)
>    7. Re: possible bug in tutorial code for creating sourcemodel
>       (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 10 Dec 2015 11:13:10 -0800
> From: "Nicholas A. Peatfield" <nick.peatfield at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID:
>         <CADzq99=
> 3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:
>
> > Dear all,
> >
> > I'm just starting to work on a cluster-based permutation test script
> based
> > on the tutorial for within-subject designs on the fieldtrip website. I
> ran
> > into an issue when computing the [stat] matrix. I used the code as it was
> > on the website:
> >
> > [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
> >
> > with the Correct and Incorrect matrices looking as follows:
> >
> > Correct{1}
> >
> >         avg: [34x600 double]
> >        time: [1x600 double]
> >     fsample: '500'
> >       label: {34x1 cell}
> >      dimord: 'chan_time'
> >         dof: [34x600 double]
> >         var: [34x600 double]
> >
> > The function runs without problems, i.e I don't get any error messages.
> > However, the result seems incomplete.
> >
> > stat =
> >                    prob: [25x1 double]
> >             posclusters: []
> >     posclusterslabelmat: [25x1 double]
> >         posdistribution: [1x500 double]
> >             negclusters: [1x1 struct]
> >     negclusterslabelmat: [25x1 double]
> >         negdistribution: [1x500 double]
> >                 cirange: [25x1 double]
> >                    mask: [25x1 logical]
> >                    stat: [25x1 double]
> >                     ref: [25x1 double]
> >                  dimord: 'chan_time'
> >                   label: {25x1 cell}
> >                    time: 0
> >                     cfg: [1x1 struct]
> >
> > Specifically, I later run into trouble with the stat.posclusterslabelmat
> > and stat.negclusterslabelmat matrices which should apparantly contain far
> > more values something more like 25x500 instead of 25x1. When calling
> > neg_int = all(neg(:, m(k):m(k+1)), 2)
> > I get the "Index exceeds matrix dimensions" error message which I assume
> > has to do with the fact that "neg" does not have the appropriate matrix
> > dimensions
> > (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
> >
> > Where is the error / where should I look for the error?
> >
> > Some further design details:
> > Nsubj = 24
> > 2 conditions = Correct, Incorrect
> > Within-subject design
> > sampling rate = 500
> > 34 channels
> >
> > I hope I gave enough / the necessary information for someone to help me
> > out.
> >
> > Thanks in advance!
> >
> > Best,
> > Anne
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Nicholas Peatfield, PhD
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 3
> Date: Thu, 10 Dec 2015 19:36:45 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Anne,
>
> I agree with Nick, some more information would be helpful. At this stage
> my wild guess (assuming that you did not constrain your ?search space?,
> using cfg.channel and cfg.latency before calling ft_timelockstatistics)
> would be that there?s a major discrepancy in the descriptive dimensions of
> your data (i.e. the ?labels? and the time points) across the input
> arguments. FieldTrip does an explicit check on the labels and time points,
> it only proceeds to do calculations on the channels and time points that
> are present in each and every input argument. With respect to time points:
> this could even mean that numerical inaccuracies are the showstopper here.
> These inaccuracies could be easily introduced when e.g. downsampling.
>
> Best,
> Jan-Mathijs
>
>
> On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <
> nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:
> amickan1990 at gmail.com>> wrote:
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Nicholas Peatfield, PhD
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Dec 2015 12:00:39 +0530
> From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <
> CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
> wrote:
>
> > Hi Aishwarya,
> >
> > I faced the similar problem. You are supposed to change your data
> > (.mat format) in a data structure that is read by fieldtrip. For that
> > you need at least following information
> > 1. Channel label and their location (If you don't have this file you
> > can use standard file available in Fieldtrip and you can include only
> > those electrode that you have been using in your experiment)
> > 2. sampling rate of the data (that you would have done while recording
> the
> > data)
> > 3. time vector
> > 4. no. of trials
> >
> > You can create them in MATLAB and put them together in a structure
> > along with your recorded data. This worked for me.
> >
> > --
> > Ashutosh Mishra
> > 5th year Integrated BS-MS student
> > Department of Physical Sciences
> > Indian Institute of Science Education and Research, Kolkata
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Dec 2015 08:09:14 +0000
> From: "Pelt, S. van (Stan)" <stan.vanpelt at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0 at exprd03.hosting.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Aishwarya,
>
> The data structure should look something like this:
>
> % 1. Load data
> load EEGdata.mat
>
> % 2. Make FieldTrip structure, manually
> data.label={'Channel1Name?,?Channel2Name?,?Channel3Name?}; %your channel
> names
> data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each
> trial: channelsxtimepoints data
> data.fsample=500; %your recording sampling frequency
> data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data
> sample (e.g: [0 0.02 0.04 0.06 etc])
>
> Going through the Walktrough Tutorial will be the best starting point when
> you just started to use FieldTrip:
> http://www.fieldtriptoolbox.org/walkthrough
> After that, you may go through the other Tutorial documentation or Example
> Matlab scripts.
>
> Best,
> Stan
>
> --
> Stan van Pelt, PhD
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University
> Montessorilaan 3, B.01.34
> 6525 HR Nijmegen, the Netherlands
> tel: +31 24 3616288
>
> From: fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
> Sent: vrijdag 11 december 2015 7:31
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] filed trip
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com
> <mailto:mishra408 at gmail.com>> wrote:
> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Dec 2015 11:43:05 +0100
> From: Juan <juangpc at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID:
>         <CAPO7YL+ufEwMRmBZk=
> XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831>
> ?"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
> the coordinate system
>  % segment the template brain and construct a volume conduction model
> (i.e. head model): % this is needed to describe the boundary that
> define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
> Convert the vol to cm, because the CTF convenction is to express
> everything in cm.
>  % construct the dipole grid in the template brain coordinates% the
> negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html
> >.resolution
> = 1;
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
>  = 'yes';
> cfg.inwardshift = -1.5;
> ??
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ?this line:
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html
> >hold
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where one
> is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
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> >
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Dec 2015 10:54:54 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Juan,
>
> We?ll look into this specific issue soon, it should work without
> specifying sensor positions. However, for now and in general I would
> recommend just using a pre-cooked template grid. These can be found in
> fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I
> will make this more explicit shortly.
>
> Best,
>
> Jan-Mathijs
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:
> juangpc at gmail.com>> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data<http://goog_2124598831/>
> ?<http:/>"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
> coordinate system
>
> % segment the template brain and construct a volume conduction model (i.e.
> head model):
> % this is needed to describe the boundary that define which dipole
> locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert
> the vol to cm, because the CTF convenction is to express everything in cm.
>
> % construct the dipole grid in the template brain coordinates
> % the negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
> = 1;
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
> = 'yes';
> cfg.inwardshift = -1.5;
>
> ??
> cfg.headmodel   = template_headmodel;
>
>
> The problem occurs when I execute ?this line:
>
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
>
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> % make a figure with the template head model and dipole grid
> figure<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
> hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto: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 61, Issue 7
> ****************************************
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From LordJojo at gmx.de  Sat Dec 12 19:59:26 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Sat, 12 Dec 2015 19:59:26 +0100
Subject: [FieldTrip] channel problem ft_freqstatistics
Message-ID: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>

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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sun Dec 13 12:12:40 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sun, 13 Dec 2015 11:12:40 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
Message-ID: <CAJT2k_85VtNAPj4J2tib5c2C4ZnJn6xZm6qr7GqceAAH2EA6=A@mail.gmail.com>

Hi Anne,

It looks like you're running stats on grand-average structures created with
cfg.keepindividual='no' (because your Correct and Incorrect structures have
an .avg field). I always do stats on a grand-average structure created with
cfg.keepindividual='yes' (which will yield a structure with no .avg field,
and instead an .individual field, which in your case will be 24x34x600,
since you have participants). Do things work out better if you try it that
way?

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
>
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From recasensmarc at gmail.com  Sun Dec 13 16:07:08 2015
From: recasensmarc at gmail.com (Marc Recasens)
Date: Sun, 13 Dec 2015 15:07:08 +0000
Subject: [FieldTrip] channel problem ft_freqstatistics
In-Reply-To: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
Message-ID: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>

Hi Johannes,

I think the same problem has been reported before in:
http://mailman.science.ru.nl/pipermail/fieldtrip/2015-November/009789.html

Roy Cox looked into the problem with quite detail and found the bug in
the ft_get_selection
function, line 630-631 during a call to "*label = union(label,
selchannel);"*. I recently had the same problem and it was solved after
commenting that line. However it might be better if you update FieldTrip to
the last version where this issue is fixed.

Hope that helps.

Best wishes
Marc

On Sat, Dec 12, 2015 at 6:59 PM, Jojo Klemt <LordJojo at gmx.de> wrote:

> Dear community
>
> My name is Johannes Klemt and I'm analysing eeg/emg-power data of patients
> and healthy controls for my medical doctorate in Tübingen.
> I have a small problem using ft_freqstatistics. After performing an
> independent samples t-test, the channels are suddenly ordered alphabeticaly.
> The preprocessing and power analysis were not performed in field trip.
> The electrode labels and neighbours were defined and put into the
> following cfg:
> cfg.elec
> cfg.neighbours
> The statistics were then calculated using montecarlo method, but the
> channel order in stat.label is changed into alphabetical order, so the stat
> plot looks nice but is quite useless.
> Colleagues of mine used ft_freqgrandaverage as input data and did not have
> the problem, but I can't find the bug.
> I designed a file containing the layout structure and tried putting it in
> by using
> cfg.layout
> but it was ignored.
>
> Any help would be deeply appreciated.
>
> Yours sincerely
>
> Johannes Klemt
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Marc Recasens
Tel.: +34 639 24 15 98
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From federica.ma at gmail.com  Mon Dec 14 12:30:33 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 12:30:33 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Message-ID: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing
to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of
epochs), however the output of the function (namely TFRhann.powspctrm)
always gives me power data for the same number of epochs, namely 41,
unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in
steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
= 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from
-0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica
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From Elana.Harris at cchmc.org  Mon Dec 14 13:12:29 2015
From: Elana.Harris at cchmc.org (Harris, Elana)
Date: Mon, 14 Dec 2015 12:12:29 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
Message-ID: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>

cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


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From stan.vanpelt at donders.ru.nl  Mon Dec 14 13:21:41 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 12:21:41 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>

Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288


From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


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From federica.ma at gmail.com  Mon Dec 14 13:41:27 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 13:41:27 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute
fft for single trials, since TFRhann.powspctrm is by definition an average
along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From stan.vanpelt at donders.ru.nl  Mon Dec 14 14:30:32 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 13:30:32 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>

Hi Federica,

If you want to have an estimate for each trial separately, you should specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip?

Best,
Stan

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro
Sent: maandag 14 december 2015 13:41
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute fft for single trials, since TFRhann.powspctrm is by definition an average along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl<mailto:stan.vanpelt at donders.ru.nl>>:
Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288<tel:%2B31%2024%203616288>


From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [mailto:fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Federica Mauro [federica.ma at gmail.com<mailto:federica.ma at gmail.com>]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica



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

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From LordJojo at gmx.de  Mon Dec 14 15:24:32 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Mon, 14 Dec 2015 15:24:32 +0100
Subject: [FieldTrip]  channel problem ft_freqstatistics
In-Reply-To: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>, 
 <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
Message-ID: <trinity-fd5a5c5e-0a0b-417c-b164-249e75a4e832-1450103072262@3capp-gmx-bs08>

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From federica.ma at gmail.com  Mon Dec 14 22:51:26 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 22:51:26 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5Aoow_Gp1LZOWb2VpOLXr18c2SY+tCpyLrahcVg0miu4g@mail.gmail.com>

Hi Stan, thank you, it was really helpful.

Best,
Federica

2015-12-14 14:30 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Hi Federica,
>
>
>
> If you want to have an estimate for each trial separately, you should
> specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also
> http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip
> ?
>
>
>
> Best,
>
> Stan
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro
> *Sent:* maandag 14 december 2015 13:41
>
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> Dear Stan and Elana, thank you very much for your answers and help.
>
>
>
> Just another question: if I understood correctly, there's no way to
> compute fft for single trials, since TFRhann.powspctrm is by definition an
> average along trials. Is that true?
>
>
>
> Thanks again.
>
>
>
> Bests,
>
> Federica
>
>
>
> 2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl
> >:
>
> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
>
> _______________________________________________
> 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 S.Hanslmayr at bham.ac.uk  Wed Dec 16 12:50:48 2015
From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr)
Date: Wed, 16 Dec 2015 11:50:48 +0000
Subject: [FieldTrip] PhD studentship available at University of Birmingham
Message-ID: <257F6C65A372A04CA41056EACC0DE7CED841AC9A@EX8.adf.bham.ac.uk>

Dear Fieldtrip Community,

I take this opportunity to announce a PhD studentship that is available for talented students to work in the labs of Joff Lee and Simon Hanslmayr on a memory project involving invasive recordings of oscillations in rodents. More information about the project and instructions on how to apply can be found here: http://www.birmingham.ac.uk/research/activity/mrc-impact/imaging.aspx. Deadline for applicants is Sunday 10 January 2016.

For any questions about the project please write an email to Dr Joff Lee (J.L.C.Lee at bham.ac.uk<mailto:J.L.C.Lee at bham.ac.uk>) or myself (simon.hanslmayr at bham.ac.uk<mailto:simon.hanslmayr at bham.ac.uk>).

Seasonal greetings,
Simon


Dr. Simon Hanslmayr
Senior Lecturer
School of Psychology
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Tel +44 121 4146203
http://www.memorybham.com/people/#/simon-hanslmayr/
[http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif]

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From luke.bloy at gmail.com  Wed Dec 16 22:29:17 2015
From: luke.bloy at gmail.com (Luke Bloy)
Date: Wed, 16 Dec 2015 21:29:17 +0000
Subject: [FieldTrip] Question about ft_statfun_actvsblT
Message-ID: <CAG5Ru-pbKEF6cd2YFnkXYvGXfEVtb9YGFpw-zydJMbiKJHshsQ@mail.gmail.com>

Sorry if this is missing something fundamental but I'm abit confused about
the use of ft_statfun_actvsblT for frequency analysis and how it compares
to ft_statfun_depsamplesT.

It seems from http://www.fieldtriptoolbox.org/tutorial/salzburg (and from
trying to use it) that inorder to use ft_statfun_actvsblT the active and
baseline freq structures need to have the same time dimension. Based on
this I'm assuming that the active vs baseline comparison happens at each
time x frequency pair, but isn't this what ft_statfun_depsamplesT does?

So I guess my question is what is the difference between the two? What
exactly is the comparison being performed by ft_statfun_actvsblT?

Thanks
Luke
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From leilayou_54 at yahoo.com  Fri Dec 18 10:43:43 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
References: <807603762.476165.1450431823359.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <807603762.476165.1450431823359.JavaMail.yahoo@mail.yahoo.com>

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again. 
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
      strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load : filename     = 'mydata.edf'
 hdr   = ft_read_header(filename);
 sample.start=1
 sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
 
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Fri Dec 18 13:37:52 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Fri, 18 Dec 2015 12:37:52 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>

Hello Leila,

I think there are a few possible options for you. If you're not interested
in analyzing high frequencies, then you could import the data one sample at
a time, downsampling each channel, and then concatenate the channels into
one structure, as described in
http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
I don't know what your sampling rate was, but if your sampling rate was
extremely high then this can save you a lot of space. For example, if
you're only interested in frequencies up to high gamma (around 90-100 Hz),
then your data only need to be sampled at around 250 Hz (per the Nyquist
theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
Hz (which our EDF system does by default) or 5000 Hz then you have way more
samples than necessary; downsampling like this will greatly reduce your
array size.



If that is not an option, then you can read in a segment of data as a
'trial'. ft_preprocessing understands trial start and end times from
cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
read, and the columns are the start sample for each trial, the end sample
for each trial, and the trigger value associated with the trial; you could
just put 0 if there's no trigger). So let's say you want to read the first
through thousandth sample of the recording, then you would set up your cfg
as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of
1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an
explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them
back into continuous data (see
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for
details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/

On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
>         <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
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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 61, Issue 14
> *****************************************
>
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From anja.pflug at musterkind.eu  Fri Dec 18 14:06:32 2015
From: anja.pflug at musterkind.eu (Anja Pflug)
Date: Fri, 18 Dec 2015 14:06:32 +0100 (CET)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
Message-ID: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>

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From leilayou_54 at yahoo.com  Fri Dec 18 14:13:16 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:13:16 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <1753128777.512946.1450444396047.JavaMail.yahoo@mail.yahoo.com>

 Thanks for your reply Anja.I need to have all the channel information at a segment of time to decide if it there is seizure occurring.  Down sampling will loose the information and I am not sure if I want to go that way, as I need to do some feature extractions/classification etc on the data.
Not sure how I could cut the data in fieldtrip. Do you know?ThanksBest regards
___________________________________________________ Leila Ayoubian 

 

      From: Anja Pflug <anja.pflug at musterkind.eu>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 1:06 PM
 Subject: [FieldTrip] Importing large edf data
   
 Hello Leila,
have you tried to import only one of your 51 channels?
If this works you  could cut the data or downsample it and then combine all channels in a later step.
Best,
Anja


fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


Send fieldtrip mailing list submissions to
 fieldtrip at science.ru.nl

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 http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
or, via email, send a message with subject or body 'help' to
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 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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
 <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From jorn at artinis.com  Fri Dec 18 14:17:34 2015
From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=)
Date: Fri, 18 Dec 2015 14:17:34 +0100
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <007301d13996$7573dc60$605b9520$@artinis.com>

Hi all,

 

I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension. 

 

Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.

 

Best of luck ;)

Jörn

--
Jörn M. Horschig, PhD, Software Engineer
 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

 

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data

 

Hello Leila,

have you tried to import only one of your 51 channels?

If this works you  could cut the data or downsample it and then combine all channels in a later step.

Best,

Anja

 

 <mailto:fieldtrip-request at science.ru.nl> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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Today's Topics:

1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com <mailto:leilayou_54 at yahoo.com> >
To: "fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> " <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com <mailto:807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> >
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From leilayou_54 at yahoo.com  Fri Dec 18 14:40:59 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
References: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
Message-ID: <2054001626.533069.1450446059200.JavaMail.yahoo@mail.yahoo.com>

 Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.  Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! 

So this is what I get: 


   hdr: [1x1 struct]
         label: {51x1 cell}
          time: {1x50710 cell}
         trial: {1x50710 cell}
       fsample: 1024
    sampleinfo: [50710x2 double]
           cfg: [1x1 struct]

so the actual data which is in data.trial  is this in both cases! 
size(data.trial)

ans =

           1       50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian 

 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing. 

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

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        fieldtrip at science.ru.nl

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Today's Topics:

   1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
        <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 61, Issue 14
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From leilayou_54 at yahoo.com  Fri Dec 18 14:55:18 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:55:18 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <778201681.538338.1450446918121.JavaMail.yahoo@mail.yahoo.com>

Thanks Jorn. Appreciate your feedback.
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Jörn M. Horschig <jorn at artinis.com>
 To: 'FieldTrip discussion list' <fieldtrip at science.ru.nl> 
 Sent: Friday, December 18, 2015 1:17 PM
 Subject: Re: [FieldTrip] Importing large edf data
   
#yiv8769305188 #yiv8769305188 -- _filtered #yiv8769305188 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8769305188 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv8769305188 {font-family:Verdana;panose-1:2 11 6 4 3 5 4 4 2 4;}#yiv8769305188 #yiv8769305188 p.yiv8769305188MsoNormal, #yiv8769305188 li.yiv8769305188MsoNormal, #yiv8769305188 div.yiv8769305188MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:12.0pt;}#yiv8769305188 a:link, #yiv8769305188 span.yiv8769305188MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv8769305188 a:visited, #yiv8769305188 span.yiv8769305188MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv8769305188 p {margin-right:0in;margin-left:0in;font-size:12.0pt;}#yiv8769305188 span.yiv8769305188EmailStyle18 {color:#1F497D;}#yiv8769305188 .yiv8769305188MsoChpDefault {font-size:10.0pt;} _filtered #yiv8769305188 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv8769305188 div.yiv8769305188WordSection1 {}#yiv8769305188 Hi all,  I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.   Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.  Best of luck ;)Jörn--
Jörn M. Horschig, PhD, Software Engineer
Artinis Medical Systems  |  +31 481 350 980   From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data  Hello Leila,have you tried to import only one of your 51 channels?If this works you  could cut the data or downsample it and then combine all channels in a later step.Best,Anja  
fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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Today's Topics:

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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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*****************************************

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From a.stolk8 at gmail.com  Fri Dec 18 18:51:20 2015
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Fri, 18 Dec 2015 07:51:20 -1000
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <81DC3EE6-21D4-4BB7-80B8-AF642B616768@gmail.com>

Hi all,

Perhaps this links helps:
http://www.fieldtriptoolbox.org/getting_started/edf

Arjen

> On Dec 18, 2015, at 3:17 AM, Jörn M. Horschig <jorn at artinis.com> wrote:
> 
> Hi all,
>  
> I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.
>  
> Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.
>  
> Best of luck ;)
> Jörn
> --
> Jörn M. Horschig, PhD, Software Engineer
> Artinis Medical Systems  |  +31 481 350 980
>  
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
> Sent: Friday, December 18, 2015 14:07
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Importing large edf data
>  
> Hello Leila,
> 
> have you tried to import only one of your 51 channels?
> 
> If this works you  could cut the data or downsample it and then combine all channels in a later step.
> 
> Best,
> 
> Anja
> 
>  
> 
> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:
> 
> 
> 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. importing large edf data (Leila Ayoubian)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
> 
> Error in ReadFedfiles (line 8)
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 
> 
> 
> I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >> 
> 
> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
> Thanks again for your support and assistance. 
> We appreciate your effort.
> Kind regards
> 
> ___________________________________________________ Dr. Leila Ayoubian 
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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 61, Issue 14
> *****************************************
> 
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sat Dec 19 15:06:46 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sat, 19 Dec 2015 14:06:46 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a
sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it
worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Friday, December 18, 2015 12:37 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
>
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From senakahks at gmail.com  Sun Dec 20 12:51:47 2015
From: senakahks at gmail.com (Senaka Amarakeerthi)
Date: Sun, 20 Dec 2015 17:21:47 +0530
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data structure.
Message-ID: <CA+si8qkXe5W7J=J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg@mail.gmail.com>

Dear all,

I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
The file I am trying to process is a single trial.

The code I tried is:

%% import data from testbench emotiv edf file

[hdr, data_eeg] = edfread('emotive.edf');



%% Rearrange data to match FieldTrip Format

% Remove unnecessary columns

data.trial = data_eeg([3:16,39], : );





% Cell-array containing strings, Nchan X 1

% Based on https://emotiv.com/forum/forum14/topic1817/messages/

data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6' 'F4'
'F8' 'AF4' 'MARKER'};



% Sampling frequency in Hz, single number

data.fsample = 128;



% Setting time

[x, filelength] = size(data.trial);

data.time{1} = [1:filelength]./data.fsample;

%% Using the rearranged data





% Set the trial column name and event value (what you enter to the last
column.

% here enter number 1 as the marker)

cfg.trialdef.eventtype = 'MARKER';

cfg.trialdef.eventvalue = 1;

cfg.trialdef.eventtype = '?';

ft_definetrial(cfg);


%% Preprocessing

 cfg = [];

 cfg.channel       = 'AF3';

 cfg.lpfilter      = 'yes';

 cfg.hpfilter      = 'yes';

 cfg.bsfilter      = 'yes';

 cfg.lpfreq        = 100;

 cfg.hpfreq        = 10;

 cfg.bsfreq        = [59 61];

 cfg.lpfiltord     = 4;

 cfg.hpfiltord     = 4;

 cfg.bpfiltord     = 4;

 cfg.lpfilttype    = 'but';

 cfg.hpfilttype    = 'but';

 ecog = ft_preprocessing(cfg,data);


When I run the script. I am getting the following error.

Error in ft_trialfun_general (line 78)
hdr = ft_read_header(cfg.headerfile, 'headerformat',
cfg.headerformat);

Do I need to set the header structure as well? Can somebody help me to get
this fixed. I am reading the documentation but it seems start is bit hard!

Appreciate your support
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From leilayou_54 at yahoo.com  Mon Dec 21 10:36:27 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
References: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
Message-ID: <1459455402.1301519.1450690587900.JavaMail.yahoo@mail.yahoo.com>

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first. 
But now I see thecfg2.trialdef.triallength = 1; 
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference? Thanks again.Kind regards
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/ 
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

Send fieldtrip mailing list submissions to
? ? ? ? fieldtrip at science.ru.nl

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Today's Topics:

? ?1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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------------------------------




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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:35:23 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:35:23 +0000
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
	structure
Message-ID: <CAJT2k_-wZpxENz55hHhJDerN1RuBQH34j3dyKvhLoPHSEGfTbg@mail.gmail.com>

Hello Senaka,

I think you might be making your life more difficult by trying to directly
call edfread(), which is a low-level function. Have you tried just using
ft_preprocessing(), the high-level wrapper function, as described in the
tutorial on the fieldtrip wiki? In my experience, this function reads EDF
data straightforwardly.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 20 Dec 2015 17:21:47 +0530
> From: Senaka Amarakeerthi <senakahks at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
>         structure.
> Message-ID:
>         <CA+si8qkXe5W7J=
> J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
> The file I am trying to process is a single trial.
>
> The code I tried is:
>
> %% import data from testbench emotiv edf file
>
> [hdr, data_eeg] = edfread('emotive.edf');
>
>
>
> %% Rearrange data to match FieldTrip Format
>
> % Remove unnecessary columns
>
> data.trial = data_eeg([3:16,39], : );
>
>
>
>
>
> % Cell-array containing strings, Nchan X 1
>
> % Based on https://emotiv.com/forum/forum14/topic1817/messages/
>
> data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6'
> 'F4'
> 'F8' 'AF4' 'MARKER'};
>
>
>
> % Sampling frequency in Hz, single number
>
> data.fsample = 128;
>
>
>
> % Setting time
>
> [x, filelength] = size(data.trial);
>
> data.time{1} = [1:filelength]./data.fsample;
>
> %% Using the rearranged data
>
>
>
>
>
> % Set the trial column name and event value (what you enter to the last
> column.
>
> % here enter number 1 as the marker)
>
> cfg.trialdef.eventtype = 'MARKER';
>
> cfg.trialdef.eventvalue = 1;
>
> cfg.trialdef.eventtype = '?';
>
> ft_definetrial(cfg);
>
>
> %% Preprocessing
>
>  cfg = [];
>
>  cfg.channel       = 'AF3';
>
>  cfg.lpfilter      = 'yes';
>
>  cfg.hpfilter      = 'yes';
>
>  cfg.bsfilter      = 'yes';
>
>  cfg.lpfreq        = 100;
>
>  cfg.hpfreq        = 10;
>
>  cfg.bsfreq        = [59 61];
>
>  cfg.lpfiltord     = 4;
>
>  cfg.hpfiltord     = 4;
>
>  cfg.bpfiltord     = 4;
>
>  cfg.lpfilttype    = 'but';
>
>  cfg.hpfilttype    = 'but';
>
>  ecog = ft_preprocessing(cfg,data);
>
>
> When I run the script. I am getting the following error.
>
> Error in ft_trialfun_general (line 78)
> hdr = ft_read_header(cfg.headerfile, 'headerformat',
> cfg.headerformat);
>
> Do I need to set the header structure as well? Can somebody help me to get
> this fixed. I am reading the documentation but it seems start is bit hard!
>
> Appreciate your support
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:39:56 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:39:56 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>

Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
needed if all you want to do is read a single segment of continuous data
based on predetermined latencies; you may notice that, in the sample code
snippets I sent in my last message, I did not use this function at all, I
just hard-coded the latency range in cfg.trl (and then passed this cfg
structure to ft_preprocessing() ). So, if this is all you need to do, there
is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into
one dataset (which is what you would accomplish by using
cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
it's not working for you at the moment; I would have to see your code to be
able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Saturday, December 19, 2015 2:06 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
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> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
>
>
>
>
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From leilayou_54 at yahoo.com  Mon Dec 21 13:04:36 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:04:36 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <1581782628.1312312.1450699476132.JavaMail.yahoo@mail.yahoo.com>

 You are absolutely right. It is either using the fix cfg.trl to choose the begining and end of the samples or to choose the cfg2.trialdef.triallength =5. 
In your initial code you had them together, and that is why I was confused. So basically there are two ways to segment the file.
Thanks you very much. You have been very helpful.
My questions are endless. I have another one for you! Sorry!
When loading edf+ the events are lost. using cfg2.trialdef.eventtype  = '?' gives me no events detected.
Any idea how I could go about it?
Thanks again for your help. I really appreciate it.Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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
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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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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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 leilayou_54 at yahoo.com  Mon Dec 21 13:59:38 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <916358647.1306232.1450702778200.JavaMail.yahoo@mail.yahoo.com>

Dear Steve,I have shared my data file in drop box with you. 
I am trying to read the events in this file and I get 0 events. cfg2.trialdef.eventtype  = '?'
Could you please help me out?
Thanks __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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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 leilayou_54 at yahoo.com  Mon Dec 21 16:49:12 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
Subject: [FieldTrip] EDF+ annotations
References: <782532884.1387709.1450712952642.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <782532884.1387709.1450712952642.JavaMail.yahoo@mail.yahoo.com>

Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab and read the events/annotations. These annotations are usually seizure, or spikes....
The files are EEG data from nicollet one, lengthy data for epileptic patients.
This is how I try to look at the events:

cfg2 = [];

cfg2.dataset = 'For leila.edf';
cfg2.trialdef.eventtype  = '?'
cfg2 = ft_definetrial( cfg2 );


cfg2.continuous = 'yes';
data2 = ft_preprocessing(cfg2);
However the output for events are always empty.Does anyone have an idea how I could extract the events/annotation on these files? 

 Thanks in advance for your assistance.
Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 

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From weston.pack at yale.edu  Mon Dec 21 18:56:11 2015
From: weston.pack at yale.edu (Pack, Weston)
Date: Mon, 21 Dec 2015 17:56:11 +0000
Subject: [FieldTrip] How to implement the .pl2 patch for Plexon data
Message-ID: <46289A1970E74F4888AA0D7E75AAB1E6210097A4@x10-mbx13.yu.yale.edu>

Greetings FieldTrip community,

I am new to using FieldTrip, but am well versed in Matlab. I would like to use FieldTrip to analyze Plexon data from LFP recordings and am working with the .pl2 format. I have read through the current documentation (very short) about the patch for loading .pl2 files, but I still have no idea how to install and use the patch as this is not documented (that I can find). The following is provided but with no explanation of how to implement it:

“ (filetype = plexon_plx_v2) “

I have added the path of the Plexon SDK folder using:
“ addpath ('E:\MatlabOfflineFilesSDK')”

I have download the .diff patch file as well as the .zip folder “ft_plexon” but I don’t know where to put them. Does the “plexon” folder inside go in the main FieldTrip directory, the main Plexon SDK directory (currently listed above), or somewhere else? The same question applies to the .diff file.
Thank you in advance for your assistance. Once I get FieldTrip figured out, I intend to create a thorough, novice-friendly tutorial with step-by-step instructions how to work with .pl2 files for LFP analysis. I’ve spent the better part a week fumbling through the tutorials and I’m certain I can write a novice-friendly tutorial on the wiki that will only take a few hours at most for beginners to master. My goal is first to understand how to utilize FieldTrip, at which point I can document my struggles and successes so that future users (especially my lab-mates) can obtain competency with far more efficiency.

Thanks again in advance. I hope to contribute significantly to the community. Happy Holidays!

Weston Pack, PhD

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From jochem.rieger at uni-oldenburg.de  Mon Dec 21 20:00:15 2015
From: jochem.rieger at uni-oldenburg.de (Jochem Rieger)
Date: Mon, 21 Dec 2015 20:00:15 +0100
Subject: [FieldTrip] Job vacancies: MEG-physicist/engineer and
 MRI-physicist/engineer at Oldenburg University, Germany
Message-ID: <56784C3F.4050501@uni-oldenburg.de>

The newly founded Neuroimaging Center at the University of Oldenburg,
Germany,
offers the following two positions


*1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) *

* *

*2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years)*

 

The positions are suitable for part-time work.

 

The Neuroimaging Center hosts a state of the art magnetoencephalograph
(ElektaTriux)
and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded
in an
excellent interdisciplinary scientific environment with a strong
research focus on
neurosensory, neurocognitive, and medical research. 

 

We seek for highly motivated post-doctoral candidates  (with PhD) with
an academic university degree in physics, engineering or related fields,
with documented research experience in magnetoencephalography (position
1) or magnetic resonance imaging (position 2). For both positions,
fluency in English is necessary. German and experience in the design of
neurocognitive experiments are desirable.

 

Successful candidates will be responsible for the operation and
administration of the
MEG-system and MRI-system respectively, their infrastructure, the
development and
improvement of measurement and analyses techniques and user consultancy.

 

The University of Oldenburg is rapidly growing and offers a vibrant
scientific environment with strong foci on cognitive and sensory
neuroscience and a new medical school. The European Medical School is a
cooperation project between the Universities of Oldenburg and Groningen
and three local hospitals. Oldenburg is an attractive city in Germany's
northwest with excellent quality of life. It is close to Bremen,
Hamburg, Groningen, and approx. 1 h from the north sea.

 

The University of Oldenburg is dedicated to increasing the percentage of
women in science. Therefore, female candidates are particularly
encouraged to apply and will be given preference in cases of equal
qualification. Handicapped applicants will be given preference if
equally qualified.

 

Electronic applications (one pdf file) are preferred and can be send to:
Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de
<mailto:Jochem.rieger at uni-oldenburg.de> 

Applications by mail should be sent to

Prof. Jochem Rieger

Universität Oldenburg

Kuepkersweg 74 (W30)

26129 Oldenburg

Germany

 

The application process is open until January 31st 2016. Applications
should include
your CV, a list of most recent publications, and a statement (max. 3
pages).
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From plyons at udel.edu  Mon Dec 21 20:39:59 2015
From: plyons at udel.edu (Peter Lyons)
Date: Mon, 21 Dec 2015 14:39:59 -0500
Subject: [FieldTrip] Clarification on plotting WPLI
Message-ID: <CALq-V2q-ubebB0u1S_wa_RFpfW4gAFXntNb4C+SC8uHT2QpPzw@mail.gmail.com>

Hello Everyone,

I have a question regarding the interpretation of negative values in the
debiased wPLI. Although the reference page on the debiased wPLI notes that
estimates are computed by squaring the wPLI values, I and others have
noticed that some of the values in the debiased wPLI spectrum are negative.
How should these negative values be interpreted in reference to 0?

To view the results of the debiased wPLI connectivity analysis
(ft_connectivity analysis with cfg.method = 'wpli_debiased'), I've been
using the ft_topoplotER function. However, I'm concerned that the default
scaling (zlim = 'maxmin') of the plot does not seem to register the
negative values in the debiased wPLI spectrum. That is, the negative values
are not being plotted. It is curious, however, that the ft_topoplotER
does register the negative values in the *non-debiased *wPLI spectrum.

Is there a reason why the ft_topoplotER function is treating the negative
values from the debiased vs. non-debiased wPLI spectrums differently? Is
there perhaps a more appropriate plotting function I should be using to
view the debiased wPLI output?

I would greatly appreciate any guidance in this.

Thank you!

Peter
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From shlomitbeker at gmail.com  Tue Dec 22 07:42:31 2015
From: shlomitbeker at gmail.com (Shlomit Beker)
Date: Tue, 22 Dec 2015 06:42:31 +0000
Subject: [FieldTrip] Please remove me from mailing list
Message-ID: <7fa9847a19964083a25ceb552d18577f@EXPRD01.hosting.ru.nl>




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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Tue Dec 22 18:48:01 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Tue, 22 Dec 2015 12:48:01 -0500
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k__yFvF-Khymgo7fVLyZnCUdsb9htcC-kFGqDZ1JM=1Akg@mail.gmail.com>

Hi Leila,

According to the warning messages that pop up, the annotation channel is
not being read because it is at a different sampling rate than the data.
>From what I can tell, this appears to be a common problem.
http://www.fieldtriptoolbox.org/getting_started/edf explains a workaround;
have you tried this?

Alternatively, you could consider trying some other toolboxes---I believe
mne-python is capable of handling this issue with EDF triggers
straightforwardly, or you could use one of the softwares that is
specifically made for EDF (such as EDFViewer or EDFBrowser) to export your
annotations into a format that is more easily readable and then use that to
create your cfg.trl structure for Fieldtrip.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 4
> Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <916358647.1306232.1450702778200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Steve,I have shared my data file in drop box with you.
> I am trying to read the events in this file and I get 0 events.
> cfg2.trialdef.eventtype? = '?'
> Could you please help me out?
> Thanks?__________________________________________________ Leila Ayoubian,
> PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Monday, December 21, 2015 11:39 AM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
> needed if all you want to do is read a single segment of continuous data
> based on predetermined latencies; you may notice that, in the sample code
> snippets I sent in my last message, I did not use this function at all, I
> just hard-coded the latency range in cfg.trl (and then passed this cfg
> structure to ft_preprocessing() ). So, if this is all you need to do, there
> is no need to worry about these additional parameters.
>
> If you are trying to read multiple segments of data as separate epochs
> into one dataset (which is what you would accomplish by using
> cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
> it's not working for you at the moment; I would have to see your code to be
> able to diagnose what might be going on.
>
> Best,
> Steve
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> ?
>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Saturday, December 19, 2015 2:06 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
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>
>
>
>
> ?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> ------------------------------
>
> Message: 5
> Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] EDF+ annotations
> Message-ID:
>         <782532884.1387709.1450712952642.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab
> and read the events/annotations. These annotations are usually seizure, or
> spikes....
> The files are EEG data from nicollet one, lengthy data for epileptic
> patients.
> This is how I try to look at the events:
>
> cfg2 = [];
>
> cfg2.dataset = 'For leila.edf';
> cfg2.trialdef.eventtype? = '?'
> cfg2 = ft_definetrial( cfg2 );
>
>
> cfg2.continuous = 'yes';
> data2 = ft_preprocessing(cfg2);
> However the output for events are always empty.Does anyone have an idea
> how I could extract the events/annotation on these files?
>
>  Thanks in advance for your assistance.
> Best regards
> __________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
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From fanshine at yeah.net  Wed Dec 23 09:55:28 2015
From: fanshine at yeah.net (Hanson)
Date: Wed, 23 Dec 2015 16:55:28 +0800 (CST)
Subject: [FieldTrip] Make a custom layout
Message-ID: <7af7ec0c.1eaf.151ce0cdf79.Coremail.fanshine@yeah.net>

Dear all,

I am new to FieldTrip and  trying to  do the time-frequency analysis of my eeg data , however it seems that no suitable layout. And I use ft_prepare_layout function to make a custom layout(electrode_position32.mat).
%% Time-frequency analysis 
cfg              = [];
cfg.output       = 'pow';
cfg.channel      = 'EEG';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 2:2:30;                           
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   
cfg.toi          = -0.5:0.05:1.5;                   
TFRhann = ft_freqanalysis(cfg, data);


cfg = [];       
cfg.showlabels   = 'yes';
cfg.layout       = 'electrode_position32.mat';
figure 
ft_multiplotTFR(cfg, TFRhann);


cfg = [];
cfg.channel      = 'C4';
figure 
ft_singleplotTFR(cfg, TFRhann);


cfg = [];
cfg.layout = 'electrode_position32.mat';
figure 
ft_topoplotTFR(cfg, TFRhann);


When I run the script. I am getting the following error.


Warning: (one of the) axis is/are not evenly spaced, but plots are made as if axis are linear 
> In ft_multiplotTFR at 405
  In TFanalysis_zhs_2 at 52 
the call to "ft_multiplotTFR" took 0 seconds
the call to "ft_singleplotTFR" took 0 seconds
reading layout from file electrode_position32.mat
the call to "ft_prepare_layout" took 0 seconds
Warning: Some points fall outside the outline, please consider using another layout 
> In ft_plot_topo at 171
  In fieldtrip\private\topoplot_common at 731
  In ft_topoplotTFR at 192
  In TFanalysis_zhs_2 at 62 
Index exceeds matrix dimensions.


Error in ft_plot_topo (line 182)
    mask{i}(end+1, :) = mask{i}(1, :);                   % force them to be closed


Error in topoplot_common (line 731)
  ft_plot_topo(chanX,chanY,datavector,opt{:});


Error in ft_topoplotTFR (line 192)
[cfg] = topoplot_common(cfg, varargin{:});


Error in TFanalysis_zhs_2 (line 62)
ft_topoplotTFR(cfg, TFRhann);


Do you have any suggestion about it?
Thank you very much for your attention.


Kind Regards,
Hanson
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From daria.laptinskaya at googlemail.com  Tue Dec  1 09:58:46 2015
From: daria.laptinskaya at googlemail.com (Daria Laptinskaya)
Date: Tue, 1 Dec 2015 09:58:46 +0100
Subject: [FieldTrip] SCD and coherence analysis
In-Reply-To: <52d6-565c1c80-25-55c3b400@102538225>
References: <52d6-565c1c80-25-55c3b400@102538225>
Message-ID: <CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ@mail.gmail.com>

Hi Barbara,

try this:
 sens=ft_read_sens('GSN-HydroCel-257.sfp');
 cfg=[];
 cfg.elec=sens;

Hope it helps :-)
Daria






2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:

> Dear Fieltripers,
>
> I would like to do coherence analysis. I did a SCD analysis on my data
> first ('finite' method), and want to run ft_mvaranalysis now. I get
> the error
>
> Error using ft_datatype_sens (line 186)
> inconsistent number of channels in sensor description
>
> As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> fieldtrip (my raw data set has 257 channels), but there are only 256
> channels left after the SCD analysis. Can this cause the problem?
>
> Has anyone had this problem before and can provide a solution? I only
> found one prior entry with this topic, but there was no final solution for
> it.
>
>
> Thanks and all the best,
> Barbara
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From barbara.schorr at uni-ulm.de  Tue Dec  1 15:18:31 2015
From: barbara.schorr at uni-ulm.de (Barbara Schorr)
Date: Tue, 01 Dec 2015 15:18:31 +0100
Subject: [FieldTrip] =?utf-8?q?SCD_and_coherence_analysis?=
In-Reply-To: <mailman.19.1448967602.14550.fieldtrip@science.ru.nl>
Message-ID: <38ba-565dac00-3-4dd4ed00@147935417>

Dear Daria,

I did exactly this. 
The problem occurs afterwards, when I want to run ft_mvaranalysis on the data that result from ft_scalpcurrentdensity.
In the fieldtrip document it states, that the output data of  ft_scalpcurrentdensity has the same format as the input data.
When I run ft_mvaranalysis on the original data, everything works fine, but with the SCD data I get this error that the number of channels in sensor description is inconsistent.

Has anyone else experienced this problem?

Best,
Barbara


Am Dienstag, 01. Dezember 2015 12:00 CET, fieldtrip-request at science.ru.nl schrieb: 
 
> 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: power suppression during DICS beamforming ?
>       (Mait? Crespo Garc?a)
>    2. Re: SCD and coherence analysis (Daria Laptinskaya)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 30 Nov 2015 15:31:20 +0000 (UTC)
> From: Mait? Crespo Garc?a <maity_winky at yahoo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] power suppression during DICS beamforming ?
> Message-ID:
> 	<1881724873.21184223.1448897480847.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Fr?d?ri,
> maybe you have the solution already.
> In case not, could you explain how did you get the last two plots? Are spectra computed after averaging across all virtual channel spectra or you are representing the spectrum of the source with maximal power?
> Best,Maite
> 
> 
> 
>     El Jueves 26 de noviembre de 2015 13:55, Fr?d?ric Roux <f.roux at bcbl.eu> escribi?:
>  
> 
>  Dear all,
> 
> I am observing a counter-intuitive result after applying the spatial filters obtained from DICS beamforming to my MEG data.
> 
> The plot in the attachment summarizes the issue: The raw data shows a clear peak of activity at 10 Hz, however, after applying the spatial filter to the MEG data the spectrum of the virtual channels shows that power in this frequency band is reduced. The same also happens when I apply a spatial filter in the gamma range for power at 70 Hz to the raw MEG signals.
> 
> Is this something that falls out of the beamformer math due to the fact how the algorithm suppresses power at all locations by minimizing the noise level, or is there something wrong with my code? I (maybe naively) assumed that the results should come out the opposite. On the other hand, when plotting the noise normalized maps (NAI) of both the alpha and gamma beamformers the sources look quite accurate. Should I normalize with the level of noise first before plotting the spectrum to see the expected results (ie an upregulation of power instead of a downregulation of power)?
>  
> The code that I use to generate the figures is:
> 
> % 1) compute CSD matrix
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.foilim = [10 10];
> cfg.tapsmofrq = 2;
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> 
> [csd] = ft_freqanalysis(cfg,meg_data);
> 
> 
> % 2) compute DICS filter
> cfg = [];
> cfg.method = 'dics';
> cfg.grad = meg_data.grad;
> cfg.headmodel = vol;
> cfg.frequency = csd.freq;
> 
> cfg.dics.realfiter = 'yes';
> cfg.dics.fixedori = 'yes';
> 
> [alpha_filter]= ft_sourceanalysis(cfg,csd);
> 
> % 3) compute the virtual channel data
> 
> VC = meg_data;
> VC.trial = cell(1,length(meg_data.trial));
> VC.label = cell(1,length(alpha_filter.avg.pow));
> 
> for i = 1:length(VC.trial)
> ? for j = 1:length(VC.label)
> 
> ? ? ? VC.trial{i}(j,:) = alpha_filter{j}*meg_data.trial{i};
> ? ? ? VC.label(j) = {['virtual_channel',num2str(j)]};
> ? end;
> end;
> 
> % 4) compute the spectrum of the virtual channel data
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> cfg.tapsmofrq = 1;
> cfg.foi = 0.1:100;
> 
> [pow] = ft_freqanalysis(cfg,VC);
> 
> 
> Any help or suggestions would be greatly appreciated.
> 
> Fred
> 
> --
> Fr?d?ric Roux
> Postdoctoral Scientist, Marie-Curie fellow
> BCBL. Basque Center on Cognition, Brain & Language.
> 
> f.roux at bcbl.eu
> Tel: +34 943 309 300 Ext 211
> Fax: +34 943 309 052
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> ---------------------------------------------------------------------------
> 
> ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
>   
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> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 1 Dec 2015 09:58:46 +0100
> From: Daria Laptinskaya <daria.laptinskaya at googlemail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] SCD and coherence analysis
> Message-ID:
> 	<CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Barbara,
> 
> try this:
>  sens=ft_read_sens('GSN-HydroCel-257.sfp');
>  cfg=[];
>  cfg.elec=sens;
> 
> Hope it helps :-)
> Daria
> 
> 
> 
> 
> 
> 
> 2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:
> 
> > Dear Fieltripers,
> >
> > I would like to do coherence analysis. I did a SCD analysis on my data
> > first ('finite' method), and want to run ft_mvaranalysis now. I get
> > the error
> >
> > Error using ft_datatype_sens (line 186)
> > inconsistent number of channels in sensor description
> >
> > As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> > fieldtrip (my raw data set has 257 channels), but there are only 256
> > channels left after the SCD analysis. Can this cause the problem?
> >
> > Has anyone had this problem before and can provide a solution? I only
> > found one prior entry with this topic, but there was no final solution for
> > it.
> >
> >
> > Thanks and all the best,
> > Barbara
> >
> >
> > _______________________________________________
> > 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 61, Issue 1
> ****************************************
 
 
 
 





From eriksenj at ohsu.edu  Wed Dec  2 03:04:56 2015
From: eriksenj at ohsu.edu (K Jeffrey Eriksen)
Date: Wed, 2 Dec 2015 02:04:56 +0000
Subject: [FieldTrip] accommodating air pockets in FEM head model
Message-ID: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>

Hi,

I am reading the FieldTrip documentation on creating an FEM model and see that the following tissue types are output from the segmentation process:

Gray
White
Csf
Skull
Scalp

Q1: Since I am using a 256 channel EGI system with electrodes over the lower part of the head and face, I absolutely need to be able to include air voxels as well. Anyone have any knowledge of such a possibility?

Q2: Beyond that I would also like to include other tissue types such as fat, muscle, and eyeball (vitrious). I suppose I could find other segmentation software to simply create a more varied segmentation and insert it in the processing pipeline, but would like to know if that would mess anything up.

Q3: Next, can the FEM handle anisotropic conductivities for white matter and skull?

Q4: has anyone out there actually used the FDM model?

Thanks,
-Jeff Eriksen

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From carsten.wolters at uni-muenster.de  Wed Dec  2 08:53:17 2015
From: carsten.wolters at uni-muenster.de (Carsten Wolters)
Date: Wed, 2 Dec 2015 08:53:17 +0100
Subject: [FieldTrip] accommodating air pockets in FEM head model
In-Reply-To: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
References: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
Message-ID: <565EA36D.5030005@uni-muenster.de>

Hi Jeff,

Q3:
yes, FEM can model anisotropy and white matter is anisotropic, but skull 
is a three-layered-structure
consisting of spongiosa and compacta, see
http://www.ncbi.nlm.nih.gov/pubmed/20690140

For Q4:
FEM allows geometry-adaptation, see
http://www.ncbi.nlm.nih.gov/pubmed/17694865
As far as I know, modeling using irregular meshes might get difficult to 
implement within an FDM framework.

For Q1 and Q2:
Mainly tissues between sources and electrodes are important to be 
modeled (so white matter anisotropy
is only important for deeper sources) and FSL and freesurfer can do a 
good job on segmentation.
Air-compartments can possibly best be modeled by hand-correction of the 
FSL output.
Please see
http://www.ncbi.nlm.nih.gov/pubmed/24671208
on how we solve forward modeling to be able to combine EEG and MEG.

More infos are available in the two following theses:
http://www.sci.utah.edu/~wolters/PaperWolters/2014/Lanfer_Dissertation_July2-2014.pdf
http://www.sci.utah.edu/~wolters/PaperWolters/2015/Umit_Aydin_Dissertation_2015.pdf


Best regards
      Carsten

Am 02.12.2015 um 03:04 schrieb K Jeffrey Eriksen:
>
> Hi,
>
> I am reading the FieldTrip documentation on creating an FEM model and 
> see that the following tissue types are output from the segmentation 
> process:
>
> Gray
>
> White
>
> Csf
>
> Skull
>
> Scalp
>
> Q1: Since I am using a 256 channel EGI system with electrodes over the 
> lower part of the head and face, I absolutely need to be able to 
> include air voxels as well. Anyone have any knowledge of such a 
> possibility?
>
> Q2: Beyond that I would also like to include other tissue types such 
> as fat, muscle, and eyeball (vitrious). I suppose I could find other 
> segmentation software to simply create a more varied segmentation and 
> insert it in the processing pipeline, but would like to know if that 
> would mess anything up.
>
> Q3: Next, can the FEM handle anisotropic conductivities for white 
> matter and skull?
>
> Q4: has anyone out there actually used the FDM model?
>
> Thanks,
>
> -Jeff Eriksen
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From RICHARDS at mailbox.sc.edu  Wed Dec  2 14:55:57 2015
From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN)
Date: Wed, 2 Dec 2015 13:55:57 +0000
Subject: [FieldTrip] Head segmentation
Message-ID: <A84D7FC4-B8F0-4D9D-8EF0-8190153B1580@mailbox.sc.edu>

Jeff

The resources from Carsten Wolters and the answers were right on.

We have a 128 channel system.

We add “nasal cavity” which includes nasal, throat, and sinuses in our FEM model.  We do a lot of the segmenting with FSL (bet, fast, betsur, SPMf) and custom programs, and then do manual editing to identify the air passages.  The separate segments are then put together with a custom program. The air cavities might be important for the 256-channel EGI system, where on the sides and front of the face the electrodes could have some dipolar sources and the places in between would affect the source estimation.  Anything below the skull, not air cavity, we give a conductivity of muscle, which is very close to scalp; again the electrodes below the skull are over something and I presume would need a realistic estimated head media and conductivity.

As I wrote earlier, we have been using FT for FEM recently; also have gotten good (similar to FEM) results with the Dipoli BEM model. I have one already-published supplemental information that briefly describes our FEM model, and one in-press supplemental information, both articles using the EMSE program.  I am working on our first publication using the FEM from FT.

Re “Mainly tissues between sources and electrodes are important to be modeled (so white matter anisotropy is only important for deeper sources)”.  This may be practically correct, but I have suspected (and EGI’s rationale for whole-head coverage) that to get a good measure of a dipolar source whose positive or negative pole land somewhere below the skull area, one needs a good model of the head over all the places where the current flow is manifested.  We have some prefrontal  sources with large negative potentials exhibiting on the frontal-central 10-10 electrodes, and which have a large positive scalp potential on the “Oz” electrodes.  However, it turns out these potentials show up on Iz and in the EGI electrodes below Iz (128 channel), so having a model for scalp and muscle over the neck might be important.  I don’t know what the effect is of leaving these out, but I have preferred to do the whole head segmentation in case these have some effect.

One last consideration.  Most BEM and FEM models on the FT site use the segmentation of the brain, skull, and scalp about at the level of the MNI head.  This does not include the electrodes below the horizon of the MNI head, and there is a lot of area below the MNI head that is covered by the EGI 128 and 256 channel systems.  This adds significantly to the volume of the voxels used for the FEM estimation.  For BEM models we cut the head off at about 10% below the level of the lowest EGI 128 channel electrodes, and generally have done so also for the FEM models we use in FT. The electrodes are located on the places below the MNI head, so one has to have a “head” model with positions below those typically used in the FT’s demo programs.  We do a whole head MRI down to the neck, and then use a custom program to get a MRI volume with a head that extends about 10% lower than the lowest EGI-128 electrodes.

John


***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<mailto:richards-john at sc.edu>
HTTP: jerlab.psych.sc.edu
***********************************************

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From francois.tadel at mcgill.ca  Wed Dec  2 22:03:33 2015
From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=)
Date: Wed, 2 Dec 2015 16:03:33 -0500
Subject: [FieldTrip] Error in ft_dipolefitting.m ?
Message-ID: <565F5CA5.9080409@mcgill.ca>

Hello,

When fitting single dipoles on multiple time points at once, I have an 
error line 578:
     source.dip.unit = headmodel.unit;
The syntax is incorrect that source.dip is an array with multiple 
dipoles. Should this be replaced with the following line ?
     [source.dip.unit] = deal(headmodel.unit);

Cheers,
Francois


From erin.white at sickkids.ca  Wed Dec  2 22:55:40 2015
From: erin.white at sickkids.ca (Erin White)
Date: Wed, 2 Dec 2015 21:55:40 +0000
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
 multiplotER and multiplotTFR images
In-Reply-To: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
References: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
Message-ID: <0D4EE8880DEE3047BEC905C0EC463F8C2769EBD7@SKMBXX03.sickkids.ca>

Hi Steve,
Thanks so much for your helpful comment!
I'll give this a try!

All the best

Erin

----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [stephen.politzer-ahles at ling-phil.ox.ac.uk]
Sent: November 27, 2015 7:28 AM
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] Adding tick marks to the X and Y axes in multiplotER and multiplotTFR images

Hi Erin,

I don't use the multiplot functions much, so my solution is clunky and there may be others on the list with a better way to do this. But just in case, here's how I do it:

Rather than using multiplot, I make each plot individually, and use the subplot() command to arrange multiple plots into a figure. Within each subplot, I just use some custom code to draw the ticks. For example:

tickspots = [-200:200:1000]; % one tick every 200 ms, from -200 to 1000 ms
tickheight = [-.5 .5]; % how high and low the ticks will go

for tickspots = tickspot % iterate through tick spots
plot( [tickspot tickspot], tickheight, 'k' ); % plot each tick as a black line
end;


Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab, Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/<https://urldefense.proofpoint.com/v2/url?u=http-3A__users.ox.ac.uk_-7Ecpgl0080_&d=BQMFaQ&c=Dvjge31PR3JZstzk2paJYiflTxRSxp35GBhsbHdd2Zw&r=I8lBTmv7Y9oqVGvTj_vgdd74EEIPprGsdbxcnXduG2k&m=lnKeei_k8PbT5JQEFb_AdyFHThYK07IvJphgqiA4pd8&s=yHg_UuAaKeXLiYDOWrOeEtt0pDtbBRlk3w7TC1hOKdw&e=>


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

Message: 2
Date: Thu, 26 Nov 2015 12:48:25 +0000
From: Erin White <erin.white at sickkids.ca<mailto:erin.white at sickkids.ca>>
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
        multiplotER and multiplotTFR images
Message-ID:
        <0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca<mailto:0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
I'm new at programming and was wondering if someone could help with something that I'm sure is simple.
I'd like to add tick marks to my multiplotER and multiplotTFR figures so that the timing and amplitude (for multiplotER) and timing and frequency (for multiplotTFR) scales are presented clearly. For example, I'd like a tick mark on my X axes every 200 ms, and on the y axes, every 2 mV for ER images and every 5 Hz for TFR images.

Could anyone suggest what I should add to my code to show this?

Thanks very much!

Erin












----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813<tel:%28647%29834-7813>

________________________________

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*****************************************

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From p.babaeeghazvini at vu.nl  Fri Dec  4 20:14:26 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Fri, 4 Dec 2015 19:14:26 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
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From ronny.ibrahim at mq.edu.au  Mon Dec  7 05:36:14 2015
From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim)
Date: Mon, 7 Dec 2015 15:36:14 +1100
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency
	data
Message-ID: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a
time-frequency datasets that I've acquired using the ft_freqanalysis
function. When I run ft_freqstatistics on the data it would give me stats
result which is based on comparing the absolute values of power spectrum
instead the relative change with respect to the baseline. I have tried to
perform to do my relative change power spectrum data manually but it seems
that when I run the ft_freqstatistics it produces an error of which I could
not figure out on why.

Here is my code:



C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6}
outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13}
outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};



C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6}
outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13}
outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};



%% Performing cluster statistics for the paradigm

cfg                  = [];

cfg.layout           = 'EEG_KR.lay';

lay                  = ft_prepare_layout(cfg);

% Needs to change this

cfg.latency          = [0 0.6]; %Need to look this up according to what

cfg.frequency        = [8 12];% Need to do it for different frequency bands
(theta, alpha, beta, gamma).

cfg.channel          = 'all';

cfg.avgovertime      = 'no';

cfg.avgoverfreq      = 'yes';

cfg.avgoverchan      = 'no';

cfg.statistic        = 'ft_statfun_indepsamplesT';

cfg.numrandomization = 1000;

cfg.correctm         = 'cluster';

cfg.method           = 'montecarlo';

cfg.computeprob    = 'yes';

cfg.computecritval = 'yes';

cfg.clusteralpha     = 0.05;

cfg.clusterstatistic = 'maxsum';

cfg.minnbchan        = 3;

cfg.tail             = 0;

cfg.clustertail      = 0;

cfg.alpha            = 0.05;

cfg_neighb.layout    = lay;

cfg_neighb.method    = 'triangulation';

cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);

cfg.ivar             = 1;

cfg.design = [ones(1,18) 2*ones(1,18)];

stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});



%% Plotting significant clusters



cfg                  = [];

cfg.alpha            = 0.05;

cfg.parameter        = 'stat';

cfg.layout           = lay;

ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output
structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny
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From j.herring at donders.ru.nl  Mon Dec  7 09:24:32 2015
From: j.herring at donders.ru.nl (Herring, J.D. (Jim))
Date: Mon, 7 Dec 2015 08:24:32 +0000
Subject: [FieldTrip] Clusterstatistics on relative change (%) time
 frequency	data
In-Reply-To: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
References: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
Message-ID: <3D00B7615FB58D46A0B49B9AD67A33EB279C7AFB@exprd01.hosting.ru.nl>

Dear Ronny,

What error do you get when running this code?

You can perform a (relative) baseline correction using ft_freqbaseline with cfg.baselinetype = ‘relative’ or ‘relchange’ and cfg.baseline = [your baseline window];. If your code works on absolute values it should also work on baseline-corrected values using ft_freqbaseline.

Best,

Jim

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Ronny Ibrahim
Sent: maandag 7 december 2015 5:36
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency data

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a time-frequency datasets that I've acquired using the ft_freqanalysis function. When I run ft_freqstatistics on the data it would give me stats result which is based on comparing the absolute values of power spectrum instead the relative change with respect to the baseline. I have tried to perform to do my relative change power spectrum data manually but it seems that when I run the ft_freqstatistics it produces an error of which I could not figure out on why.

Here is my code:

C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6} outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13} outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};

C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6} outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13} outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};

%% Performing cluster statistics for the paradigm
cfg                  = [];
cfg.layout           = 'EEG_KR.lay';
lay                  = ft_prepare_layout(cfg);
% Needs to change this
cfg.latency          = [0 0.6]; %Need to look this up according to what
cfg.frequency        = [8 12];% Need to do it for different frequency bands (theta, alpha, beta, gamma).
cfg.channel          = 'all';
cfg.avgovertime      = 'no';
cfg.avgoverfreq      = 'yes';
cfg.avgoverchan      = 'no';
cfg.statistic        = 'ft_statfun_indepsamplesT';
cfg.numrandomization = 1000;
cfg.correctm         = 'cluster';
cfg.method           = 'montecarlo';
cfg.computeprob    = 'yes';
cfg.computecritval = 'yes';
cfg.clusteralpha     = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan        = 3;
cfg.tail             = 0;
cfg.clustertail      = 0;
cfg.alpha            = 0.05;
cfg_neighb.layout    = lay;
cfg_neighb.method    = 'triangulation';
cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);
cfg.ivar             = 1;
cfg.design = [ones(1,18) 2*ones(1,18)];
stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});

%% Plotting significant clusters

cfg                  = [];
cfg.alpha            = 0.05;
cfg.parameter        = 'stat';
cfg.layout           = lay;
ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny

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From julian.keil at gmail.com  Mon Dec  7 09:30:25 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 09:30:25 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
Message-ID: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

> Hello
> 
> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> Not from the voxel indicating maximum power ([maxval,
>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
> 
> Regards,
> Parinaz.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From p.babaeeghazvini at vu.nl  Mon Dec  7 12:52:55 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 11:52:55 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From julian.keil at gmail.com  Mon Dec  7 17:57:10 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 17:57:10 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
Message-ID: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>

Hi Parinaz,

> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

> How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

> Hi Julian,
> 
> Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:
> 
> cfg = []
> 
> cfg.atlas = atlas;
> 
> cfg.roi = atlas.tissuelabel(1)
> 
> cfg.inputcoord = 'mni';
> 
> mas = ft_volumelookup(cfg,grid);
> 
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.xgrid      =
> 
> cfg.grid.ygrid      =
> 
> cfg.grid.zgrid      =
> 
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> 
> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.
> 
> an other question that I have is that: when I compute the maximum index from
>  [maxvalr, maxpowindxr] = max(srcetask.avg.pow)
> 
> How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)
> 
> Regards,
> Parinaz.
> 
> 
> 
> 
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
> Sent: Monday, December 07, 2015 9:30 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch
> 
> Hi Parinaz,
> 
> I'm not sure if I understood your question correctly.
> Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?
> 
> In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
> In the second case, it's a tad more complicated, but here's how I do it:
> 1. Compute the virtual channels for all grid points in the cortex
> 2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
> 3. Build a high-resolution 3D-Grid on the standard MRI
> 4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
> 5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.
> 
> I hope this helps, let me know otherwise.
> 
> Julian
> 
> Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:
> 
>> Hello
>> 
>> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = hdm;
>> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.keepfilter   = 'yes';
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> Not from the voxel indicating maximum power ([maxval,
>>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
>> 
>> Regards,
>> Parinaz.
>> _______________________________________________
>> 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 p.babaeeghazvini at vu.nl  Mon Dec  7 20:20:15 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 19:20:15 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>,
 <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C29CB@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your help now it is completely clear for me.

Parinaz.
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 5:57 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Julian Keil [julian.keil at gmail.com<mailto:julian.keil at gmail.com>]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
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

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From amickan1990 at gmail.com  Thu Dec 10 18:14:10 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Thu, 10 Dec 2015 18:14:10 +0100
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation test
Message-ID: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>

Dear all,

I'm just starting to work on a cluster-based permutation test script based
on the tutorial for within-subject designs on the fieldtrip website. I ran
into an issue when computing the [stat] matrix. I used the code as it was
on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages.
However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat
and stat.negclusterslabelmat matrices which should apparantly contain far
more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume
has to do with the fact that "neg" does not have the appropriate matrix
dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me
out.

Thanks in advance!

Best,
Anne
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From nick.peatfield at gmail.com  Thu Dec 10 20:13:10 2015
From: nick.peatfield at gmail.com (Nicholas A. Peatfield)
Date: Thu, 10 Dec 2015 11:13:10 -0800
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
In-Reply-To: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
Message-ID: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>

Hi Anne,

To get an answer/suggestion you should provide the part of your script
detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:

> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Nicholas Peatfield, PhD
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From jan.schoffelen at donders.ru.nl  Thu Dec 10 20:36:45 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 10 Dec 2015 19:36:45 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based
	permutation	test
In-Reply-To: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
 <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9@fcdonders.ru.nl>

Hi Anne,

I agree with Nick, some more information would be helpful. At this stage my wild guess (assuming that you did not constrain your ‘search space’, using cfg.channel and cfg.latency before calling ft_timelockstatistics) would be that there’s a major discrepancy in the descriptive dimensions of your data (i.e. the ‘labels’ and the time points) across the input arguments. FieldTrip does an explicit check on the labels and time points, it only proceeds to do calculations on the channels and time points that are present in each and every input argument. With respect to time points: this could even mean that numerical inaccuracies are the showstopper here. These inaccuracies could be easily introduced when e.g. downsampling.

Best,
Jan-Mathijs


On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:

Hi Anne,

To get an answer/suggestion you should provide the part of your script detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:amickan1990 at gmail.com>> wrote:
Dear all,

I'm just starting to work on a cluster-based permutation test script based on the tutorial for within-subject designs on the fieldtrip website. I ran into an issue when computing the [stat] matrix. I used the code as it was on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages. However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat and stat.negclusterslabelmat matrices which should apparantly contain far more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume has to do with the fact that "neg" does not have the appropriate matrix dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me out.

Thanks in advance!

Best,
Anne


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



--
Nicholas Peatfield, PhD

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

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From aishwaryaselvaraj1708 at gmail.com  Fri Dec 11 07:30:39 2015
From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj)
Date: Fri, 11 Dec 2015 12:00:39 +0530
Subject: [FieldTrip] filed trip
In-Reply-To: <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
Message-ID: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
wrote:

> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Regards,
Aishwarya Selvaraj
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From stan.vanpelt at donders.ru.nl  Fri Dec 11 09:09:14 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Fri, 11 Dec 2015 08:09:14 +0000
Subject: [FieldTrip] filed trip
In-Reply-To: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
 <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0@exprd03.hosting.ru.nl>

Dear Aishwarya,

The data structure should look something like this:

% 1. Load data
load EEGdata.mat

% 2. Make FieldTrip structure, manually
data.label={'Channel1Name’,’Channel2Name’,’Channel3Name’}; %your channel names
data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each trial: channelsxtimepoints data
data.fsample=500; %your recording sampling frequency
data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data sample (e.g: [0 0.02 0.04 0.06 etc])

Going through the Walktrough Tutorial will be the best starting point when you just started to use FieldTrip: http://www.fieldtriptoolbox.org/walkthrough
After that, you may go through the other Tutorial documentation or Example Matlab scripts.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
Sent: vrijdag 11 december 2015 7:31
To: FieldTrip discussion list
Subject: Re: [FieldTrip] filed trip

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com<mailto:mishra408 at gmail.com>> wrote:
Hi Aishwarya,

I faced the similar problem. You are supposed to change your data
(.mat format) in a data structure that is read by fieldtrip. For that
you need at least following information
1. Channel label and their location (If you don't have this file you
can use standard file available in Fieldtrip and you can include only
those electrode that you have been using in your experiment)
2. sampling rate of the data (that you would have done while recording the data)
3. time vector
4. no. of trials

You can create them in MATLAB and put them together in a structure
along with your recorded data. This worked for me.

--
Ashutosh Mishra
5th year Integrated BS-MS student
Department of Physical Sciences
Indian Institute of Science Education and Research, Kolkata
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--
Regards,
Aishwarya Selvaraj
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From juangpc at gmail.com  Fri Dec 11 11:43:05 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 11:43:05 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating sourcemodel
Message-ID: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for
source-reconstruction of MEG or EEG data <http://goog_2124598831>
​"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized
space
​" procedure , there is an example code. This code throws an error when I
execute it with a version of Fieldtrip I downloaded yesterday. I think I
have downloaded correctly all the required info (Subject01.zip).

​Code:

% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
the coordinate system
 % segment the template brain and construct a volume conduction model
(i.e. head model): % this is needed to describe the boundary that
define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
Convert the vol to cm, because the CTF convenction is to express
everything in cm.
 % construct the dipole grid in the template brain coordinates% the
negative inwardshift means an outward shift of the brain surface for
inside/outside detection
cfg = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
= 1;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
 = 'yes';
cfg.inwardshift = -1.5;
​​
cfg.headmodel   = template_headmodel;

The problem occurs when I execute ​this line:

​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position
information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required
"sensor position information" by executing this code just before
(considering the folder with the information downloaded for this subject is
located just there:

​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';

Then the rest of the sample code in the tutorial can be executed with no
issues.

template_grid   = ft_prepare_sourcemodel(cfg);
 % make a figure with the template head model and dipole gridfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
'none');alpha 0.5; camlight
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));


My questions:

​Is there a better solution for this problem? Maybe I can learn a little
bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one
is placing the downloaded subject's data, and it is platform dependent.
Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan
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From jan.schoffelen at donders.ru.nl  Fri Dec 11 11:54:54 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 10:54:54 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925@fcdonders.ru.nl>

Hi Juan,

We’ll look into this specific issue soon, it should work without specifying sensor positions. However, for now and in general I would recommend just using a pre-cooked template grid. These can be found in fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I will make this more explicit shortly.

Best,

Jan-Mathijs

On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From jan.schoffelen at donders.ru.nl  Fri Dec 11 13:19:39 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 12:19:39 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>

Hi Juan,

I could reproduce your issue, and have done 2 things:
- I updated the wiki to make it clear that it would be easier to use a pre-cooked grid.
- I adjusted ft_prepare_sourcemodel so that it also works when only providing the template_headmodel, as per the example code.
The new version of ft_prepare_sourcemodel will become available in tonight’s release on the ftp-server.

Best wishes, and thanks for noticing.
Jan-Mathijs


On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From juangpc at gmail.com  Fri Dec 11 13:55:57 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 13:55:57 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating
	sourcemodel
In-Reply-To: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
 <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
Message-ID: <CAPO7YLJFQ=qB0xVBBS8WEiD2PW4OzaOnZX=xVzn_rgxd-vm9HQ@mail.gmail.com>

Hi Jan-Mathijs,

Thanks for your quick response, H2H. I've actually learned about precooked
models with your answer. Many thanks.

In the same page, in the part "Make the individual subjects' grid", there
seems to be a unit-related problem. One can find this code

% read the single subject anatomical MRI
mri = ft_read_mri('Subject01.mri');
 % segment the anatomical MRI
cfg        = [];
cfg.output = 'brain';
seg        = ft_volumesegment(cfg, mri);
 % construct the volume conductor model (i.e. head model) for each
subject% this is optional, and for the purpose of this tutorial only
required for% plotting, later on
cfg        = [];
cfg.method = 'singleshell';
headmodel  = ft_prepare_headmodel(cfg, seg);
 % create the subject specific grid, using the template grid that has
just been created
cfg                = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.warpmni
  = 'yes';
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.template
 = template_grid;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.nonlinear
= 'yes'; % use non-linear normalization
cfg.mri            = mri;grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>
             = ft_prepare_sourcemodel(cfg);
 % make a figure of the single subject headmodel, and grid
positionsfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>;
hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on;
ft_plot_vol(headmodel, 'edgecolor', 'none', 'facealpha', 0.4);
ft_plot_mesh(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.pos(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.inside,:));

When executing it, there seems to be a problem with dimensions. "headmodel"
struct is in mm and "grid" struct is in cm. So unfortunately the resulting
figure ends up being something like
[image: Inline image 1]

I've tested to specify 'mm' units in the configuration struct before
calling ft_prepare_sourcemodel: cfg.grid.unit='mm';

Or by calling ft_convert_units right after ft_prepare_sourcemodel.

grid=ft_convert_units(grid,'mm');

Both solutions work fine, producing a figure very similar to the one in the
tutorial. I've included the first solution in the wiki.

I hope this is ok.

Best,



Juan

On Fri, Dec 11, 2015 at 1:19 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Juan,
>
> I could reproduce your issue, and have done 2 things:
> - I updated the wiki to make it clear that it would be easier to use a
> pre-cooked grid.
> - I adjusted ft_prepare_sourcemodel so that it also works when only
> providing the template_headmodel, as per the example code.
> The new version of ft_prepare_sourcemodel will become available in
> tonight’s release on the ftp-server.
>
> Best wishes, and thanks for noticing.
> Jan-Mathijs
>
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831/>
> ​ <http:/>"
> ​​
>
> ​ ​when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ​" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ​Code:
>
> % NOTE: the path to the template file is user-specific
> template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system
>  % segment the template brain and construct a volume conduction model (i.e. head model): % this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.
>  % construct the dipole grid in the template brain coordinates% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
> cfg = [];
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
> cfg.inwardshift = -1.5;
> ​​
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ​this line:
>
> ​
> ​
> ​
> ​
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ​
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ​
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ​Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because​ my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ​ I figure this can be interesting to other people.​
> ​
> ​
>
> Best,
>
>
> Juan
>
> _______________________________________________
> 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 frsantos at fpce.up.pt  Fri Dec 11 13:57:52 2015
From: frsantos at fpce.up.pt (Fernando Ferreira-Santos)
Date: Fri, 11 Dec 2015 12:57:52 +0000
Subject: [FieldTrip] 3rd International Conference of the ESCAN
Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFD7B96@SRVMBX01.fpceup.psi.up.pt>

Dear Colleagues,
The 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) is accepting submissions for symposia and oral/poster presentations. The conference will take place in that will take place in Porto, Portugal, between 23-26 of June, 2016, at the Porto Palácio Congress Hotel & Spa (http://www.hotelportopalacio.com/en/hotel-overview.html).

The submission deadline is the 8th of January, 2016. Please find all the details in the conference website: www.escan2016.eu<http://www.escan2016.eu>
We would appreciate it if you could pass this information along to other colleagues and students. Attached you may find a poster with the call for submissions.

We are looking forward to seeing you in Porto in 2016!
Fernando Babosa and Fernando Ferreira-Santos (University of Porto)
Chairs of the Local Organizing Committee


P.S.: Apologies if you get multiple postings of this announcement.

--
Laboratory of Neuropsychophysiology
Faculty of Psychology and Education Sciences
University of Porto
Rua Alfredo Allen, 4200-135 Porto (Portugal)
Tel.: +351 226079700
http://www.fpce.up.pt/labpsi/

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From marlene.boenstrup at googlemail.com  Fri Dec 11 21:30:46 2015
From: marlene.boenstrup at googlemail.com (=?UTF-8?Q?Marlene_B=C3=B6nstrup?=)
Date: Fri, 11 Dec 2015 21:30:46 +0100
Subject: [FieldTrip] ft_sourceinterpolate fails when cfg.moveinward and
 cfg.inwardshift was used to create sourcemodel
Message-ID: <CAG0LeNnQE60kuJZHh7jSOYpNLOurgtnn3gBODE0LkXB_NTuzAg@mail.gmail.com>

Dear fieldtrip-community,

I struggle at plotting source reconstruction results, and my routine even
fails when using the template structural data.
I think it is based on a shortcoming of the ft_sourceinterpolation
function. This is why I am optimistic to find help in this platform:
I prepare the leadfields based on the standard_sourcemodel3d6mm, the vol
called standard_bem.mat, the electrode positions defined in
standard_1005.elc.
Since some of the dipoles that are assigned as "inside" in the
sourcemodel3d6mm are actually sticking out of the inner bem boundary,
leading to distorted leadfields, I re-prepare the sourcemodel based on the
following specifications:

mri=ft_read_mri('single_subj_T1.nii');
mri.coordsys = 'spm';
mri = ft_volumereslice([], mri);
cfg=[];
cfg.mri  = mri;
cfg.elec=elec;
cfg.vol=vol;
cfg.grid.warpmni   = 'yes';
cfg.grid.template  = grid; % sourcemodel3d6mm
cfg.grid.nonlinear = 'no';
cfg.moveinward=5;
cfg.inwardshift=0;
grid    = ft_prepare_sourcemodel(cfg);

this comes out with a vector of positions in three dimensional space, all
of them being assigned to inside and none of them as outside.
The leadfields prepared based on this sourcemodel look very convincing and
the ft_sourceanalysis function also works.
But the problem is to interpolate this on the anatomical image:
Nested in the function ft_sourceinterpolate, the function ft_checkdata,
specifically the subfunction source2volume leads to a misconfiguration with
all the positions of the functional data being distributed in to a full 3D
volume. In the end the orthoplot of the brain is a big fully activated
cube.

I hope someone has a good idea how to deal with this issue in fieldtrip and
shares his/her expertise with us.

Many greetings,

Marlene
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From amickan1990 at gmail.com  Sat Dec 12 16:12:57 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Sat, 12 Dec 2015 16:12:57 +0100
Subject: [FieldTrip] fieldtrip Digest, Vol 61, Issue 7
In-Reply-To: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
References: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
Message-ID: <CANX43OLN8qog=xL7qjDpRp_yTPjKV1oQhgbT4Wuy5z0fDmqTiw@mail.gmail.com>

Dear Nick and Jan-Mathijs,

thanks for your emails. Here is the part of the code that details the cfg
inputs. I basically stuck to what was in the tutorial:

cfg = [];
cfg.channel = 'all';

% prepare neighbouring channels

cfg_neighb = [];
cfg_neighb.method = 'distance';
cfg.channel = 'all';
cfg_neighb.feedback = 'yes';
cfg_neighb.layout = 'easycapM3.mat';

neighbours = ft_prepare_neighbours(cfg_neighb, Correct{1});

% settings for statistics

cfg = [];
cfg.channel = {'EEG'};
cfg.latency = [0 1];

cfg.method = 'montecarlo';
cfg.statistic = 'depsamplesT';
cfg.correctm = 'cluster';
cfg.clusteralpha = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan = 2;
cfg.neighbours = neighbours;
cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = 0.5;
cfg.numrandomization = 500;

% prepare design
subj = 24;
design = zeros(2,2*subj);
for i = 1:subj
  design(1,i) = i;
end
for i = 1:subj
  design(1,subj+i) = i;
end
design(2,1:subj)        = 1;
design(2,subj+1:2*subj) = 2;

cfg.design = design;
cfg.uvar  = 1;
cfg.ivar  = 2;

Best,
Anne

On Fri, Dec 11, 2015 at 12:00 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. Stats matrix incomplete - cluster-based permutation test
>       (Anne Mickan)
>    2. Re: Stats matrix incomplete - cluster-based permutation   test
>       (Nicholas A. Peatfield)
>    3. Re: Stats matrix incomplete - cluster-based       permutation
>  test
>       (Schoffelen, J.M. (Jan Mathijs))
>    4. Re: filed trip (aishwarya selvaraj)
>    5. Re: filed trip (Pelt, S. van (Stan))
>    6. possible bug in tutorial code for creating sourcemodel (Juan)
>    7. Re: possible bug in tutorial code for creating sourcemodel
>       (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
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> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 10 Dec 2015 11:13:10 -0800
> From: "Nicholas A. Peatfield" <nick.peatfield at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID:
>         <CADzq99=
> 3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:
>
> > Dear all,
> >
> > I'm just starting to work on a cluster-based permutation test script
> based
> > on the tutorial for within-subject designs on the fieldtrip website. I
> ran
> > into an issue when computing the [stat] matrix. I used the code as it was
> > on the website:
> >
> > [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
> >
> > with the Correct and Incorrect matrices looking as follows:
> >
> > Correct{1}
> >
> >         avg: [34x600 double]
> >        time: [1x600 double]
> >     fsample: '500'
> >       label: {34x1 cell}
> >      dimord: 'chan_time'
> >         dof: [34x600 double]
> >         var: [34x600 double]
> >
> > The function runs without problems, i.e I don't get any error messages.
> > However, the result seems incomplete.
> >
> > stat =
> >                    prob: [25x1 double]
> >             posclusters: []
> >     posclusterslabelmat: [25x1 double]
> >         posdistribution: [1x500 double]
> >             negclusters: [1x1 struct]
> >     negclusterslabelmat: [25x1 double]
> >         negdistribution: [1x500 double]
> >                 cirange: [25x1 double]
> >                    mask: [25x1 logical]
> >                    stat: [25x1 double]
> >                     ref: [25x1 double]
> >                  dimord: 'chan_time'
> >                   label: {25x1 cell}
> >                    time: 0
> >                     cfg: [1x1 struct]
> >
> > Specifically, I later run into trouble with the stat.posclusterslabelmat
> > and stat.negclusterslabelmat matrices which should apparantly contain far
> > more values something more like 25x500 instead of 25x1. When calling
> > neg_int = all(neg(:, m(k):m(k+1)), 2)
> > I get the "Index exceeds matrix dimensions" error message which I assume
> > has to do with the fact that "neg" does not have the appropriate matrix
> > dimensions
> > (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
> >
> > Where is the error / where should I look for the error?
> >
> > Some further design details:
> > Nsubj = 24
> > 2 conditions = Correct, Incorrect
> > Within-subject design
> > sampling rate = 500
> > 34 channels
> >
> > I hope I gave enough / the necessary information for someone to help me
> > out.
> >
> > Thanks in advance!
> >
> > Best,
> > Anne
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Nicholas Peatfield, PhD
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Thu, 10 Dec 2015 19:36:45 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Anne,
>
> I agree with Nick, some more information would be helpful. At this stage
> my wild guess (assuming that you did not constrain your ?search space?,
> using cfg.channel and cfg.latency before calling ft_timelockstatistics)
> would be that there?s a major discrepancy in the descriptive dimensions of
> your data (i.e. the ?labels? and the time points) across the input
> arguments. FieldTrip does an explicit check on the labels and time points,
> it only proceeds to do calculations on the channels and time points that
> are present in each and every input argument. With respect to time points:
> this could even mean that numerical inaccuracies are the showstopper here.
> These inaccuracies could be easily introduced when e.g. downsampling.
>
> Best,
> Jan-Mathijs
>
>
> On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <
> nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:
> amickan1990 at gmail.com>> wrote:
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Nicholas Peatfield, PhD
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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> >
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Dec 2015 12:00:39 +0530
> From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <
> CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
> wrote:
>
> > Hi Aishwarya,
> >
> > I faced the similar problem. You are supposed to change your data
> > (.mat format) in a data structure that is read by fieldtrip. For that
> > you need at least following information
> > 1. Channel label and their location (If you don't have this file you
> > can use standard file available in Fieldtrip and you can include only
> > those electrode that you have been using in your experiment)
> > 2. sampling rate of the data (that you would have done while recording
> the
> > data)
> > 3. time vector
> > 4. no. of trials
> >
> > You can create them in MATLAB and put them together in a structure
> > along with your recorded data. This worked for me.
> >
> > --
> > Ashutosh Mishra
> > 5th year Integrated BS-MS student
> > Department of Physical Sciences
> > Indian Institute of Science Education and Research, Kolkata
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
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>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Dec 2015 08:09:14 +0000
> From: "Pelt, S. van (Stan)" <stan.vanpelt at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0 at exprd03.hosting.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Aishwarya,
>
> The data structure should look something like this:
>
> % 1. Load data
> load EEGdata.mat
>
> % 2. Make FieldTrip structure, manually
> data.label={'Channel1Name?,?Channel2Name?,?Channel3Name?}; %your channel
> names
> data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each
> trial: channelsxtimepoints data
> data.fsample=500; %your recording sampling frequency
> data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data
> sample (e.g: [0 0.02 0.04 0.06 etc])
>
> Going through the Walktrough Tutorial will be the best starting point when
> you just started to use FieldTrip:
> http://www.fieldtriptoolbox.org/walkthrough
> After that, you may go through the other Tutorial documentation or Example
> Matlab scripts.
>
> Best,
> Stan
>
> --
> Stan van Pelt, PhD
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University
> Montessorilaan 3, B.01.34
> 6525 HR Nijmegen, the Netherlands
> tel: +31 24 3616288
>
> From: fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
> Sent: vrijdag 11 december 2015 7:31
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] filed trip
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com
> <mailto:mishra408 at gmail.com>> wrote:
> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Dec 2015 11:43:05 +0100
> From: Juan <juangpc at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID:
>         <CAPO7YL+ufEwMRmBZk=
> XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831>
> ?"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
> the coordinate system
>  % segment the template brain and construct a volume conduction model
> (i.e. head model): % this is needed to describe the boundary that
> define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
> Convert the vol to cm, because the CTF convenction is to express
> everything in cm.
>  % construct the dipole grid in the template brain coordinates% the
> negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html
> >.resolution
> = 1;
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
>  = 'yes';
> cfg.inwardshift = -1.5;
> ??
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ?this line:
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html
> >hold
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where one
> is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Dec 2015 10:54:54 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Juan,
>
> We?ll look into this specific issue soon, it should work without
> specifying sensor positions. However, for now and in general I would
> recommend just using a pre-cooked template grid. These can be found in
> fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I
> will make this more explicit shortly.
>
> Best,
>
> Jan-Mathijs
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:
> juangpc at gmail.com>> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data<http://goog_2124598831/>
> ?<http:/>"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
> coordinate system
>
> % segment the template brain and construct a volume conduction model (i.e.
> head model):
> % this is needed to describe the boundary that define which dipole
> locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert
> the vol to cm, because the CTF convenction is to express everything in cm.
>
> % construct the dipole grid in the template brain coordinates
> % the negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
> = 1;
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
> = 'yes';
> cfg.inwardshift = -1.5;
>
> ??
> cfg.headmodel   = template_headmodel;
>
>
> The problem occurs when I execute ?this line:
>
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
>
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> % make a figure with the template head model and dipole grid
> figure<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
> hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto: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 61, Issue 7
> ****************************************
>
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From LordJojo at gmx.de  Sat Dec 12 19:59:26 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Sat, 12 Dec 2015 19:59:26 +0100
Subject: [FieldTrip] channel problem ft_freqstatistics
Message-ID: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>

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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sun Dec 13 12:12:40 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sun, 13 Dec 2015 11:12:40 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
Message-ID: <CAJT2k_85VtNAPj4J2tib5c2C4ZnJn6xZm6qr7GqceAAH2EA6=A@mail.gmail.com>

Hi Anne,

It looks like you're running stats on grand-average structures created with
cfg.keepindividual='no' (because your Correct and Incorrect structures have
an .avg field). I always do stats on a grand-average structure created with
cfg.keepindividual='yes' (which will yield a structure with no .avg field,
and instead an .individual field, which in your case will be 24x34x600,
since you have participants). Do things work out better if you try it that
way?

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
>
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From recasensmarc at gmail.com  Sun Dec 13 16:07:08 2015
From: recasensmarc at gmail.com (Marc Recasens)
Date: Sun, 13 Dec 2015 15:07:08 +0000
Subject: [FieldTrip] channel problem ft_freqstatistics
In-Reply-To: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
Message-ID: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>

Hi Johannes,

I think the same problem has been reported before in:
http://mailman.science.ru.nl/pipermail/fieldtrip/2015-November/009789.html

Roy Cox looked into the problem with quite detail and found the bug in
the ft_get_selection
function, line 630-631 during a call to "*label = union(label,
selchannel);"*. I recently had the same problem and it was solved after
commenting that line. However it might be better if you update FieldTrip to
the last version where this issue is fixed.

Hope that helps.

Best wishes
Marc

On Sat, Dec 12, 2015 at 6:59 PM, Jojo Klemt <LordJojo at gmx.de> wrote:

> Dear community
>
> My name is Johannes Klemt and I'm analysing eeg/emg-power data of patients
> and healthy controls for my medical doctorate in Tübingen.
> I have a small problem using ft_freqstatistics. After performing an
> independent samples t-test, the channels are suddenly ordered alphabeticaly.
> The preprocessing and power analysis were not performed in field trip.
> The electrode labels and neighbours were defined and put into the
> following cfg:
> cfg.elec
> cfg.neighbours
> The statistics were then calculated using montecarlo method, but the
> channel order in stat.label is changed into alphabetical order, so the stat
> plot looks nice but is quite useless.
> Colleagues of mine used ft_freqgrandaverage as input data and did not have
> the problem, but I can't find the bug.
> I designed a file containing the layout structure and tried putting it in
> by using
> cfg.layout
> but it was ignored.
>
> Any help would be deeply appreciated.
>
> Yours sincerely
>
> Johannes Klemt
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Marc Recasens
Tel.: +34 639 24 15 98
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From federica.ma at gmail.com  Mon Dec 14 12:30:33 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 12:30:33 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Message-ID: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing
to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of
epochs), however the output of the function (namely TFRhann.powspctrm)
always gives me power data for the same number of epochs, namely 41,
unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in
steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
= 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from
-0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica
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From Elana.Harris at cchmc.org  Mon Dec 14 13:12:29 2015
From: Elana.Harris at cchmc.org (Harris, Elana)
Date: Mon, 14 Dec 2015 12:12:29 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
Message-ID: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>

cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


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From stan.vanpelt at donders.ru.nl  Mon Dec 14 13:21:41 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 12:21:41 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>

Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288


From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


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From federica.ma at gmail.com  Mon Dec 14 13:41:27 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 13:41:27 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute
fft for single trials, since TFRhann.powspctrm is by definition an average
along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From stan.vanpelt at donders.ru.nl  Mon Dec 14 14:30:32 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 13:30:32 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>

Hi Federica,

If you want to have an estimate for each trial separately, you should specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip?

Best,
Stan

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro
Sent: maandag 14 december 2015 13:41
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute fft for single trials, since TFRhann.powspctrm is by definition an average along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl<mailto:stan.vanpelt at donders.ru.nl>>:
Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288<tel:%2B31%2024%203616288>


From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [mailto:fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Federica Mauro [federica.ma at gmail.com<mailto:federica.ma at gmail.com>]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica



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

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From LordJojo at gmx.de  Mon Dec 14 15:24:32 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Mon, 14 Dec 2015 15:24:32 +0100
Subject: [FieldTrip]  channel problem ft_freqstatistics
In-Reply-To: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>, 
 <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
Message-ID: <trinity-fd5a5c5e-0a0b-417c-b164-249e75a4e832-1450103072262@3capp-gmx-bs08>

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From federica.ma at gmail.com  Mon Dec 14 22:51:26 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 22:51:26 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5Aoow_Gp1LZOWb2VpOLXr18c2SY+tCpyLrahcVg0miu4g@mail.gmail.com>

Hi Stan, thank you, it was really helpful.

Best,
Federica

2015-12-14 14:30 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Hi Federica,
>
>
>
> If you want to have an estimate for each trial separately, you should
> specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also
> http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip
> ?
>
>
>
> Best,
>
> Stan
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro
> *Sent:* maandag 14 december 2015 13:41
>
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> Dear Stan and Elana, thank you very much for your answers and help.
>
>
>
> Just another question: if I understood correctly, there's no way to
> compute fft for single trials, since TFRhann.powspctrm is by definition an
> average along trials. Is that true?
>
>
>
> Thanks again.
>
>
>
> Bests,
>
> Federica
>
>
>
> 2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl
> >:
>
> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
>
> _______________________________________________
> 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 S.Hanslmayr at bham.ac.uk  Wed Dec 16 12:50:48 2015
From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr)
Date: Wed, 16 Dec 2015 11:50:48 +0000
Subject: [FieldTrip] PhD studentship available at University of Birmingham
Message-ID: <257F6C65A372A04CA41056EACC0DE7CED841AC9A@EX8.adf.bham.ac.uk>

Dear Fieldtrip Community,

I take this opportunity to announce a PhD studentship that is available for talented students to work in the labs of Joff Lee and Simon Hanslmayr on a memory project involving invasive recordings of oscillations in rodents. More information about the project and instructions on how to apply can be found here: http://www.birmingham.ac.uk/research/activity/mrc-impact/imaging.aspx. Deadline for applicants is Sunday 10 January 2016.

For any questions about the project please write an email to Dr Joff Lee (J.L.C.Lee at bham.ac.uk<mailto:J.L.C.Lee at bham.ac.uk>) or myself (simon.hanslmayr at bham.ac.uk<mailto:simon.hanslmayr at bham.ac.uk>).

Seasonal greetings,
Simon


Dr. Simon Hanslmayr
Senior Lecturer
School of Psychology
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Tel +44 121 4146203
http://www.memorybham.com/people/#/simon-hanslmayr/
[http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif]

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From luke.bloy at gmail.com  Wed Dec 16 22:29:17 2015
From: luke.bloy at gmail.com (Luke Bloy)
Date: Wed, 16 Dec 2015 21:29:17 +0000
Subject: [FieldTrip] Question about ft_statfun_actvsblT
Message-ID: <CAG5Ru-pbKEF6cd2YFnkXYvGXfEVtb9YGFpw-zydJMbiKJHshsQ@mail.gmail.com>

Sorry if this is missing something fundamental but I'm abit confused about
the use of ft_statfun_actvsblT for frequency analysis and how it compares
to ft_statfun_depsamplesT.

It seems from http://www.fieldtriptoolbox.org/tutorial/salzburg (and from
trying to use it) that inorder to use ft_statfun_actvsblT the active and
baseline freq structures need to have the same time dimension. Based on
this I'm assuming that the active vs baseline comparison happens at each
time x frequency pair, but isn't this what ft_statfun_depsamplesT does?

So I guess my question is what is the difference between the two? What
exactly is the comparison being performed by ft_statfun_actvsblT?

Thanks
Luke
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From leilayou_54 at yahoo.com  Fri Dec 18 10:43:43 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
References: <807603762.476165.1450431823359.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <807603762.476165.1450431823359.JavaMail.yahoo@mail.yahoo.com>

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again. 
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
      strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load : filename     = 'mydata.edf'
 hdr   = ft_read_header(filename);
 sample.start=1
 sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
 
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Fri Dec 18 13:37:52 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Fri, 18 Dec 2015 12:37:52 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>

Hello Leila,

I think there are a few possible options for you. If you're not interested
in analyzing high frequencies, then you could import the data one sample at
a time, downsampling each channel, and then concatenate the channels into
one structure, as described in
http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
I don't know what your sampling rate was, but if your sampling rate was
extremely high then this can save you a lot of space. For example, if
you're only interested in frequencies up to high gamma (around 90-100 Hz),
then your data only need to be sampled at around 250 Hz (per the Nyquist
theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
Hz (which our EDF system does by default) or 5000 Hz then you have way more
samples than necessary; downsampling like this will greatly reduce your
array size.



If that is not an option, then you can read in a segment of data as a
'trial'. ft_preprocessing understands trial start and end times from
cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
read, and the columns are the start sample for each trial, the end sample
for each trial, and the trigger value associated with the trial; you could
just put 0 if there's no trigger). So let's say you want to read the first
through thousandth sample of the recording, then you would set up your cfg
as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of
1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an
explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them
back into continuous data (see
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for
details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/

On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
>         <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
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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 61, Issue 14
> *****************************************
>
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From anja.pflug at musterkind.eu  Fri Dec 18 14:06:32 2015
From: anja.pflug at musterkind.eu (Anja Pflug)
Date: Fri, 18 Dec 2015 14:06:32 +0100 (CET)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
Message-ID: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>

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From leilayou_54 at yahoo.com  Fri Dec 18 14:13:16 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:13:16 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <1753128777.512946.1450444396047.JavaMail.yahoo@mail.yahoo.com>

 Thanks for your reply Anja.I need to have all the channel information at a segment of time to decide if it there is seizure occurring.  Down sampling will loose the information and I am not sure if I want to go that way, as I need to do some feature extractions/classification etc on the data.
Not sure how I could cut the data in fieldtrip. Do you know?ThanksBest regards
___________________________________________________ Leila Ayoubian 

 

      From: Anja Pflug <anja.pflug at musterkind.eu>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 1:06 PM
 Subject: [FieldTrip] Importing large edf data
   
 Hello Leila,
have you tried to import only one of your 51 channels?
If this works you  could cut the data or downsample it and then combine all channels in a later step.
Best,
Anja


fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
 <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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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 61, Issue 14
*****************************************

_______________________________________________
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From jorn at artinis.com  Fri Dec 18 14:17:34 2015
From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=)
Date: Fri, 18 Dec 2015 14:17:34 +0100
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <007301d13996$7573dc60$605b9520$@artinis.com>

Hi all,

 

I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension. 

 

Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.

 

Best of luck ;)

Jörn

--
Jörn M. Horschig, PhD, Software Engineer
 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

 

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data

 

Hello Leila,

have you tried to import only one of your 51 channels?

If this works you  could cut the data or downsample it and then combine all channels in a later step.

Best,

Anja

 

 <mailto:fieldtrip-request at science.ru.nl> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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Today's Topics:

1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com <mailto:leilayou_54 at yahoo.com> >
To: "fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> " <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com <mailto:807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> >
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From leilayou_54 at yahoo.com  Fri Dec 18 14:40:59 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
References: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
Message-ID: <2054001626.533069.1450446059200.JavaMail.yahoo@mail.yahoo.com>

 Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.  Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! 

So this is what I get: 


   hdr: [1x1 struct]
         label: {51x1 cell}
          time: {1x50710 cell}
         trial: {1x50710 cell}
       fsample: 1024
    sampleinfo: [50710x2 double]
           cfg: [1x1 struct]

so the actual data which is in data.trial  is this in both cases! 
size(data.trial)

ans =

           1       50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian 

 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing. 

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

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Today's Topics:

   1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
        <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 61, Issue 14
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From leilayou_54 at yahoo.com  Fri Dec 18 14:55:18 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:55:18 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <778201681.538338.1450446918121.JavaMail.yahoo@mail.yahoo.com>

Thanks Jorn. Appreciate your feedback.
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Jörn M. Horschig <jorn at artinis.com>
 To: 'FieldTrip discussion list' <fieldtrip at science.ru.nl> 
 Sent: Friday, December 18, 2015 1:17 PM
 Subject: Re: [FieldTrip] Importing large edf data
   
#yiv8769305188 #yiv8769305188 -- _filtered #yiv8769305188 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8769305188 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv8769305188 {font-family:Verdana;panose-1:2 11 6 4 3 5 4 4 2 4;}#yiv8769305188 #yiv8769305188 p.yiv8769305188MsoNormal, #yiv8769305188 li.yiv8769305188MsoNormal, #yiv8769305188 div.yiv8769305188MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:12.0pt;}#yiv8769305188 a:link, #yiv8769305188 span.yiv8769305188MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv8769305188 a:visited, #yiv8769305188 span.yiv8769305188MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv8769305188 p {margin-right:0in;margin-left:0in;font-size:12.0pt;}#yiv8769305188 span.yiv8769305188EmailStyle18 {color:#1F497D;}#yiv8769305188 .yiv8769305188MsoChpDefault {font-size:10.0pt;} _filtered #yiv8769305188 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv8769305188 div.yiv8769305188WordSection1 {}#yiv8769305188 Hi all,  I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.   Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.  Best of luck ;)Jörn--
Jörn M. Horschig, PhD, Software Engineer
Artinis Medical Systems  |  +31 481 350 980   From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data  Hello Leila,have you tried to import only one of your 51 channels?If this works you  could cut the data or downsample it and then combine all channels in a later step.Best,Anja  
fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 61, Issue 14
*****************************************

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From a.stolk8 at gmail.com  Fri Dec 18 18:51:20 2015
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Fri, 18 Dec 2015 07:51:20 -1000
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <81DC3EE6-21D4-4BB7-80B8-AF642B616768@gmail.com>

Hi all,

Perhaps this links helps:
http://www.fieldtriptoolbox.org/getting_started/edf

Arjen

> On Dec 18, 2015, at 3:17 AM, Jörn M. Horschig <jorn at artinis.com> wrote:
> 
> Hi all,
>  
> I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.
>  
> Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.
>  
> Best of luck ;)
> Jörn
> --
> Jörn M. Horschig, PhD, Software Engineer
> Artinis Medical Systems  |  +31 481 350 980
>  
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
> Sent: Friday, December 18, 2015 14:07
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Importing large edf data
>  
> Hello Leila,
> 
> have you tried to import only one of your 51 channels?
> 
> If this works you  could cut the data or downsample it and then combine all channels in a later step.
> 
> Best,
> 
> Anja
> 
>  
> 
> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:
> 
> 
> 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. importing large edf data (Leila Ayoubian)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
> 
> Error in ReadFedfiles (line 8)
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 
> 
> 
> I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >> 
> 
> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
> Thanks again for your support and assistance. 
> We appreciate your effort.
> Kind regards
> 
> ___________________________________________________ Dr. Leila Ayoubian 
> -------------- next part --------------
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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 61, Issue 14
> *****************************************
> 
> _______________________________________________
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sat Dec 19 15:06:46 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sat, 19 Dec 2015 14:06:46 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a
sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it
worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Friday, December 18, 2015 12:37 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
>
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From senakahks at gmail.com  Sun Dec 20 12:51:47 2015
From: senakahks at gmail.com (Senaka Amarakeerthi)
Date: Sun, 20 Dec 2015 17:21:47 +0530
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data structure.
Message-ID: <CA+si8qkXe5W7J=J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg@mail.gmail.com>

Dear all,

I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
The file I am trying to process is a single trial.

The code I tried is:

%% import data from testbench emotiv edf file

[hdr, data_eeg] = edfread('emotive.edf');



%% Rearrange data to match FieldTrip Format

% Remove unnecessary columns

data.trial = data_eeg([3:16,39], : );





% Cell-array containing strings, Nchan X 1

% Based on https://emotiv.com/forum/forum14/topic1817/messages/

data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6' 'F4'
'F8' 'AF4' 'MARKER'};



% Sampling frequency in Hz, single number

data.fsample = 128;



% Setting time

[x, filelength] = size(data.trial);

data.time{1} = [1:filelength]./data.fsample;

%% Using the rearranged data





% Set the trial column name and event value (what you enter to the last
column.

% here enter number 1 as the marker)

cfg.trialdef.eventtype = 'MARKER';

cfg.trialdef.eventvalue = 1;

cfg.trialdef.eventtype = '?';

ft_definetrial(cfg);


%% Preprocessing

 cfg = [];

 cfg.channel       = 'AF3';

 cfg.lpfilter      = 'yes';

 cfg.hpfilter      = 'yes';

 cfg.bsfilter      = 'yes';

 cfg.lpfreq        = 100;

 cfg.hpfreq        = 10;

 cfg.bsfreq        = [59 61];

 cfg.lpfiltord     = 4;

 cfg.hpfiltord     = 4;

 cfg.bpfiltord     = 4;

 cfg.lpfilttype    = 'but';

 cfg.hpfilttype    = 'but';

 ecog = ft_preprocessing(cfg,data);


When I run the script. I am getting the following error.

Error in ft_trialfun_general (line 78)
hdr = ft_read_header(cfg.headerfile, 'headerformat',
cfg.headerformat);

Do I need to set the header structure as well? Can somebody help me to get
this fixed. I am reading the documentation but it seems start is bit hard!

Appreciate your support
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From leilayou_54 at yahoo.com  Mon Dec 21 10:36:27 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
References: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
Message-ID: <1459455402.1301519.1450690587900.JavaMail.yahoo@mail.yahoo.com>

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first. 
But now I see thecfg2.trialdef.triallength = 1; 
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference? Thanks again.Kind regards
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/ 
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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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 stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:35:23 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:35:23 +0000
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
	structure
Message-ID: <CAJT2k_-wZpxENz55hHhJDerN1RuBQH34j3dyKvhLoPHSEGfTbg@mail.gmail.com>

Hello Senaka,

I think you might be making your life more difficult by trying to directly
call edfread(), which is a low-level function. Have you tried just using
ft_preprocessing(), the high-level wrapper function, as described in the
tutorial on the fieldtrip wiki? In my experience, this function reads EDF
data straightforwardly.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 20 Dec 2015 17:21:47 +0530
> From: Senaka Amarakeerthi <senakahks at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
>         structure.
> Message-ID:
>         <CA+si8qkXe5W7J=
> J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
> The file I am trying to process is a single trial.
>
> The code I tried is:
>
> %% import data from testbench emotiv edf file
>
> [hdr, data_eeg] = edfread('emotive.edf');
>
>
>
> %% Rearrange data to match FieldTrip Format
>
> % Remove unnecessary columns
>
> data.trial = data_eeg([3:16,39], : );
>
>
>
>
>
> % Cell-array containing strings, Nchan X 1
>
> % Based on https://emotiv.com/forum/forum14/topic1817/messages/
>
> data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6'
> 'F4'
> 'F8' 'AF4' 'MARKER'};
>
>
>
> % Sampling frequency in Hz, single number
>
> data.fsample = 128;
>
>
>
> % Setting time
>
> [x, filelength] = size(data.trial);
>
> data.time{1} = [1:filelength]./data.fsample;
>
> %% Using the rearranged data
>
>
>
>
>
> % Set the trial column name and event value (what you enter to the last
> column.
>
> % here enter number 1 as the marker)
>
> cfg.trialdef.eventtype = 'MARKER';
>
> cfg.trialdef.eventvalue = 1;
>
> cfg.trialdef.eventtype = '?';
>
> ft_definetrial(cfg);
>
>
> %% Preprocessing
>
>  cfg = [];
>
>  cfg.channel       = 'AF3';
>
>  cfg.lpfilter      = 'yes';
>
>  cfg.hpfilter      = 'yes';
>
>  cfg.bsfilter      = 'yes';
>
>  cfg.lpfreq        = 100;
>
>  cfg.hpfreq        = 10;
>
>  cfg.bsfreq        = [59 61];
>
>  cfg.lpfiltord     = 4;
>
>  cfg.hpfiltord     = 4;
>
>  cfg.bpfiltord     = 4;
>
>  cfg.lpfilttype    = 'but';
>
>  cfg.hpfilttype    = 'but';
>
>  ecog = ft_preprocessing(cfg,data);
>
>
> When I run the script. I am getting the following error.
>
> Error in ft_trialfun_general (line 78)
> hdr = ft_read_header(cfg.headerfile, 'headerformat',
> cfg.headerformat);
>
> Do I need to set the header structure as well? Can somebody help me to get
> this fixed. I am reading the documentation but it seems start is bit hard!
>
> Appreciate your support
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:39:56 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:39:56 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>

Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
needed if all you want to do is read a single segment of continuous data
based on predetermined latencies; you may notice that, in the sample code
snippets I sent in my last message, I did not use this function at all, I
just hard-coded the latency range in cfg.trl (and then passed this cfg
structure to ft_preprocessing() ). So, if this is all you need to do, there
is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into
one dataset (which is what you would accomplish by using
cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
it's not working for you at the moment; I would have to see your code to be
able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Saturday, December 19, 2015 2:06 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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
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> ? ? ? ? fieldtrip-request at science.ru.nl
>
> You can reach the person managing the list at
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>
>
> Today's Topics:
>
> ? ?1. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
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From leilayou_54 at yahoo.com  Mon Dec 21 13:04:36 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:04:36 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <1581782628.1312312.1450699476132.JavaMail.yahoo@mail.yahoo.com>

 You are absolutely right. It is either using the fix cfg.trl to choose the begining and end of the samples or to choose the cfg2.trialdef.triallength =5. 
In your initial code you had them together, and that is why I was confused. So basically there are two ways to segment the file.
Thanks you very much. You have been very helpful.
My questions are endless. I have another one for you! Sorry!
When loading edf+ the events are lost. using cfg2.trialdef.eventtype  = '?' gives me no events detected.
Any idea how I could go about it?
Thanks again for your help. I really appreciate it.Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

Send fieldtrip mailing list submissions to
? ? ? ? fieldtrip at science.ru.nl

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Today's Topics:

? ?1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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------------------------------





 
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fieldtrip mailing list
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From leilayou_54 at yahoo.com  Mon Dec 21 13:59:38 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <916358647.1306232.1450702778200.JavaMail.yahoo@mail.yahoo.com>

Dear Steve,I have shared my data file in drop box with you. 
I am trying to read the events in this file and I get 0 events. cfg2.trialdef.eventtype  = '?'
Could you please help me out?
Thanks __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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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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From leilayou_54 at yahoo.com  Mon Dec 21 16:49:12 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
Subject: [FieldTrip] EDF+ annotations
References: <782532884.1387709.1450712952642.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <782532884.1387709.1450712952642.JavaMail.yahoo@mail.yahoo.com>

Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab and read the events/annotations. These annotations are usually seizure, or spikes....
The files are EEG data from nicollet one, lengthy data for epileptic patients.
This is how I try to look at the events:

cfg2 = [];

cfg2.dataset = 'For leila.edf';
cfg2.trialdef.eventtype  = '?'
cfg2 = ft_definetrial( cfg2 );


cfg2.continuous = 'yes';
data2 = ft_preprocessing(cfg2);
However the output for events are always empty.Does anyone have an idea how I could extract the events/annotation on these files? 

 Thanks in advance for your assistance.
Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 

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From weston.pack at yale.edu  Mon Dec 21 18:56:11 2015
From: weston.pack at yale.edu (Pack, Weston)
Date: Mon, 21 Dec 2015 17:56:11 +0000
Subject: [FieldTrip] How to implement the .pl2 patch for Plexon data
Message-ID: <46289A1970E74F4888AA0D7E75AAB1E6210097A4@x10-mbx13.yu.yale.edu>

Greetings FieldTrip community,

I am new to using FieldTrip, but am well versed in Matlab. I would like to use FieldTrip to analyze Plexon data from LFP recordings and am working with the .pl2 format. I have read through the current documentation (very short) about the patch for loading .pl2 files, but I still have no idea how to install and use the patch as this is not documented (that I can find). The following is provided but with no explanation of how to implement it:

“ (filetype = plexon_plx_v2) “

I have added the path of the Plexon SDK folder using:
“ addpath ('E:\MatlabOfflineFilesSDK')”

I have download the .diff patch file as well as the .zip folder “ft_plexon” but I don’t know where to put them. Does the “plexon” folder inside go in the main FieldTrip directory, the main Plexon SDK directory (currently listed above), or somewhere else? The same question applies to the .diff file.
Thank you in advance for your assistance. Once I get FieldTrip figured out, I intend to create a thorough, novice-friendly tutorial with step-by-step instructions how to work with .pl2 files for LFP analysis. I’ve spent the better part a week fumbling through the tutorials and I’m certain I can write a novice-friendly tutorial on the wiki that will only take a few hours at most for beginners to master. My goal is first to understand how to utilize FieldTrip, at which point I can document my struggles and successes so that future users (especially my lab-mates) can obtain competency with far more efficiency.

Thanks again in advance. I hope to contribute significantly to the community. Happy Holidays!

Weston Pack, PhD

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From jochem.rieger at uni-oldenburg.de  Mon Dec 21 20:00:15 2015
From: jochem.rieger at uni-oldenburg.de (Jochem Rieger)
Date: Mon, 21 Dec 2015 20:00:15 +0100
Subject: [FieldTrip] Job vacancies: MEG-physicist/engineer and
 MRI-physicist/engineer at Oldenburg University, Germany
Message-ID: <56784C3F.4050501@uni-oldenburg.de>

The newly founded Neuroimaging Center at the University of Oldenburg,
Germany,
offers the following two positions


*1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) *

* *

*2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years)*

 

The positions are suitable for part-time work.

 

The Neuroimaging Center hosts a state of the art magnetoencephalograph
(ElektaTriux)
and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded
in an
excellent interdisciplinary scientific environment with a strong
research focus on
neurosensory, neurocognitive, and medical research. 

 

We seek for highly motivated post-doctoral candidates  (with PhD) with
an academic university degree in physics, engineering or related fields,
with documented research experience in magnetoencephalography (position
1) or magnetic resonance imaging (position 2). For both positions,
fluency in English is necessary. German and experience in the design of
neurocognitive experiments are desirable.

 

Successful candidates will be responsible for the operation and
administration of the
MEG-system and MRI-system respectively, their infrastructure, the
development and
improvement of measurement and analyses techniques and user consultancy.

 

The University of Oldenburg is rapidly growing and offers a vibrant
scientific environment with strong foci on cognitive and sensory
neuroscience and a new medical school. The European Medical School is a
cooperation project between the Universities of Oldenburg and Groningen
and three local hospitals. Oldenburg is an attractive city in Germany's
northwest with excellent quality of life. It is close to Bremen,
Hamburg, Groningen, and approx. 1 h from the north sea.

 

The University of Oldenburg is dedicated to increasing the percentage of
women in science. Therefore, female candidates are particularly
encouraged to apply and will be given preference in cases of equal
qualification. Handicapped applicants will be given preference if
equally qualified.

 

Electronic applications (one pdf file) are preferred and can be send to:
Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de
<mailto:Jochem.rieger at uni-oldenburg.de> 

Applications by mail should be sent to

Prof. Jochem Rieger

Universität Oldenburg

Kuepkersweg 74 (W30)

26129 Oldenburg

Germany

 

The application process is open until January 31st 2016. Applications
should include
your CV, a list of most recent publications, and a statement (max. 3
pages).
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From plyons at udel.edu  Mon Dec 21 20:39:59 2015
From: plyons at udel.edu (Peter Lyons)
Date: Mon, 21 Dec 2015 14:39:59 -0500
Subject: [FieldTrip] Clarification on plotting WPLI
Message-ID: <CALq-V2q-ubebB0u1S_wa_RFpfW4gAFXntNb4C+SC8uHT2QpPzw@mail.gmail.com>

Hello Everyone,

I have a question regarding the interpretation of negative values in the
debiased wPLI. Although the reference page on the debiased wPLI notes that
estimates are computed by squaring the wPLI values, I and others have
noticed that some of the values in the debiased wPLI spectrum are negative.
How should these negative values be interpreted in reference to 0?

To view the results of the debiased wPLI connectivity analysis
(ft_connectivity analysis with cfg.method = 'wpli_debiased'), I've been
using the ft_topoplotER function. However, I'm concerned that the default
scaling (zlim = 'maxmin') of the plot does not seem to register the
negative values in the debiased wPLI spectrum. That is, the negative values
are not being plotted. It is curious, however, that the ft_topoplotER
does register the negative values in the *non-debiased *wPLI spectrum.

Is there a reason why the ft_topoplotER function is treating the negative
values from the debiased vs. non-debiased wPLI spectrums differently? Is
there perhaps a more appropriate plotting function I should be using to
view the debiased wPLI output?

I would greatly appreciate any guidance in this.

Thank you!

Peter
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From shlomitbeker at gmail.com  Tue Dec 22 07:42:31 2015
From: shlomitbeker at gmail.com (Shlomit Beker)
Date: Tue, 22 Dec 2015 06:42:31 +0000
Subject: [FieldTrip] Please remove me from mailing list
Message-ID: <7fa9847a19964083a25ceb552d18577f@EXPRD01.hosting.ru.nl>




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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Tue Dec 22 18:48:01 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Tue, 22 Dec 2015 12:48:01 -0500
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k__yFvF-Khymgo7fVLyZnCUdsb9htcC-kFGqDZ1JM=1Akg@mail.gmail.com>

Hi Leila,

According to the warning messages that pop up, the annotation channel is
not being read because it is at a different sampling rate than the data.
>From what I can tell, this appears to be a common problem.
http://www.fieldtriptoolbox.org/getting_started/edf explains a workaround;
have you tried this?

Alternatively, you could consider trying some other toolboxes---I believe
mne-python is capable of handling this issue with EDF triggers
straightforwardly, or you could use one of the softwares that is
specifically made for EDF (such as EDFViewer or EDFBrowser) to export your
annotations into a format that is more easily readable and then use that to
create your cfg.trl structure for Fieldtrip.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 4
> Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <916358647.1306232.1450702778200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Steve,I have shared my data file in drop box with you.
> I am trying to read the events in this file and I get 0 events.
> cfg2.trialdef.eventtype? = '?'
> Could you please help me out?
> Thanks?__________________________________________________ Leila Ayoubian,
> PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Monday, December 21, 2015 11:39 AM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
> needed if all you want to do is read a single segment of continuous data
> based on predetermined latencies; you may notice that, in the sample code
> snippets I sent in my last message, I did not use this function at all, I
> just hard-coded the latency range in cfg.trl (and then passed this cfg
> structure to ft_preprocessing() ). So, if this is all you need to do, there
> is no need to worry about these additional parameters.
>
> If you are trying to read multiple segments of data as separate epochs
> into one dataset (which is what you would accomplish by using
> cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
> it's not working for you at the moment; I would have to see your code to be
> able to diagnose what might be going on.
>
> Best,
> Steve
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> ?
>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Saturday, December 19, 2015 2:06 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
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> ------------------------------
>
>
>
>
>
> ?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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> ------------------------------
>
> Message: 5
> Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] EDF+ annotations
> Message-ID:
>         <782532884.1387709.1450712952642.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab
> and read the events/annotations. These annotations are usually seizure, or
> spikes....
> The files are EEG data from nicollet one, lengthy data for epileptic
> patients.
> This is how I try to look at the events:
>
> cfg2 = [];
>
> cfg2.dataset = 'For leila.edf';
> cfg2.trialdef.eventtype? = '?'
> cfg2 = ft_definetrial( cfg2 );
>
>
> cfg2.continuous = 'yes';
> data2 = ft_preprocessing(cfg2);
> However the output for events are always empty.Does anyone have an idea
> how I could extract the events/annotation on these files?
>
>  Thanks in advance for your assistance.
> Best regards
> __________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
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> ------------------------------
>
>
>
>
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From fanshine at yeah.net  Wed Dec 23 09:55:28 2015
From: fanshine at yeah.net (Hanson)
Date: Wed, 23 Dec 2015 16:55:28 +0800 (CST)
Subject: [FieldTrip] Make a custom layout
Message-ID: <7af7ec0c.1eaf.151ce0cdf79.Coremail.fanshine@yeah.net>

Dear all,

I am new to FieldTrip and  trying to  do the time-frequency analysis of my eeg data , however it seems that no suitable layout. And I use ft_prepare_layout function to make a custom layout(electrode_position32.mat).
%% Time-frequency analysis 
cfg              = [];
cfg.output       = 'pow';
cfg.channel      = 'EEG';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 2:2:30;                           
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   
cfg.toi          = -0.5:0.05:1.5;                   
TFRhann = ft_freqanalysis(cfg, data);


cfg = [];       
cfg.showlabels   = 'yes';
cfg.layout       = 'electrode_position32.mat';
figure 
ft_multiplotTFR(cfg, TFRhann);


cfg = [];
cfg.channel      = 'C4';
figure 
ft_singleplotTFR(cfg, TFRhann);


cfg = [];
cfg.layout = 'electrode_position32.mat';
figure 
ft_topoplotTFR(cfg, TFRhann);


When I run the script. I am getting the following error.


Warning: (one of the) axis is/are not evenly spaced, but plots are made as if axis are linear 
> In ft_multiplotTFR at 405
  In TFanalysis_zhs_2 at 52 
the call to "ft_multiplotTFR" took 0 seconds
the call to "ft_singleplotTFR" took 0 seconds
reading layout from file electrode_position32.mat
the call to "ft_prepare_layout" took 0 seconds
Warning: Some points fall outside the outline, please consider using another layout 
> In ft_plot_topo at 171
  In fieldtrip\private\topoplot_common at 731
  In ft_topoplotTFR at 192
  In TFanalysis_zhs_2 at 62 
Index exceeds matrix dimensions.


Error in ft_plot_topo (line 182)
    mask{i}(end+1, :) = mask{i}(1, :);                   % force them to be closed


Error in topoplot_common (line 731)
  ft_plot_topo(chanX,chanY,datavector,opt{:});


Error in ft_topoplotTFR (line 192)
[cfg] = topoplot_common(cfg, varargin{:});


Error in TFanalysis_zhs_2 (line 62)
ft_topoplotTFR(cfg, TFRhann);


Do you have any suggestion about it?
Thank you very much for your attention.


Kind Regards,
Hanson
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From daria.laptinskaya at googlemail.com  Tue Dec  1 09:58:46 2015
From: daria.laptinskaya at googlemail.com (Daria Laptinskaya)
Date: Tue, 1 Dec 2015 09:58:46 +0100
Subject: [FieldTrip] SCD and coherence analysis
In-Reply-To: <52d6-565c1c80-25-55c3b400@102538225>
References: <52d6-565c1c80-25-55c3b400@102538225>
Message-ID: <CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ@mail.gmail.com>

Hi Barbara,

try this:
 sens=ft_read_sens('GSN-HydroCel-257.sfp');
 cfg=[];
 cfg.elec=sens;

Hope it helps :-)
Daria






2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:

> Dear Fieltripers,
>
> I would like to do coherence analysis. I did a SCD analysis on my data
> first ('finite' method), and want to run ft_mvaranalysis now. I get
> the error
>
> Error using ft_datatype_sens (line 186)
> inconsistent number of channels in sensor description
>
> As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> fieldtrip (my raw data set has 257 channels), but there are only 256
> channels left after the SCD analysis. Can this cause the problem?
>
> Has anyone had this problem before and can provide a solution? I only
> found one prior entry with this topic, but there was no final solution for
> it.
>
>
> Thanks and all the best,
> Barbara
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From barbara.schorr at uni-ulm.de  Tue Dec  1 15:18:31 2015
From: barbara.schorr at uni-ulm.de (Barbara Schorr)
Date: Tue, 01 Dec 2015 15:18:31 +0100
Subject: [FieldTrip] =?utf-8?q?SCD_and_coherence_analysis?=
In-Reply-To: <mailman.19.1448967602.14550.fieldtrip@science.ru.nl>
Message-ID: <38ba-565dac00-3-4dd4ed00@147935417>

Dear Daria,

I did exactly this. 
The problem occurs afterwards, when I want to run ft_mvaranalysis on the data that result from ft_scalpcurrentdensity.
In the fieldtrip document it states, that the output data of  ft_scalpcurrentdensity has the same format as the input data.
When I run ft_mvaranalysis on the original data, everything works fine, but with the SCD data I get this error that the number of channels in sensor description is inconsistent.

Has anyone else experienced this problem?

Best,
Barbara


Am Dienstag, 01. Dezember 2015 12:00 CET, fieldtrip-request at science.ru.nl schrieb: 
 
> 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: power suppression during DICS beamforming ?
>       (Mait? Crespo Garc?a)
>    2. Re: SCD and coherence analysis (Daria Laptinskaya)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 30 Nov 2015 15:31:20 +0000 (UTC)
> From: Mait? Crespo Garc?a <maity_winky at yahoo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] power suppression during DICS beamforming ?
> Message-ID:
> 	<1881724873.21184223.1448897480847.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Fr?d?ri,
> maybe you have the solution already.
> In case not, could you explain how did you get the last two plots? Are spectra computed after averaging across all virtual channel spectra or you are representing the spectrum of the source with maximal power?
> Best,Maite
> 
> 
> 
>     El Jueves 26 de noviembre de 2015 13:55, Fr?d?ric Roux <f.roux at bcbl.eu> escribi?:
>  
> 
>  Dear all,
> 
> I am observing a counter-intuitive result after applying the spatial filters obtained from DICS beamforming to my MEG data.
> 
> The plot in the attachment summarizes the issue: The raw data shows a clear peak of activity at 10 Hz, however, after applying the spatial filter to the MEG data the spectrum of the virtual channels shows that power in this frequency band is reduced. The same also happens when I apply a spatial filter in the gamma range for power at 70 Hz to the raw MEG signals.
> 
> Is this something that falls out of the beamformer math due to the fact how the algorithm suppresses power at all locations by minimizing the noise level, or is there something wrong with my code? I (maybe naively) assumed that the results should come out the opposite. On the other hand, when plotting the noise normalized maps (NAI) of both the alpha and gamma beamformers the sources look quite accurate. Should I normalize with the level of noise first before plotting the spectrum to see the expected results (ie an upregulation of power instead of a downregulation of power)?
>  
> The code that I use to generate the figures is:
> 
> % 1) compute CSD matrix
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.foilim = [10 10];
> cfg.tapsmofrq = 2;
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> 
> [csd] = ft_freqanalysis(cfg,meg_data);
> 
> 
> % 2) compute DICS filter
> cfg = [];
> cfg.method = 'dics';
> cfg.grad = meg_data.grad;
> cfg.headmodel = vol;
> cfg.frequency = csd.freq;
> 
> cfg.dics.realfiter = 'yes';
> cfg.dics.fixedori = 'yes';
> 
> [alpha_filter]= ft_sourceanalysis(cfg,csd);
> 
> % 3) compute the virtual channel data
> 
> VC = meg_data;
> VC.trial = cell(1,length(meg_data.trial));
> VC.label = cell(1,length(alpha_filter.avg.pow));
> 
> for i = 1:length(VC.trial)
> ? for j = 1:length(VC.label)
> 
> ? ? ? VC.trial{i}(j,:) = alpha_filter{j}*meg_data.trial{i};
> ? ? ? VC.label(j) = {['virtual_channel',num2str(j)]};
> ? end;
> end;
> 
> % 4) compute the spectrum of the virtual channel data
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> cfg.tapsmofrq = 1;
> cfg.foi = 0.1:100;
> 
> [pow] = ft_freqanalysis(cfg,VC);
> 
> 
> Any help or suggestions would be greatly appreciated.
> 
> Fred
> 
> --
> Fr?d?ric Roux
> Postdoctoral Scientist, Marie-Curie fellow
> BCBL. Basque Center on Cognition, Brain & Language.
> 
> f.roux at bcbl.eu
> Tel: +34 943 309 300 Ext 211
> Fax: +34 943 309 052
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
> ---------------------------------------------------------------------------
> 
> ?The probability of success is difficult to estimate; but if we never search the chance of success is zero.?
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> ------------------------------
> 
> Message: 2
> Date: Tue, 1 Dec 2015 09:58:46 +0100
> From: Daria Laptinskaya <daria.laptinskaya at googlemail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] SCD and coherence analysis
> Message-ID:
> 	<CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Barbara,
> 
> try this:
>  sens=ft_read_sens('GSN-HydroCel-257.sfp');
>  cfg=[];
>  cfg.elec=sens;
> 
> Hope it helps :-)
> Daria
> 
> 
> 
> 
> 
> 
> 2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:
> 
> > Dear Fieltripers,
> >
> > I would like to do coherence analysis. I did a SCD analysis on my data
> > first ('finite' method), and want to run ft_mvaranalysis now. I get
> > the error
> >
> > Error using ft_datatype_sens (line 186)
> > inconsistent number of channels in sensor description
> >
> > As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> > fieldtrip (my raw data set has 257 channels), but there are only 256
> > channels left after the SCD analysis. Can this cause the problem?
> >
> > Has anyone had this problem before and can provide a solution? I only
> > found one prior entry with this topic, but there was no final solution for
> > it.
> >
> >
> > Thanks and all the best,
> > Barbara
> >
> >
> > _______________________________________________
> > 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 61, Issue 1
> ****************************************
 
 
 
 





From eriksenj at ohsu.edu  Wed Dec  2 03:04:56 2015
From: eriksenj at ohsu.edu (K Jeffrey Eriksen)
Date: Wed, 2 Dec 2015 02:04:56 +0000
Subject: [FieldTrip] accommodating air pockets in FEM head model
Message-ID: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>

Hi,

I am reading the FieldTrip documentation on creating an FEM model and see that the following tissue types are output from the segmentation process:

Gray
White
Csf
Skull
Scalp

Q1: Since I am using a 256 channel EGI system with electrodes over the lower part of the head and face, I absolutely need to be able to include air voxels as well. Anyone have any knowledge of such a possibility?

Q2: Beyond that I would also like to include other tissue types such as fat, muscle, and eyeball (vitrious). I suppose I could find other segmentation software to simply create a more varied segmentation and insert it in the processing pipeline, but would like to know if that would mess anything up.

Q3: Next, can the FEM handle anisotropic conductivities for white matter and skull?

Q4: has anyone out there actually used the FDM model?

Thanks,
-Jeff Eriksen

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From carsten.wolters at uni-muenster.de  Wed Dec  2 08:53:17 2015
From: carsten.wolters at uni-muenster.de (Carsten Wolters)
Date: Wed, 2 Dec 2015 08:53:17 +0100
Subject: [FieldTrip] accommodating air pockets in FEM head model
In-Reply-To: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
References: <FC8F960C75FCA14493D57C730DD538EF4779AF7F@EXMB14.ohsu.edu>
Message-ID: <565EA36D.5030005@uni-muenster.de>

Hi Jeff,

Q3:
yes, FEM can model anisotropy and white matter is anisotropic, but skull 
is a three-layered-structure
consisting of spongiosa and compacta, see
http://www.ncbi.nlm.nih.gov/pubmed/20690140

For Q4:
FEM allows geometry-adaptation, see
http://www.ncbi.nlm.nih.gov/pubmed/17694865
As far as I know, modeling using irregular meshes might get difficult to 
implement within an FDM framework.

For Q1 and Q2:
Mainly tissues between sources and electrodes are important to be 
modeled (so white matter anisotropy
is only important for deeper sources) and FSL and freesurfer can do a 
good job on segmentation.
Air-compartments can possibly best be modeled by hand-correction of the 
FSL output.
Please see
http://www.ncbi.nlm.nih.gov/pubmed/24671208
on how we solve forward modeling to be able to combine EEG and MEG.

More infos are available in the two following theses:
http://www.sci.utah.edu/~wolters/PaperWolters/2014/Lanfer_Dissertation_July2-2014.pdf
http://www.sci.utah.edu/~wolters/PaperWolters/2015/Umit_Aydin_Dissertation_2015.pdf


Best regards
      Carsten

Am 02.12.2015 um 03:04 schrieb K Jeffrey Eriksen:
>
> Hi,
>
> I am reading the FieldTrip documentation on creating an FEM model and 
> see that the following tissue types are output from the segmentation 
> process:
>
> Gray
>
> White
>
> Csf
>
> Skull
>
> Scalp
>
> Q1: Since I am using a 256 channel EGI system with electrodes over the 
> lower part of the head and face, I absolutely need to be able to 
> include air voxels as well. Anyone have any knowledge of such a 
> possibility?
>
> Q2: Beyond that I would also like to include other tissue types such 
> as fat, muscle, and eyeball (vitrious). I suppose I could find other 
> segmentation software to simply create a more varied segmentation and 
> insert it in the processing pipeline, but would like to know if that 
> would mess anything up.
>
> Q3: Next, can the FEM handle anisotropic conductivities for white 
> matter and skull?
>
> Q4: has anyone out there actually used the FDM model?
>
> Thanks,
>
> -Jeff Eriksen
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From RICHARDS at mailbox.sc.edu  Wed Dec  2 14:55:57 2015
From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN)
Date: Wed, 2 Dec 2015 13:55:57 +0000
Subject: [FieldTrip] Head segmentation
Message-ID: <A84D7FC4-B8F0-4D9D-8EF0-8190153B1580@mailbox.sc.edu>

Jeff

The resources from Carsten Wolters and the answers were right on.

We have a 128 channel system.

We add “nasal cavity” which includes nasal, throat, and sinuses in our FEM model.  We do a lot of the segmenting with FSL (bet, fast, betsur, SPMf) and custom programs, and then do manual editing to identify the air passages.  The separate segments are then put together with a custom program. The air cavities might be important for the 256-channel EGI system, where on the sides and front of the face the electrodes could have some dipolar sources and the places in between would affect the source estimation.  Anything below the skull, not air cavity, we give a conductivity of muscle, which is very close to scalp; again the electrodes below the skull are over something and I presume would need a realistic estimated head media and conductivity.

As I wrote earlier, we have been using FT for FEM recently; also have gotten good (similar to FEM) results with the Dipoli BEM model. I have one already-published supplemental information that briefly describes our FEM model, and one in-press supplemental information, both articles using the EMSE program.  I am working on our first publication using the FEM from FT.

Re “Mainly tissues between sources and electrodes are important to be modeled (so white matter anisotropy is only important for deeper sources)”.  This may be practically correct, but I have suspected (and EGI’s rationale for whole-head coverage) that to get a good measure of a dipolar source whose positive or negative pole land somewhere below the skull area, one needs a good model of the head over all the places where the current flow is manifested.  We have some prefrontal  sources with large negative potentials exhibiting on the frontal-central 10-10 electrodes, and which have a large positive scalp potential on the “Oz” electrodes.  However, it turns out these potentials show up on Iz and in the EGI electrodes below Iz (128 channel), so having a model for scalp and muscle over the neck might be important.  I don’t know what the effect is of leaving these out, but I have preferred to do the whole head segmentation in case these have some effect.

One last consideration.  Most BEM and FEM models on the FT site use the segmentation of the brain, skull, and scalp about at the level of the MNI head.  This does not include the electrodes below the horizon of the MNI head, and there is a lot of area below the MNI head that is covered by the EGI 128 and 256 channel systems.  This adds significantly to the volume of the voxels used for the FEM estimation.  For BEM models we cut the head off at about 10% below the level of the lowest EGI 128 channel electrodes, and generally have done so also for the FEM models we use in FT. The electrodes are located on the places below the MNI head, so one has to have a “head” model with positions below those typically used in the FT’s demo programs.  We do a whole head MRI down to the neck, and then use a custom program to get a MRI volume with a head that extends about 10% lower than the lowest EGI-128 electrodes.

John


***********************************************
John E. Richards Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC  29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu<mailto:richards-john at sc.edu>
HTTP: jerlab.psych.sc.edu
***********************************************

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From francois.tadel at mcgill.ca  Wed Dec  2 22:03:33 2015
From: francois.tadel at mcgill.ca (=?UTF-8?Q?Fran=c3=a7ois_Tadel?=)
Date: Wed, 2 Dec 2015 16:03:33 -0500
Subject: [FieldTrip] Error in ft_dipolefitting.m ?
Message-ID: <565F5CA5.9080409@mcgill.ca>

Hello,

When fitting single dipoles on multiple time points at once, I have an 
error line 578:
     source.dip.unit = headmodel.unit;
The syntax is incorrect that source.dip is an array with multiple 
dipoles. Should this be replaced with the following line ?
     [source.dip.unit] = deal(headmodel.unit);

Cheers,
Francois


From erin.white at sickkids.ca  Wed Dec  2 22:55:40 2015
From: erin.white at sickkids.ca (Erin White)
Date: Wed, 2 Dec 2015 21:55:40 +0000
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
 multiplotER and multiplotTFR images
In-Reply-To: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
References: <CAJT2k_8L_ykHzjuGA70TCp=QF_5C3YkeHx4mMhTTKDKDYbQSUw@mail.gmail.com>
Message-ID: <0D4EE8880DEE3047BEC905C0EC463F8C2769EBD7@SKMBXX03.sickkids.ca>

Hi Steve,
Thanks so much for your helpful comment!
I'll give this a try!

All the best

Erin

----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Stephen Politzer-Ahles [stephen.politzer-ahles at ling-phil.ox.ac.uk]
Sent: November 27, 2015 7:28 AM
To: fieldtrip at science.ru.nl
Subject: Re: [FieldTrip] Adding tick marks to the X and Y axes in multiplotER and multiplotTFR images

Hi Erin,

I don't use the multiplot functions much, so my solution is clunky and there may be others on the list with a better way to do this. But just in case, here's how I do it:

Rather than using multiplot, I make each plot individually, and use the subplot() command to arrange multiple plots into a figure. Within each subplot, I just use some custom code to draw the ticks. For example:

tickspots = [-200:200:1000]; % one tick every 200 ms, from -200 to 1000 ms
tickheight = [-.5 .5]; % how high and low the ticks will go

for tickspots = tickspot % iterate through tick spots
plot( [tickspot tickspot], tickheight, 'k' ); % plot each tick as a black line
end;


Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab, Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/<https://urldefense.proofpoint.com/v2/url?u=http-3A__users.ox.ac.uk_-7Ecpgl0080_&d=BQMFaQ&c=Dvjge31PR3JZstzk2paJYiflTxRSxp35GBhsbHdd2Zw&r=I8lBTmv7Y9oqVGvTj_vgdd74EEIPprGsdbxcnXduG2k&m=lnKeei_k8PbT5JQEFb_AdyFHThYK07IvJphgqiA4pd8&s=yHg_UuAaKeXLiYDOWrOeEtt0pDtbBRlk3w7TC1hOKdw&e=>


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

Message: 2
Date: Thu, 26 Nov 2015 12:48:25 +0000
From: Erin White <erin.white at sickkids.ca<mailto:erin.white at sickkids.ca>>
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: [FieldTrip] Adding tick marks to the X and Y axes in
        multiplotER and multiplotTFR images
Message-ID:
        <0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca<mailto:0D4EE8880DEE3047BEC905C0EC463F8C2769D79D at SKMBXX03.sickkids.ca>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,
I'm new at programming and was wondering if someone could help with something that I'm sure is simple.
I'd like to add tick marks to my multiplotER and multiplotTFR figures so that the timing and amplitude (for multiplotER) and timing and frequency (for multiplotTFR) scales are presented clearly. For example, I'd like a tick mark on my X axes every 200 ms, and on the y axes, every 2 mV for ER images and every 5 Hz for TFR images.

Could anyone suggest what I should add to my code to show this?

Thanks very much!

Erin












----------------------------------------------------
Erin White, PhD
Post-Doctoral Research Fellow
Neurosciences and Mental Health
The Hospital for Sick Children
555 University Avenue
Toronto, Ontario
Canada
Telephone: (647)834-7813<tel:%28647%29834-7813>

________________________________

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
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------------------------------

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fieldtrip mailing list
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End of fieldtrip Digest, Vol 60, Issue 23
*****************************************

________________________________

This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.
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From p.babaeeghazvini at vu.nl  Fri Dec  4 20:14:26 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Fri, 4 Dec 2015 19:14:26 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
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From ronny.ibrahim at mq.edu.au  Mon Dec  7 05:36:14 2015
From: ronny.ibrahim at mq.edu.au (Ronny Ibrahim)
Date: Mon, 7 Dec 2015 15:36:14 +1100
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency
	data
Message-ID: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a
time-frequency datasets that I've acquired using the ft_freqanalysis
function. When I run ft_freqstatistics on the data it would give me stats
result which is based on comparing the absolute values of power spectrum
instead the relative change with respect to the baseline. I have tried to
perform to do my relative change power spectrum data manually but it seems
that when I run the ft_freqstatistics it produces an error of which I could
not figure out on why.

Here is my code:



C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6}
outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13}
outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};



C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6}
outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13}
outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};



%% Performing cluster statistics for the paradigm

cfg                  = [];

cfg.layout           = 'EEG_KR.lay';

lay                  = ft_prepare_layout(cfg);

% Needs to change this

cfg.latency          = [0 0.6]; %Need to look this up according to what

cfg.frequency        = [8 12];% Need to do it for different frequency bands
(theta, alpha, beta, gamma).

cfg.channel          = 'all';

cfg.avgovertime      = 'no';

cfg.avgoverfreq      = 'yes';

cfg.avgoverchan      = 'no';

cfg.statistic        = 'ft_statfun_indepsamplesT';

cfg.numrandomization = 1000;

cfg.correctm         = 'cluster';

cfg.method           = 'montecarlo';

cfg.computeprob    = 'yes';

cfg.computecritval = 'yes';

cfg.clusteralpha     = 0.05;

cfg.clusterstatistic = 'maxsum';

cfg.minnbchan        = 3;

cfg.tail             = 0;

cfg.clustertail      = 0;

cfg.alpha            = 0.05;

cfg_neighb.layout    = lay;

cfg_neighb.method    = 'triangulation';

cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);

cfg.ivar             = 1;

cfg.design = [ones(1,18) 2*ones(1,18)];

stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});



%% Plotting significant clusters



cfg                  = [];

cfg.alpha            = 0.05;

cfg.parameter        = 'stat';

cfg.layout           = lay;

ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output
structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny
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From j.herring at donders.ru.nl  Mon Dec  7 09:24:32 2015
From: j.herring at donders.ru.nl (Herring, J.D. (Jim))
Date: Mon, 7 Dec 2015 08:24:32 +0000
Subject: [FieldTrip] Clusterstatistics on relative change (%) time
 frequency	data
In-Reply-To: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
References: <CAE1JevtMhcDEgz8CDOM7Vg9v_qikSWwejwm=bBveS3J4q+-b=w@mail.gmail.com>
Message-ID: <3D00B7615FB58D46A0B49B9AD67A33EB279C7AFB@exprd01.hosting.ru.nl>

Dear Ronny,

What error do you get when running this code?

You can perform a (relative) baseline correction using ft_freqbaseline with cfg.baselinetype = ‘relative’ or ‘relchange’ and cfg.baseline = [your baseline window];. If your code works on absolute values it should also work on baseline-corrected values using ft_freqbaseline.

Best,

Jim

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Ronny Ibrahim
Sent: maandag 7 december 2015 5:36
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Clusterstatistics on relative change (%) time frequency data

Dear fellow fieldtrip users,
I would like to implement a clusterstatistics independentT test on a time-frequency datasets that I've acquired using the ft_freqanalysis function. When I run ft_freqstatistics on the data it would give me stats result which is based on comparing the absolute values of power spectrum instead the relative change with respect to the baseline. I have tried to perform to do my relative change power spectrum data manually but it seems that when I run the ft_freqstatistics it produces an error of which I could not figure out on why.

Here is my code:

C_1 = {outP10{1} outP10{2} outP10{3} outP10{4} outP10{5} outP10{6} outP10{7} outP10{8} outP10{9} outP10{10} outP10{11} outP10{12} outP10{13} outP10{14} outP10{15} outP10{16} outP10{17} outP10{18}};

C_2 = {outM10{1} outM10{2} outM10{3} outM10{4} outM10{5} outM10{6} outM10{7} outM10{8} outM10{9} outM10{10} outM10{11} outM10{12} outM10{13} outM10{14} outM10{15} outM10{16} outM10{17} outM10{18}};

%% Performing cluster statistics for the paradigm
cfg                  = [];
cfg.layout           = 'EEG_KR.lay';
lay                  = ft_prepare_layout(cfg);
% Needs to change this
cfg.latency          = [0 0.6]; %Need to look this up according to what
cfg.frequency        = [8 12];% Need to do it for different frequency bands (theta, alpha, beta, gamma).
cfg.channel          = 'all';
cfg.avgovertime      = 'no';
cfg.avgoverfreq      = 'yes';
cfg.avgoverchan      = 'no';
cfg.statistic        = 'ft_statfun_indepsamplesT';
cfg.numrandomization = 1000;
cfg.correctm         = 'cluster';
cfg.method           = 'montecarlo';
cfg.computeprob    = 'yes';
cfg.computecritval = 'yes';
cfg.clusteralpha     = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan        = 3;
cfg.tail             = 0;
cfg.clustertail      = 0;
cfg.alpha            = 0.05;
cfg_neighb.layout    = lay;
cfg_neighb.method    = 'triangulation';
cfg.neighbours       = ft_prepare_neighbours(cfg_neighb);
cfg.ivar             = 1;
cfg.design = [ones(1,18) 2*ones(1,18)];
stat                 = ft_freqstatistics(cfg, C_2{:}, C_1{:});

%% Plotting significant clusters

cfg                  = [];
cfg.alpha            = 0.05;
cfg.parameter        = 'stat';
cfg.layout           = lay;
ft_clusterplot(cfg, stat);


where the variable out is essentially my time-frequency data output structure.

I would greatly appreciate the input and assistance. Thank you.

Kind Regards,

Ronny

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From julian.keil at gmail.com  Mon Dec  7 09:30:25 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 09:30:25 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>
Message-ID: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

> Hello
> 
> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> Not from the voxel indicating maximum power ([maxval,
>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
> 
> Regards,
> Parinaz.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From p.babaeeghazvini at vu.nl  Mon Dec  7 12:52:55 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 11:52:55 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From julian.keil at gmail.com  Mon Dec  7 17:57:10 2015
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 7 Dec 2015 17:57:10 +0100
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>
Message-ID: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>

Hi Parinaz,

> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

> How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

> Hi Julian,
> 
> Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:
> 
> cfg = []
> 
> cfg.atlas = atlas;
> 
> cfg.roi = atlas.tissuelabel(1)
> 
> cfg.inputcoord = 'mni';
> 
> mas = ft_volumelookup(cfg,grid);
> 
> cfg              = [];
> cfg.method       = 'lcmv';
> cfg.vol          = hdm;
> cfg.grid.xgrid      =
> 
> cfg.grid.ygrid      =
> 
> cfg.grid.zgrid      =
> 
> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
> cfg.grid.outside = [];
> cfg.keepfilter   = 'yes';
> source_idx       = ft_sourceanalysis(cfg, tlock);
> 
> My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.
> 
> an other question that I have is that: when I compute the maximum index from
>  [maxvalr, maxpowindxr] = max(srcetask.avg.pow)
> 
> How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)
> 
> Regards,
> Parinaz.
> 
> 
> 
> 
> From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
> Sent: Monday, December 07, 2015 9:30 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch
> 
> Hi Parinaz,
> 
> I'm not sure if I understood your question correctly.
> Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?
> 
> In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
> In the second case, it's a tad more complicated, but here's how I do it:
> 1. Compute the virtual channels for all grid points in the cortex
> 2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
> 3. Build a high-resolution 3D-Grid on the standard MRI
> 4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
> 5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.
> 
> I hope this helps, let me know otherwise.
> 
> Julian
> 
> Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:
> 
>> Hello
>> 
>> I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors
>> cfg              = [];
>> cfg.method       = 'lcmv';
>> cfg.vol          = hdm;
>> cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
>> cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
>> cfg.grid.outside = [];
>> cfg.keepfilter   = 'yes';
>> source_idx       = ft_sourceanalysis(cfg, tlock);
>> Not from the voxel indicating maximum power ([maxval,
>>  maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos
>>  = sourcemodel.pos([maxcohindx maxpowindx], :)).
>> 
>> Regards,
>> Parinaz.
>> _______________________________________________
>> 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 p.babaeeghazvini at vu.nl  Mon Dec  7 20:20:15 2015
From: p.babaeeghazvini at vu.nl (Babaeeghazvini, P.)
Date: Mon, 7 Dec 2015 19:20:15 +0000
Subject: [FieldTrip] Extracting virtual EEG channel from a patch
In-Reply-To: <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
References: <561966C5AD6B9647B14A89A8189322E02F0C01C6@PEXMB100A.vu.local>
 <561966C5AD6B9647B14A89A8189322E02F0C020E@PEXMB100A.vu.local>,
 <54D55463-2B37-4AEB-ABA8-0B5EFCAB3564@gmail.com>
 <561966C5AD6B9647B14A89A8189322E02F0C2859@PEXMB100A.vu.local>,
 <F7E8A24A-4192-46BB-9CEA-9EA40401A1C2@gmail.com>
Message-ID: <561966C5AD6B9647B14A89A8189322E02F0C29CB@PEXMB100A.vu.local>

Hi Julian,

Thank you very much for your help now it is completely clear for me.

Parinaz.
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Julian Keil [julian.keil at gmail.com]
Sent: Monday, December 07, 2015 5:57 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

You don't. You compute your virtual channels for a regular grid (something like -20:1:20 for x,y and z) and select the virtual channels in your ROI in a second step.
This might be a bit of an overkill, as you don't use most of your channels later on, but maybe you want to extend your analysis to other cortical areas - you never know.

Anyways, to be more clear: You compute your virtual electrodes on a predefined grid. To find your ROI, you use ft_volumelookup to get a binary matrix which tells you, which voxels of the standard MRI are in your ROI. Then you build a high-resolution grid based on the standard MRI (It's important to use one grid point per voxel). Using pythagoras, you can now find the closest high-resolution grid points for each of your virtual electrodes. As soon as you have these, you can see which of them have a value of 1 in your binary matrix of ft_volumelookup. Now you know which virtual electrodes are inside your ROI.

So for example, you have 2000 virtual electrodes on a -20:1:20 regular grid. You then compute a binary matrix and a high-resolution grid based on the standard MRI resulting in ~900000 grid points on a 91x109x91 grid. Using pythagoras, you find that grid point 6000 is closest to virtual electrode #1. Then you can see if element 6000 from your binary matrix is a 1. If so, your virtual electrode #1 is in your ROI, if not, your virtual electrode is not in your ROI.

How I can find the atlas position to this maximum point in my code

Do you want to have the coordinates or the actual label? A while ago, I hacked the ft_sourceplot-function to give me the coordinate position as an output, but I can't find the code anymore. I'm sure you can edit the function to also output the label, as this has to be included as a text element somewhere in the function. But please be aware that editing the FT-functions can severely compromise the functionality.

Good luck,

Julian



Am 07.12.2015 um 12:52 schrieb Babaeeghazvini, P.:

Hi Julian,

Thank you very much for your kind reply. Yes I want to compute virtual channel from an atlas area like whole Precentral_L (not from one voxel in this area). So your second explanation helps me. If I understood correctly in the code below I should use all grid points belong to atlas:


cfg = []

cfg.atlas = atlas;

cfg.roi = atlas.tissuelabel(1)

cfg.inputcoord = 'mni';

mas = ft_volumelookup(cfg,grid);

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;


cfg.grid.xgrid      =

cfg.grid.ygrid      =

cfg.grid.zgrid      =

cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

My problem is how I should use the output of volumelookup here for cfg.grid.xgrid, cfg.grid.ygrid and cfg.grid.zgrid.

an other question that I have is that: when I compute the maximum index from
 [maxvalr, maxpowindxr] = max(srcetask.avg.pow)

How I can find the atlas position to this maximum point in my code (I can see this atlas label in the figure that I get from sourceplot, but I want to report this label in matlab)

Regards,
Parinaz.



From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Julian Keil [julian.keil at gmail.com<mailto:julian.keil at gmail.com>]
Sent: Monday, December 07, 2015 9:30 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Extracting virtual EEG channel from a patch

Hi Parinaz,

I'm not sure if I understood your question correctly.
Do you want to find the atlas label to a given virtual channel? Or do you want to compute a virtual channel on a given atlas label?

In the first case, you can simply interpolate your virtual EEG channels to the standard MRI and use source plot with an atlas to find the corresponding label.
In the second case, it's a tad more complicated, but here's how I do it:
1. Compute the virtual channels for all grid points in the cortex
2. If you have computed the virtual channels on an individual MRI, make sure that the positions correspond to the standard MRI (I think that's described in the source analysis-tutorial)
3. Build a high-resolution 3D-Grid on the standard MRI
4. Select all grid points from the grid of step 3 which belong to an atlas (see ft_volumelookup)
5. Use pythagoras to find the virtual channels from step 2 closest to the grid points from step 4.

I hope this helps, let me know otherwise.

Julian

Am 04.12.2015 um 20:14 schrieb Babaeeghazvini, P.:

Hello

I want to reconstruct a source signal the same as below in page  http://www.fieldtriptoolbox.org/tutorial/shared/virtual_sensors

cfg              = [];
cfg.method       = 'lcmv';
cfg.vol          = hdm;
cfg.grid.pos     = sourcemodel.pos([maxcohindx maxpowindx], :);
cfg.grid.inside  = 1:size(cfg.grid.pos, 1);
cfg.grid.outside = [];
cfg.keepfilter   = 'yes';
source_idx       = ft_sourceanalysis(cfg, tlock);

Not from the voxel indicating maximum power ([maxval, maxpowindx] = max(source_diff.avg.pow);), but from the atlas area which this voxel belongs to, such as Supp_Motor_Area_L. So my question is: How I can get the atlas range and atlas label belong to a voxel, and how I can use this atlas area range in this code to reconstruct a signal instead of using (cfg.grid.pos = sourcemodel.pos([maxcohindx maxpowindx], :)).

Regards,
Parinaz.
_______________________________________________
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

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From amickan1990 at gmail.com  Thu Dec 10 18:14:10 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Thu, 10 Dec 2015 18:14:10 +0100
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation test
Message-ID: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>

Dear all,

I'm just starting to work on a cluster-based permutation test script based
on the tutorial for within-subject designs on the fieldtrip website. I ran
into an issue when computing the [stat] matrix. I used the code as it was
on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages.
However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat
and stat.negclusterslabelmat matrices which should apparantly contain far
more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume
has to do with the fact that "neg" does not have the appropriate matrix
dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me
out.

Thanks in advance!

Best,
Anne
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From nick.peatfield at gmail.com  Thu Dec 10 20:13:10 2015
From: nick.peatfield at gmail.com (Nicholas A. Peatfield)
Date: Thu, 10 Dec 2015 11:13:10 -0800
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
In-Reply-To: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
Message-ID: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>

Hi Anne,

To get an answer/suggestion you should provide the part of your script
detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:

> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Nicholas Peatfield, PhD
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From jan.schoffelen at donders.ru.nl  Thu Dec 10 20:36:45 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Thu, 10 Dec 2015 19:36:45 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based
	permutation	test
In-Reply-To: <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
References: <CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA@mail.gmail.com>
 <CADzq99=3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ@mail.gmail.com>
Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9@fcdonders.ru.nl>

Hi Anne,

I agree with Nick, some more information would be helpful. At this stage my wild guess (assuming that you did not constrain your ‘search space’, using cfg.channel and cfg.latency before calling ft_timelockstatistics) would be that there’s a major discrepancy in the descriptive dimensions of your data (i.e. the ‘labels’ and the time points) across the input arguments. FieldTrip does an explicit check on the labels and time points, it only proceeds to do calculations on the channels and time points that are present in each and every input argument. With respect to time points: this could even mean that numerical inaccuracies are the showstopper here. These inaccuracies could be easily introduced when e.g. downsampling.

Best,
Jan-Mathijs


On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:

Hi Anne,

To get an answer/suggestion you should provide the part of your script detailing your cfg inputs.

Cheers,

Nick

On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:amickan1990 at gmail.com>> wrote:
Dear all,

I'm just starting to work on a cluster-based permutation test script based on the tutorial for within-subject designs on the fieldtrip website. I ran into an issue when computing the [stat] matrix. I used the code as it was on the website:

[stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});

with the Correct and Incorrect matrices looking as follows:

Correct{1}

        avg: [34x600 double]
       time: [1x600 double]
    fsample: '500'
      label: {34x1 cell}
     dimord: 'chan_time'
        dof: [34x600 double]
        var: [34x600 double]

The function runs without problems, i.e I don't get any error messages. However, the result seems incomplete.

stat =
                   prob: [25x1 double]
            posclusters: []
    posclusterslabelmat: [25x1 double]
        posdistribution: [1x500 double]
            negclusters: [1x1 struct]
    negclusterslabelmat: [25x1 double]
        negdistribution: [1x500 double]
                cirange: [25x1 double]
                   mask: [25x1 logical]
                   stat: [25x1 double]
                    ref: [25x1 double]
                 dimord: 'chan_time'
                  label: {25x1 cell}
                   time: 0
                    cfg: [1x1 struct]

Specifically, I later run into trouble with the stat.posclusterslabelmat and stat.negclusterslabelmat matrices which should apparantly contain far more values something more like 25x500 instead of 25x1. When calling
neg_int = all(neg(:, m(k):m(k+1)), 2)
I get the "Index exceeds matrix dimensions" error message which I assume has to do with the fact that "neg" does not have the appropriate matrix dimensions
(neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )

Where is the error / where should I look for the error?

Some further design details:
Nsubj = 24
2 conditions = Correct, Incorrect
Within-subject design
sampling rate = 500
34 channels

I hope I gave enough / the necessary information for someone to help me out.

Thanks in advance!

Best,
Anne


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



--
Nicholas Peatfield, PhD

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

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From aishwaryaselvaraj1708 at gmail.com  Fri Dec 11 07:30:39 2015
From: aishwaryaselvaraj1708 at gmail.com (aishwarya selvaraj)
Date: Fri, 11 Dec 2015 12:00:39 +0530
Subject: [FieldTrip] filed trip
In-Reply-To: <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
Message-ID: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
wrote:

> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Regards,
Aishwarya Selvaraj
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From stan.vanpelt at donders.ru.nl  Fri Dec 11 09:09:14 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Fri, 11 Dec 2015 08:09:14 +0000
Subject: [FieldTrip] filed trip
In-Reply-To: <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
References: <5bd6dabc93ec431694d6c282894f6b62@EXPRD02.hosting.ru.nl>
 <CAAiwptSDx8LBUmER+6UOYpEii-Kwm5K+S_-VX4R9haNB1GDFsw@mail.gmail.com>
 <CAL6=h-OS9aNjyQ5qdf4th56N18kHLCZviBOBvXiPR-wDUnSpEw@mail.gmail.com>
 <CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0@exprd03.hosting.ru.nl>

Dear Aishwarya,

The data structure should look something like this:

% 1. Load data
load EEGdata.mat

% 2. Make FieldTrip structure, manually
data.label={'Channel1Name’,’Channel2Name’,’Channel3Name’}; %your channel names
data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each trial: channelsxtimepoints data
data.fsample=500; %your recording sampling frequency
data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data sample (e.g: [0 0.02 0.04 0.06 etc])

Going through the Walktrough Tutorial will be the best starting point when you just started to use FieldTrip: http://www.fieldtriptoolbox.org/walkthrough
After that, you may go through the other Tutorial documentation or Example Matlab scripts.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
Sent: vrijdag 11 december 2015 7:31
To: FieldTrip discussion list
Subject: Re: [FieldTrip] filed trip

do you still have that   m file with you??
could you share ??

On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com<mailto:mishra408 at gmail.com>> wrote:
Hi Aishwarya,

I faced the similar problem. You are supposed to change your data
(.mat format) in a data structure that is read by fieldtrip. For that
you need at least following information
1. Channel label and their location (If you don't have this file you
can use standard file available in Fieldtrip and you can include only
those electrode that you have been using in your experiment)
2. sampling rate of the data (that you would have done while recording the data)
3. time vector
4. no. of trials

You can create them in MATLAB and put them together in a structure
along with your recorded data. This worked for me.

--
Ashutosh Mishra
5th year Integrated BS-MS student
Department of Physical Sciences
Indian Institute of Science Education and Research, Kolkata
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--
Regards,
Aishwarya Selvaraj
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From juangpc at gmail.com  Fri Dec 11 11:43:05 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 11:43:05 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating sourcemodel
Message-ID: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for
source-reconstruction of MEG or EEG data <http://goog_2124598831>
​"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized
space
​" procedure , there is an example code. This code throws an error when I
execute it with a version of Fieldtrip I downloaded yesterday. I think I
have downloaded correctly all the required info (Subject01.zip).

​Code:

% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
the coordinate system
 % segment the template brain and construct a volume conduction model
(i.e. head model): % this is needed to describe the boundary that
define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
Convert the vol to cm, because the CTF convenction is to express
everything in cm.
 % construct the dipole grid in the template brain coordinates% the
negative inwardshift means an outward shift of the brain surface for
inside/outside detection
cfg = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
= 1;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
 = 'yes';
cfg.inwardshift = -1.5;
​​
cfg.headmodel   = template_headmodel;

The problem occurs when I execute ​this line:

​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position
information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required
"sensor position information" by executing this code just before
(considering the folder with the information downloaded for this subject is
located just there:

​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';

Then the rest of the sample code in the tutorial can be executed with no
issues.

template_grid   = ft_prepare_sourcemodel(cfg);
 % make a figure with the template head model and dipole gridfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
'none');alpha 0.5; camlight
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));


My questions:

​Is there a better solution for this problem? Maybe I can learn a little
bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one
is placing the downloaded subject's data, and it is platform dependent.
Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan
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From jan.schoffelen at donders.ru.nl  Fri Dec 11 11:54:54 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 10:54:54 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925@fcdonders.ru.nl>

Hi Juan,

We’ll look into this specific issue soon, it should work without specifying sensor positions. However, for now and in general I would recommend just using a pre-cooked template grid. These can be found in fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I will make this more explicit shortly.

Best,

Jan-Mathijs

On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From jan.schoffelen at donders.ru.nl  Fri Dec 11 13:19:39 2015
From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs))
Date: Fri, 11 Dec 2015 12:19:39 +0000
Subject: [FieldTrip] possible bug in tutorial code for creating
 sourcemodel
In-Reply-To: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
Message-ID: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>

Hi Juan,

I could reproduce your issue, and have done 2 things:
- I updated the wiki to make it clear that it would be easier to use a pre-cooked grid.
- I adjusted ft_prepare_sourcemodel so that it also works when only providing the template_headmodel, as per the example code.
The new version of ft_prepare_sourcemodel will become available in tonight’s release on the ftp-server.

Best wishes, and thanks for noticing.
Jan-Mathijs


On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:juangpc at gmail.com>> wrote:

Dear Community,

My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab. Currently I am learning to do beamforming source analysis using Fieldtrip.

While following the tutorial: "Creating a sourcemodel for source-reconstruction of MEG or EEG data<http://goog_2124598831/>
​<http:/>"
​​

​ ​when I reach "
Subject-specific grids that are equivalent across subjects in normalized space
​" procedure , there is an example code. This code throws an error when I execute it with a version of Fieldtrip I downloaded yesterday. I think I have downloaded correctly all the required info (Subject01.zip).

​Code:


% NOTE: the path to the template file is user-specific
template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system

% segment the template brain and construct a volume conduction model (i.e. head model):
% this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
cfg          = [];
template_seg = ft_volumesegment(cfg, template);

cfg          = [];
cfg.method   = 'singleshell';
template_headmodel = ft_prepare_headmodel(cfg, template_seg);
template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.

% construct the dipole grid in the template brain coordinates
% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
cfg = [];
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
cfg.grid<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
cfg.inwardshift = -1.5;

​​
cfg.headmodel   = template_headmodel;


The problem occurs when I execute ​this line:


​
​
​
​
template_grid   = ft_prepare_sourcemodel(cfg);

Matlab's output:
​
>> template_grid   = ft_prepare_sourcemodel(cfg);
creating dipole grid based on automatic 3D grid with specified resolution
Error using ft_prepare_sourcemodel (line 317)
creating a 3D-grid sourcemodel this way requires sensor position information to estimate the extent of the brain
​


I have managed to look around and found that you can specify the required "sensor position information" by executing this code just before (considering the folder with the information downloaded for this subject is located just there:


​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';



Then the rest of the sample code in the tutorial can be executed with no issues.


template_grid   = ft_prepare_sourcemodel(cfg);

% make a figure with the template head model and dipole grid
figure<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
ft_plot_mesh(template_grid.pos(template_grid.inside,:));

My questions:

​Is there a better solution for this problem? Maybe I can learn a little bit more about the toolbox with your answers.

I didn't want to correct the wiki because​ my solution depends on where one is placing the downloaded subject's data, and it is platform dependent. Should I add something to the tutorial anyway?
​ I figure this can be interesting to other people.​
​
​

Best,


Juan

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

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From juangpc at gmail.com  Fri Dec 11 13:55:57 2015
From: juangpc at gmail.com (Juan)
Date: Fri, 11 Dec 2015 13:55:57 +0100
Subject: [FieldTrip] possible bug in tutorial code for creating
	sourcemodel
In-Reply-To: <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
References: <CAPO7YL+ufEwMRmBZk=XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w@mail.gmail.com>
 <1556EC3A-15DD-4A75-BB39-228DB6545073@fcdonders.ru.nl>
Message-ID: <CAPO7YLJFQ=qB0xVBBS8WEiD2PW4OzaOnZX=xVzn_rgxd-vm9HQ@mail.gmail.com>

Hi Jan-Mathijs,

Thanks for your quick response, H2H. I've actually learned about precooked
models with your answer. Many thanks.

In the same page, in the part "Make the individual subjects' grid", there
seems to be a unit-related problem. One can find this code

% read the single subject anatomical MRI
mri = ft_read_mri('Subject01.mri');
 % segment the anatomical MRI
cfg        = [];
cfg.output = 'brain';
seg        = ft_volumesegment(cfg, mri);
 % construct the volume conductor model (i.e. head model) for each
subject% this is optional, and for the purpose of this tutorial only
required for% plotting, later on
cfg        = [];
cfg.method = 'singleshell';
headmodel  = ft_prepare_headmodel(cfg, seg);
 % create the subject specific grid, using the template grid that has
just been created
cfg                = [];
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.warpmni
  = 'yes';
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.template
 = template_grid;
cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.nonlinear
= 'yes'; % use non-linear normalization
cfg.mri            = mri;grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>
             = ft_prepare_sourcemodel(cfg);
 % make a figure of the single subject headmodel, and grid
positionsfigure
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>;
hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
on;
ft_plot_vol(headmodel, 'edgecolor', 'none', 'facealpha', 0.4);
ft_plot_mesh(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.pos(grid
<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.inside,:));

When executing it, there seems to be a problem with dimensions. "headmodel"
struct is in mm and "grid" struct is in cm. So unfortunately the resulting
figure ends up being something like
[image: Inline image 1]

I've tested to specify 'mm' units in the configuration struct before
calling ft_prepare_sourcemodel: cfg.grid.unit='mm';

Or by calling ft_convert_units right after ft_prepare_sourcemodel.

grid=ft_convert_units(grid,'mm');

Both solutions work fine, producing a figure very similar to the one in the
tutorial. I've included the first solution in the wiki.

I hope this is ok.

Best,



Juan

On Fri, Dec 11, 2015 at 1:19 PM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Juan,
>
> I could reproduce your issue, and have done 2 things:
> - I updated the wiki to make it clear that it would be easier to use a
> pre-cooked grid.
> - I adjusted ft_prepare_sourcemodel so that it also works when only
> providing the template_headmodel, as per the example code.
> The new version of ft_prepare_sourcemodel will become available in
> tonight’s release on the ftp-server.
>
> Best wishes, and thanks for noticing.
> Jan-Mathijs
>
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831/>
> ​ <http:/>"
> ​​
>
> ​ ​when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ​" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ​Code:
>
> % NOTE: the path to the template file is user-specific
> template = ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the coordinate system
>  % segment the template brain and construct a volume conduction model (i.e. head model): % this is needed to describe the boundary that define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert the vol to cm, because the CTF convenction is to express everything in cm.
>  % construct the dipole grid in the template brain coordinates% the negative inwardshift means an outward shift of the brain surface for inside/outside detection
> cfg = [];
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution = 1;
> cfg.grid <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight  = 'yes';
> cfg.inwardshift = -1.5;
> ​​
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ​this line:
>
> ​
> ​
> ​
> ​
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ​
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ​
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ​cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>hold <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor', 'none');alpha 0.5; camlight <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ​Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because​ my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ​ I figure this can be interesting to other people.​
> ​
> ​
>
> Best,
>
>
> Juan
>
> _______________________________________________
> 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 frsantos at fpce.up.pt  Fri Dec 11 13:57:52 2015
From: frsantos at fpce.up.pt (Fernando Ferreira-Santos)
Date: Fri, 11 Dec 2015 12:57:52 +0000
Subject: [FieldTrip] 3rd International Conference of the ESCAN
Message-ID: <2BAB036A9BAEA44984A131DFCE446108010BFD7B96@SRVMBX01.fpceup.psi.up.pt>

Dear Colleagues,
The 3rd International Conference of the European Society for Cognitive and Affective Neuroscience (ESCAN) is accepting submissions for symposia and oral/poster presentations. The conference will take place in that will take place in Porto, Portugal, between 23-26 of June, 2016, at the Porto Palácio Congress Hotel & Spa (http://www.hotelportopalacio.com/en/hotel-overview.html).

The submission deadline is the 8th of January, 2016. Please find all the details in the conference website: www.escan2016.eu<http://www.escan2016.eu>
We would appreciate it if you could pass this information along to other colleagues and students. Attached you may find a poster with the call for submissions.

We are looking forward to seeing you in Porto in 2016!
Fernando Babosa and Fernando Ferreira-Santos (University of Porto)
Chairs of the Local Organizing Committee


P.S.: Apologies if you get multiple postings of this announcement.

--
Laboratory of Neuropsychophysiology
Faculty of Psychology and Education Sciences
University of Porto
Rua Alfredo Allen, 4200-135 Porto (Portugal)
Tel.: +351 226079700
http://www.fpce.up.pt/labpsi/

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From marlene.boenstrup at googlemail.com  Fri Dec 11 21:30:46 2015
From: marlene.boenstrup at googlemail.com (=?UTF-8?Q?Marlene_B=C3=B6nstrup?=)
Date: Fri, 11 Dec 2015 21:30:46 +0100
Subject: [FieldTrip] ft_sourceinterpolate fails when cfg.moveinward and
 cfg.inwardshift was used to create sourcemodel
Message-ID: <CAG0LeNnQE60kuJZHh7jSOYpNLOurgtnn3gBODE0LkXB_NTuzAg@mail.gmail.com>

Dear fieldtrip-community,

I struggle at plotting source reconstruction results, and my routine even
fails when using the template structural data.
I think it is based on a shortcoming of the ft_sourceinterpolation
function. This is why I am optimistic to find help in this platform:
I prepare the leadfields based on the standard_sourcemodel3d6mm, the vol
called standard_bem.mat, the electrode positions defined in
standard_1005.elc.
Since some of the dipoles that are assigned as "inside" in the
sourcemodel3d6mm are actually sticking out of the inner bem boundary,
leading to distorted leadfields, I re-prepare the sourcemodel based on the
following specifications:

mri=ft_read_mri('single_subj_T1.nii');
mri.coordsys = 'spm';
mri = ft_volumereslice([], mri);
cfg=[];
cfg.mri  = mri;
cfg.elec=elec;
cfg.vol=vol;
cfg.grid.warpmni   = 'yes';
cfg.grid.template  = grid; % sourcemodel3d6mm
cfg.grid.nonlinear = 'no';
cfg.moveinward=5;
cfg.inwardshift=0;
grid    = ft_prepare_sourcemodel(cfg);

this comes out with a vector of positions in three dimensional space, all
of them being assigned to inside and none of them as outside.
The leadfields prepared based on this sourcemodel look very convincing and
the ft_sourceanalysis function also works.
But the problem is to interpolate this on the anatomical image:
Nested in the function ft_sourceinterpolate, the function ft_checkdata,
specifically the subfunction source2volume leads to a misconfiguration with
all the positions of the functional data being distributed in to a full 3D
volume. In the end the orthoplot of the brain is a big fully activated
cube.

I hope someone has a good idea how to deal with this issue in fieldtrip and
shares his/her expertise with us.

Many greetings,

Marlene
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From amickan1990 at gmail.com  Sat Dec 12 16:12:57 2015
From: amickan1990 at gmail.com (Anne Mickan)
Date: Sat, 12 Dec 2015 16:12:57 +0100
Subject: [FieldTrip] fieldtrip Digest, Vol 61, Issue 7
In-Reply-To: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
References: <mailman.13.1449831602.10347.fieldtrip@science.ru.nl>
Message-ID: <CANX43OLN8qog=xL7qjDpRp_yTPjKV1oQhgbT4Wuy5z0fDmqTiw@mail.gmail.com>

Dear Nick and Jan-Mathijs,

thanks for your emails. Here is the part of the code that details the cfg
inputs. I basically stuck to what was in the tutorial:

cfg = [];
cfg.channel = 'all';

% prepare neighbouring channels

cfg_neighb = [];
cfg_neighb.method = 'distance';
cfg.channel = 'all';
cfg_neighb.feedback = 'yes';
cfg_neighb.layout = 'easycapM3.mat';

neighbours = ft_prepare_neighbours(cfg_neighb, Correct{1});

% settings for statistics

cfg = [];
cfg.channel = {'EEG'};
cfg.latency = [0 1];

cfg.method = 'montecarlo';
cfg.statistic = 'depsamplesT';
cfg.correctm = 'cluster';
cfg.clusteralpha = 0.05;
cfg.clusterstatistic = 'maxsum';
cfg.minnbchan = 2;
cfg.neighbours = neighbours;
cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = 0.5;
cfg.numrandomization = 500;

% prepare design
subj = 24;
design = zeros(2,2*subj);
for i = 1:subj
  design(1,i) = i;
end
for i = 1:subj
  design(1,subj+i) = i;
end
design(2,1:subj)        = 1;
design(2,subj+1:2*subj) = 2;

cfg.design = design;
cfg.uvar  = 1;
cfg.ivar  = 2;

Best,
Anne

On Fri, Dec 11, 2015 at 12:00 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. Stats matrix incomplete - cluster-based permutation test
>       (Anne Mickan)
>    2. Re: Stats matrix incomplete - cluster-based permutation   test
>       (Nicholas A. Peatfield)
>    3. Re: Stats matrix incomplete - cluster-based       permutation
>  test
>       (Schoffelen, J.M. (Jan Mathijs))
>    4. Re: filed trip (aishwarya selvaraj)
>    5. Re: filed trip (Pelt, S. van (Stan))
>    6. possible bug in tutorial code for creating sourcemodel (Juan)
>    7. Re: possible bug in tutorial code for creating sourcemodel
>       (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
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> >
>
> ------------------------------
>
> Message: 2
> Date: Thu, 10 Dec 2015 11:13:10 -0800
> From: "Nicholas A. Peatfield" <nick.peatfield at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID:
>         <CADzq99=
> 3Ew0_4-mB9CxchT0CSQSKDo4e1JCkEtmdCxp-CWhYtQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com> wrote:
>
> > Dear all,
> >
> > I'm just starting to work on a cluster-based permutation test script
> based
> > on the tutorial for within-subject designs on the fieldtrip website. I
> ran
> > into an issue when computing the [stat] matrix. I used the code as it was
> > on the website:
> >
> > [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
> >
> > with the Correct and Incorrect matrices looking as follows:
> >
> > Correct{1}
> >
> >         avg: [34x600 double]
> >        time: [1x600 double]
> >     fsample: '500'
> >       label: {34x1 cell}
> >      dimord: 'chan_time'
> >         dof: [34x600 double]
> >         var: [34x600 double]
> >
> > The function runs without problems, i.e I don't get any error messages.
> > However, the result seems incomplete.
> >
> > stat =
> >                    prob: [25x1 double]
> >             posclusters: []
> >     posclusterslabelmat: [25x1 double]
> >         posdistribution: [1x500 double]
> >             negclusters: [1x1 struct]
> >     negclusterslabelmat: [25x1 double]
> >         negdistribution: [1x500 double]
> >                 cirange: [25x1 double]
> >                    mask: [25x1 logical]
> >                    stat: [25x1 double]
> >                     ref: [25x1 double]
> >                  dimord: 'chan_time'
> >                   label: {25x1 cell}
> >                    time: 0
> >                     cfg: [1x1 struct]
> >
> > Specifically, I later run into trouble with the stat.posclusterslabelmat
> > and stat.negclusterslabelmat matrices which should apparantly contain far
> > more values something more like 25x500 instead of 25x1. When calling
> > neg_int = all(neg(:, m(k):m(k+1)), 2)
> > I get the "Index exceeds matrix dimensions" error message which I assume
> > has to do with the fact that "neg" does not have the appropriate matrix
> > dimensions
> > (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
> >
> > Where is the error / where should I look for the error?
> >
> > Some further design details:
> > Nsubj = 24
> > 2 conditions = Correct, Incorrect
> > Within-subject design
> > sampling rate = 500
> > 34 channels
> >
> > I hope I gave enough / the necessary information for someone to help me
> > out.
> >
> > Thanks in advance!
> >
> > Best,
> > Anne
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Nicholas Peatfield, PhD
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>
> ------------------------------
>
> Message: 3
> Date: Thu, 10 Dec 2015 19:36:45 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation     test
> Message-ID: <7CAF2781-D756-4C0B-9B56-F05642437AF9 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="windows-1252"
>
> Hi Anne,
>
> I agree with Nick, some more information would be helpful. At this stage
> my wild guess (assuming that you did not constrain your ?search space?,
> using cfg.channel and cfg.latency before calling ft_timelockstatistics)
> would be that there?s a major discrepancy in the descriptive dimensions of
> your data (i.e. the ?labels? and the time points) across the input
> arguments. FieldTrip does an explicit check on the labels and time points,
> it only proceeds to do calculations on the channels and time points that
> are present in each and every input argument. With respect to time points:
> this could even mean that numerical inaccuracies are the showstopper here.
> These inaccuracies could be easily introduced when e.g. downsampling.
>
> Best,
> Jan-Mathijs
>
>
> On Dec 10, 2015, at 8:13 PM, Nicholas A. Peatfield <
> nick.peatfield at gmail.com<mailto:nick.peatfield at gmail.com>> wrote:
>
> Hi Anne,
>
> To get an answer/suggestion you should provide the part of your script
> detailing your cfg inputs.
>
> Cheers,
>
> Nick
>
> On 10 December 2015 at 09:14, Anne Mickan <amickan1990 at gmail.com<mailto:
> amickan1990 at gmail.com>> wrote:
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Nicholas Peatfield, PhD
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Dec 2015 12:00:39 +0530
> From: aishwarya selvaraj <aishwaryaselvaraj1708 at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <
> CACWTKSojvkrwtTLFGpsh2H6CtHXY7-krT7C5-NBjqXdHPs1Ljg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com>
> wrote:
>
> > Hi Aishwarya,
> >
> > I faced the similar problem. You are supposed to change your data
> > (.mat format) in a data structure that is read by fieldtrip. For that
> > you need at least following information
> > 1. Channel label and their location (If you don't have this file you
> > can use standard file available in Fieldtrip and you can include only
> > those electrode that you have been using in your experiment)
> > 2. sampling rate of the data (that you would have done while recording
> the
> > data)
> > 3. time vector
> > 4. no. of trials
> >
> > You can create them in MATLAB and put them together in a structure
> > along with your recorded data. This worked for me.
> >
> > --
> > Ashutosh Mishra
> > 5th year Integrated BS-MS student
> > Department of Physical Sciences
> > Indian Institute of Science Education and Research, Kolkata
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
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>
> ------------------------------
>
> Message: 5
> Date: Fri, 11 Dec 2015 08:09:14 +0000
> From: "Pelt, S. van (Stan)" <stan.vanpelt at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] filed trip
> Message-ID:
>         <7CCA2706D7A4DA45931A892DF3C2894C2A2801E0 at exprd03.hosting.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Aishwarya,
>
> The data structure should look something like this:
>
> % 1. Load data
> load EEGdata.mat
>
> % 2. Make FieldTrip structure, manually
> data.label={'Channel1Name?,?Channel2Name?,?Channel3Name?}; %your channel
> names
> data.trial{1}=[Channel1Data; Channel2Data; Channel3Data]'; % do for each
> trial: channelsxtimepoints data
> data.fsample=500; %your recording sampling frequency
> data.time{1}=[Trial1Timepoints]; % for each trial: timepoints per data
> sample (e.g: [0 0.02 0.04 0.06 etc])
>
> Going through the Walktrough Tutorial will be the best starting point when
> you just started to use FieldTrip:
> http://www.fieldtriptoolbox.org/walkthrough
> After that, you may go through the other Tutorial documentation or Example
> Matlab scripts.
>
> Best,
> Stan
>
> --
> Stan van Pelt, PhD
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University
> Montessorilaan 3, B.01.34
> 6525 HR Nijmegen, the Netherlands
> tel: +31 24 3616288
>
> From: fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] On Behalf Of aishwarya selvaraj
> Sent: vrijdag 11 december 2015 7:31
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] filed trip
>
> do you still have that   m file with you??
> could you share ??
>
> On Fri, Nov 20, 2015 at 12:18 PM, Ashutosh Mishra <mishra408 at gmail.com
> <mailto:mishra408 at gmail.com>> wrote:
> Hi Aishwarya,
>
> I faced the similar problem. You are supposed to change your data
> (.mat format) in a data structure that is read by fieldtrip. For that
> you need at least following information
> 1. Channel label and their location (If you don't have this file you
> can use standard file available in Fieldtrip and you can include only
> those electrode that you have been using in your experiment)
> 2. sampling rate of the data (that you would have done while recording the
> data)
> 3. time vector
> 4. no. of trials
>
> You can create them in MATLAB and put them together in a structure
> along with your recorded data. This worked for me.
>
> --
> Ashutosh Mishra
> 5th year Integrated BS-MS student
> Department of Physical Sciences
> Indian Institute of Science Education and Research, Kolkata
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Regards,
> Aishwarya Selvaraj
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 6
> Date: Fri, 11 Dec 2015 11:43:05 +0100
> From: Juan <juangpc at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID:
>         <CAPO7YL+ufEwMRmBZk=
> XT8P5jeAp7-C4TDBNN1Aoe8X_mtYLh8w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data <http://goog_2124598831>
> ?"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret
> the coordinate system
>  % segment the template brain and construct a volume conduction model
> (i.e. head model): % this is needed to describe the boundary that
> define which dipole locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); %
> Convert the vol to cm, because the CTF convenction is to express
> everything in cm.
>  % construct the dipole grid in the template brain coordinates% the
> negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html
> >.resolution
> = 1;
> cfg.grid <
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
>  = 'yes';
> cfg.inwardshift = -1.5;
> ??
> cfg.headmodel   = template_headmodel;
>
> The problem occurs when I execute ?this line:
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>  % make a figure with the template head model and dipole gridfigure
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html
> >hold
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight
> <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where one
> is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
> -------------- next part --------------
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> >
>
> ------------------------------
>
> Message: 7
> Date: Fri, 11 Dec 2015 10:54:54 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] possible bug in tutorial code for creating
>         sourcemodel
> Message-ID: <93DA3667-0D6E-45A6-8387-1C01B51D7925 at fcdonders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Juan,
>
> We?ll look into this specific issue soon, it should work without
> specifying sensor positions. However, for now and in general I would
> recommend just using a pre-cooked template grid. These can be found in
> fieldtrip/template/sourcemodel. This is mentioned in the tutorial, and I
> will make this more explicit shortly.
>
> Best,
>
> Jan-Mathijs
>
> On Dec 11, 2015, at 11:43 AM, Juan <juangpc at gmail.com<mailto:
> juangpc at gmail.com>> wrote:
>
> Dear Community,
>
> My name is Juan Garcia-Prieto and I am working in Madrid's MEG Lab.
> Currently I am learning to do beamforming source analysis using Fieldtrip.
>
> While following the tutorial: "Creating a sourcemodel for
> source-reconstruction of MEG or EEG data<http://goog_2124598831/>
> ?<http:/>"
> ??
>
> ? ?when I reach "
> Subject-specific grids that are equivalent across subjects in normalized
> space
> ?" procedure , there is an example code. This code throws an error when I
> execute it with a version of Fieldtrip I downloaded yesterday. I think I
> have downloaded correctly all the required info (Subject01.zip).
>
> ?Code:
>
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('~/matlab/fieldtrip/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
> coordinate system
>
> % segment the template brain and construct a volume conduction model (i.e.
> head model):
> % this is needed to describe the boundary that define which dipole
> locations are 'inside' the brain.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_headmodel = ft_prepare_headmodel(cfg, template_seg);
> template_headmodel = ft_convert_units(template_headmodel, 'cm'); % Convert
> the vol to cm, because the CTF convenction is to express everything in cm.
>
> % construct the dipole grid in the template brain coordinates
> % the negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.resolution
> = 1;
> cfg.grid<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/grid.html>.tight
> = 'yes';
> cfg.inwardshift = -1.5;
>
> ??
> cfg.headmodel   = template_headmodel;
>
>
> The problem occurs when I execute ?this line:
>
>
> ?
> ?
> ?
> ?
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> Matlab's output:
> ?
> >> template_grid   = ft_prepare_sourcemodel(cfg);
> creating dipole grid based on automatic 3D grid with specified resolution
> Error using ft_prepare_sourcemodel (line 317)
> creating a 3D-grid sourcemodel this way requires sensor position
> information to estimate the extent of the brain
> ?
>
>
> I have managed to look around and found that you can specify the required
> "sensor position information" by executing this code just before
> (considering the folder with the information downloaded for this subject is
> located just there:
>
>
> ?cfg.gradfile='Subject01\Subject01.ds\Subject01.res4';
>
>
>
> Then the rest of the sample code in the tutorial can be executed with no
> issues.
>
>
> template_grid   = ft_prepare_sourcemodel(cfg);
>
> % make a figure with the template head model and dipole grid
> figure<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>
> hold<http://www.mathworks.com/access/helpdesk/help/techdoc/ref/hold.html>
> on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight<
> http://www.mathworks.com/access/helpdesk/help/techdoc/ref/camlight.html>;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
>
> My questions:
>
> ?Is there a better solution for this problem? Maybe I can learn a little
> bit more about the toolbox with your answers.
>
> I didn't want to correct the wiki because? my solution depends on where
> one is placing the downloaded subject's data, and it is platform dependent.
> Should I add something to the tutorial anyway?
> ? I figure this can be interesting to other people.?
> ?
> ?
>
> Best,
>
>
> Juan
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto: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 61, Issue 7
> ****************************************
>
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From LordJojo at gmx.de  Sat Dec 12 19:59:26 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Sat, 12 Dec 2015 19:59:26 +0100
Subject: [FieldTrip] channel problem ft_freqstatistics
Message-ID: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>

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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sun Dec 13 12:12:40 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sun, 13 Dec 2015 11:12:40 +0000
Subject: [FieldTrip] Stats matrix incomplete - cluster-based permutation
	test
Message-ID: <CAJT2k_85VtNAPj4J2tib5c2C4ZnJn6xZm6qr7GqceAAH2EA6=A@mail.gmail.com>

Hi Anne,

It looks like you're running stats on grand-average structures created with
cfg.keepindividual='no' (because your Correct and Incorrect structures have
an .avg field). I always do stats on a grand-average structure created with
cfg.keepindividual='yes' (which will yield a structure with no .avg field,
and instead an .individual field, which in your case will be 24x34x600,
since you have participants). Do things work out better if you try it that
way?

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 1
> Date: Thu, 10 Dec 2015 18:14:10 +0100
> From: Anne Mickan <amickan1990 at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Stats matrix incomplete - cluster-based
>         permutation test
> Message-ID:
>         <
> CANX43OJN4h_1jEuDKMNwQC4sHeW+E2_StnS3WLkEbOkVpMerQA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I'm just starting to work on a cluster-based permutation test script based
> on the tutorial for within-subject designs on the fieldtrip website. I ran
> into an issue when computing the [stat] matrix. I used the code as it was
> on the website:
>
> [stat] = ft_timelockstatistics(cfg, Correct{:}, Incorrect{:});
>
> with the Correct and Incorrect matrices looking as follows:
>
> Correct{1}
>
>         avg: [34x600 double]
>        time: [1x600 double]
>     fsample: '500'
>       label: {34x1 cell}
>      dimord: 'chan_time'
>         dof: [34x600 double]
>         var: [34x600 double]
>
> The function runs without problems, i.e I don't get any error messages.
> However, the result seems incomplete.
>
> stat =
>                    prob: [25x1 double]
>             posclusters: []
>     posclusterslabelmat: [25x1 double]
>         posdistribution: [1x500 double]
>             negclusters: [1x1 struct]
>     negclusterslabelmat: [25x1 double]
>         negdistribution: [1x500 double]
>                 cirange: [25x1 double]
>                    mask: [25x1 logical]
>                    stat: [25x1 double]
>                     ref: [25x1 double]
>                  dimord: 'chan_time'
>                   label: {25x1 cell}
>                    time: 0
>                     cfg: [1x1 struct]
>
> Specifically, I later run into trouble with the stat.posclusterslabelmat
> and stat.negclusterslabelmat matrices which should apparantly contain far
> more values something more like 25x500 instead of 25x1. When calling
> neg_int = all(neg(:, m(k):m(k+1)), 2)
> I get the "Index exceeds matrix dimensions" error message which I assume
> has to do with the fact that "neg" does not have the appropriate matrix
> dimensions
> (neg = ismember(stat.negclusterslabelmat, neg_signif_clust); )
>
> Where is the error / where should I look for the error?
>
> Some further design details:
> Nsubj = 24
> 2 conditions = Correct, Incorrect
> Within-subject design
> sampling rate = 500
> 34 channels
>
> I hope I gave enough / the necessary information for someone to help me
> out.
>
> Thanks in advance!
>
> Best,
> Anne
>
>
>
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From recasensmarc at gmail.com  Sun Dec 13 16:07:08 2015
From: recasensmarc at gmail.com (Marc Recasens)
Date: Sun, 13 Dec 2015 15:07:08 +0000
Subject: [FieldTrip] channel problem ft_freqstatistics
In-Reply-To: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>
Message-ID: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>

Hi Johannes,

I think the same problem has been reported before in:
http://mailman.science.ru.nl/pipermail/fieldtrip/2015-November/009789.html

Roy Cox looked into the problem with quite detail and found the bug in
the ft_get_selection
function, line 630-631 during a call to "*label = union(label,
selchannel);"*. I recently had the same problem and it was solved after
commenting that line. However it might be better if you update FieldTrip to
the last version where this issue is fixed.

Hope that helps.

Best wishes
Marc

On Sat, Dec 12, 2015 at 6:59 PM, Jojo Klemt <LordJojo at gmx.de> wrote:

> Dear community
>
> My name is Johannes Klemt and I'm analysing eeg/emg-power data of patients
> and healthy controls for my medical doctorate in Tübingen.
> I have a small problem using ft_freqstatistics. After performing an
> independent samples t-test, the channels are suddenly ordered alphabeticaly.
> The preprocessing and power analysis were not performed in field trip.
> The electrode labels and neighbours were defined and put into the
> following cfg:
> cfg.elec
> cfg.neighbours
> The statistics were then calculated using montecarlo method, but the
> channel order in stat.label is changed into alphabetical order, so the stat
> plot looks nice but is quite useless.
> Colleagues of mine used ft_freqgrandaverage as input data and did not have
> the problem, but I can't find the bug.
> I designed a file containing the layout structure and tried putting it in
> by using
> cfg.layout
> but it was ignored.
>
> Any help would be deeply appreciated.
>
> Yours sincerely
>
> Johannes Klemt
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Marc Recasens
Tel.: +34 639 24 15 98
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From federica.ma at gmail.com  Mon Dec 14 12:30:33 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 12:30:33 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Message-ID: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing
to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of
epochs), however the output of the function (namely TFRhann.powspctrm)
always gives me power data for the same number of epochs, namely 41,
unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in
steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
= 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from
-0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica
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From Elana.Harris at cchmc.org  Mon Dec 14 13:12:29 2015
From: Elana.Harris at cchmc.org (Harris, Elana)
Date: Mon, 14 Dec 2015 12:12:29 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
Message-ID: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>

cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


-------------- next part --------------
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From stan.vanpelt at donders.ru.nl  Mon Dec 14 13:21:41 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 12:21:41 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>

Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288


From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl] on behalf of Federica Mauro [federica.ma at gmail.com]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica


-------------- next part --------------
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From federica.ma at gmail.com  Mon Dec 14 13:41:27 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 13:41:27 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute
fft for single trials, since TFRhann.powspctrm is by definition an average
along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From stan.vanpelt at donders.ru.nl  Mon Dec 14 14:30:32 2015
From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan))
Date: Mon, 14 Dec 2015 13:30:32 +0000
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>

Hi Federica,

If you want to have an estimate for each trial separately, you should specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip?

Best,
Stan

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro
Sent: maandag 14 december 2015 13:41
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output

Dear Stan and Elana, thank you very much for your answers and help.

Just another question: if I understood correctly, there's no way to compute fft for single trials, since TFRhann.powspctrm is by definition an average along trials. Is that true?

Thanks again.

Bests,
Federica

2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl<mailto:stan.vanpelt at donders.ru.nl>>:
Dear Elana,

The 50ms timesteps result in the 41 timebins. Per timebin, the average power spectrum (TFRhann.powspctrm) is computed over all trials that have data in that specific time bin. In your case, the power in the earlier time bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that of the later ones (e.g. 1.95-2.0s), because of your variable trial length.

If you specify cfg.keeptrials=’yes’, you can see that the individual trial’s TFRs will have different amount of data points.

Hope that helps.

Best,
Stan

--
Stan van Pelt, PhD
Donders Institute for Brain, Cognition and Behaviour
Radboud University
Montessorilaan 3, B.01.34
6525 HR Nijmegen, the Netherlands
tel: +31 24 3616288<tel:%2B31%2024%203616288>


From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [mailto:fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] On Behalf Of Harris, Elana
Sent: maandag 14 december 2015 13:12
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Number of epochs in the ft_freqanalysis output


cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)



I just noticed this line has an error should be -0.5:0.5:2



Sorry, I am new to fieldtrip myself and can't be more helpful yet.



Cheers,



Elana

________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Federica Mauro [federica.ma at gmail.com<mailto:federica.ma at gmail.com>]
Sent: Monday, December 14, 2015 6:30 AM
To: FieldTrip discussion list
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
Dear all,

I'm having a problem in using the ft_freqanalysis function, so I'm writing to ask your help.
I'm trying to get power data for each 2-seconds epochs of my eeg files.
My eeg files are not of the same length (they don't have the same number of epochs), however the output of the function (namely TFRhann.powspctrm) always gives me power data for the same number of epochs, namely 41, unregarding of the effective number of epochs.

Here is the code I'm using:

cfg              = [];
cfg.output       = 'pow';
% cfg.channel
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz in steps of 2 Hz
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window = 0.5 sec
cfg.toi          = -0:0.05:2;                  % time window "slides" from -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
TFRhann = ft_freqanalysis(cfg, eeg);

Do you have any suggestion about it?
Thank you very much for your attention.

Worm regards,
Federica



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

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From LordJojo at gmx.de  Mon Dec 14 15:24:32 2015
From: LordJojo at gmx.de (Jojo Klemt)
Date: Mon, 14 Dec 2015 15:24:32 +0100
Subject: [FieldTrip]  channel problem ft_freqstatistics
In-Reply-To: <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
References: <trinity-809c2780-e086-4b2c-8fa6-141cde8728a0-1449946766830@3capp-gmx-bs41>, 
 <CACKY2qPjROCSsmekAamkuDRs-M0yAFaBGQ+BcPrqQ4it-QW5AQ@mail.gmail.com>
Message-ID: <trinity-fd5a5c5e-0a0b-417c-b164-249e75a4e832-1450103072262@3capp-gmx-bs08>

An HTML attachment was scrubbed...
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From federica.ma at gmail.com  Mon Dec 14 22:51:26 2015
From: federica.ma at gmail.com (Federica Mauro)
Date: Mon, 14 Dec 2015 22:51:26 +0100
Subject: [FieldTrip] Number of epochs in the ft_freqanalysis output
In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
References: <CABX-y5BTKKXB0Xb_utW8ytB9v8v+SJ798i3et0mw3sPyKY5DNg@mail.gmail.com>
 <B622DB18EE766C4BBAA34EA95310C34C4FF9166E@MCEXMB3.chmccorp.cchmc.org>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282A3C@exprd03.hosting.ru.nl>
 <CABX-y5A31+=NmZ5svPH-YnnhemFX-6UC7MsNmuqcW3dhY7ky6w@mail.gmail.com>
 <7CCA2706D7A4DA45931A892DF3C2894C2A282AB6@exprd03.hosting.ru.nl>
Message-ID: <CABX-y5Aoow_Gp1LZOWb2VpOLXr18c2SY+tCpyLrahcVg0miu4g@mail.gmail.com>

Hi Stan, thank you, it was really helpful.

Best,
Federica

2015-12-14 14:30 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl>:

> Hi Federica,
>
>
>
> If you want to have an estimate for each trial separately, you should
> specify cfg.keeptrials=’yes’ when calling ft_freqanalysis. See also
> http://www.fieldtriptoolbox.org/faq/in_what_way_can_frequency_domain_data_be_represented_in_fieldtrip
> ?
>
>
>
> Best,
>
> Stan
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro
> *Sent:* maandag 14 december 2015 13:41
>
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> Dear Stan and Elana, thank you very much for your answers and help.
>
>
>
> Just another question: if I understood correctly, there's no way to
> compute fft for single trials, since TFRhann.powspctrm is by definition an
> average along trials. Is that true?
>
>
>
> Thanks again.
>
>
>
> Bests,
>
> Federica
>
>
>
> 2015-12-14 13:21 GMT+01:00 Pelt, S. van (Stan) <stan.vanpelt at donders.ru.nl
> >:
>
> Dear Elana,
>
>
>
> The 50ms timesteps result in the 41 timebins. Per timebin, the average
> power spectrum (TFRhann.powspctrm) is computed over all trials that have
> data in that specific time bin. In your case, the power in the earlier time
> bins (e.g. 0.0s-0.05s) will be based on more data points (trials) than that
> of the later ones (e.g. 1.95-2.0s), because of your variable trial length.
>
>
>
> If you specify cfg.keeptrials=’yes’, you can see that the individual
> trial’s TFRs will have different amount of data points.
>
>
>
> Hope that helps.
>
>
>
> Best,
>
> Stan
>
>
>
> --
>
> Stan van Pelt, PhD
>
> Donders Institute for Brain, Cognition and Behaviour
>
> Radboud University
>
> Montessorilaan 3, B.01.34
>
> 6525 HR Nijmegen, the Netherlands
>
> tel: +31 24 3616288
>
>
>
>
>
> *From:* fieldtrip-bounces at science.ru.nl [mailto:
> fieldtrip-bounces at science.ru.nl] *On Behalf Of *Harris, Elana
> *Sent:* maandag 14 december 2015 13:12
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] Number of epochs in the ft_freqanalysis output
>
>
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
>
>
> I just noticed this line has an error should be -0.5:0.5:2
>
>
>
> Sorry, I am new to fieldtrip myself and can't be more helpful yet.
>
>
>
> Cheers,
>
>
>
> Elana
> ------------------------------
>
> *From:* fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]
> on behalf of Federica Mauro [federica.ma at gmail.com]
> *Sent:* Monday, December 14, 2015 6:30 AM
> *To:* FieldTrip discussion list
> *Subject:* [FieldTrip] Number of epochs in the ft_freqanalysis output
>
> Dear all,
>
>
>
> I'm having a problem in using the ft_freqanalysis function, so I'm writing
> to ask your help.
>
> I'm trying to get power data for each 2-seconds epochs of my eeg files.
>
> My eeg files are not of the same length (they don't have the same number
> of epochs), however the output of the function (namely TFRhann.powspctrm)
> always gives me power data for the same number of epochs, namely 41,
> unregarding of the effective number of epochs.
>
>
>
> Here is the code I'm using:
>
>
>
> cfg              = [];
>
> cfg.output       = 'pow';
>
> % cfg.channel
>
> cfg.method       = 'mtmconvol';
>
> cfg.taper        = 'hanning';
>
> cfg.foi          = 4:1:40;                         % analysis 2 to 30 Hz
> in steps of 2 Hz
>
> cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   % length of time window
> = 0.5 sec
>
> cfg.toi          = -0:0.05:2;                  % time window "slides" from
> -0.5 to 1.5 sec in steps of 0.05 sec (50 ms)
>
> TFRhann = ft_freqanalysis(cfg, eeg);
>
>
>
> Do you have any suggestion about it?
>
> Thank you very much for your attention.
>
>
>
> Worm regards,
>
> Federica
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
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From S.Hanslmayr at bham.ac.uk  Wed Dec 16 12:50:48 2015
From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr)
Date: Wed, 16 Dec 2015 11:50:48 +0000
Subject: [FieldTrip] PhD studentship available at University of Birmingham
Message-ID: <257F6C65A372A04CA41056EACC0DE7CED841AC9A@EX8.adf.bham.ac.uk>

Dear Fieldtrip Community,

I take this opportunity to announce a PhD studentship that is available for talented students to work in the labs of Joff Lee and Simon Hanslmayr on a memory project involving invasive recordings of oscillations in rodents. More information about the project and instructions on how to apply can be found here: http://www.birmingham.ac.uk/research/activity/mrc-impact/imaging.aspx. Deadline for applicants is Sunday 10 January 2016.

For any questions about the project please write an email to Dr Joff Lee (J.L.C.Lee at bham.ac.uk<mailto:J.L.C.Lee at bham.ac.uk>) or myself (simon.hanslmayr at bham.ac.uk<mailto:simon.hanslmayr at bham.ac.uk>).

Seasonal greetings,
Simon


Dr. Simon Hanslmayr
Senior Lecturer
School of Psychology
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Tel +44 121 4146203
http://www.memorybham.com/people/#/simon-hanslmayr/
[http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif]

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From luke.bloy at gmail.com  Wed Dec 16 22:29:17 2015
From: luke.bloy at gmail.com (Luke Bloy)
Date: Wed, 16 Dec 2015 21:29:17 +0000
Subject: [FieldTrip] Question about ft_statfun_actvsblT
Message-ID: <CAG5Ru-pbKEF6cd2YFnkXYvGXfEVtb9YGFpw-zydJMbiKJHshsQ@mail.gmail.com>

Sorry if this is missing something fundamental but I'm abit confused about
the use of ft_statfun_actvsblT for frequency analysis and how it compares
to ft_statfun_depsamplesT.

It seems from http://www.fieldtriptoolbox.org/tutorial/salzburg (and from
trying to use it) that inorder to use ft_statfun_actvsblT the active and
baseline freq structures need to have the same time dimension. Based on
this I'm assuming that the active vs baseline comparison happens at each
time x frequency pair, but isn't this what ft_statfun_depsamplesT does?

So I guess my question is what is the difference between the two? What
exactly is the comparison being performed by ft_statfun_actvsblT?

Thanks
Luke
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From leilayou_54 at yahoo.com  Fri Dec 18 10:43:43 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
References: <807603762.476165.1450431823359.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <807603762.476165.1450431823359.JavaMail.yahoo@mail.yahoo.com>

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again. 
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
      dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
      strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load : filename     = 'mydata.edf'
 hdr   = ft_read_header(filename);
 sample.start=1
 sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
  dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
    dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
 
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Fri Dec 18 13:37:52 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Fri, 18 Dec 2015 12:37:52 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>

Hello Leila,

I think there are a few possible options for you. If you're not interested
in analyzing high frequencies, then you could import the data one sample at
a time, downsampling each channel, and then concatenate the channels into
one structure, as described in
http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
I don't know what your sampling rate was, but if your sampling rate was
extremely high then this can save you a lot of space. For example, if
you're only interested in frequencies up to high gamma (around 90-100 Hz),
then your data only need to be sampled at around 250 Hz (per the Nyquist
theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
Hz (which our EDF system does by default) or 5000 Hz then you have way more
samples than necessary; downsampling like this will greatly reduce your
array size.



If that is not an option, then you can read in a segment of data as a
'trial'. ft_preprocessing understands trial start and end times from
cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
read, and the columns are the start sample for each trial, the end sample
for each trial, and the trigger value associated with the trial; you could
just put 0 if there's no trigger). So let's say you want to read the first
through thousandth sample of the recording, then you would set up your cfg
as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of
1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an
explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them
back into continuous data (see
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for
details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/

On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
>         <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
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> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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> *****************************************
>
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From anja.pflug at musterkind.eu  Fri Dec 18 14:06:32 2015
From: anja.pflug at musterkind.eu (Anja Pflug)
Date: Fri, 18 Dec 2015 14:06:32 +0100 (CET)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
Message-ID: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>

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From leilayou_54 at yahoo.com  Fri Dec 18 14:13:16 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:13:16 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <1753128777.512946.1450444396047.JavaMail.yahoo@mail.yahoo.com>

 Thanks for your reply Anja.I need to have all the channel information at a segment of time to decide if it there is seizure occurring.  Down sampling will loose the information and I am not sure if I want to go that way, as I need to do some feature extractions/classification etc on the data.
Not sure how I could cut the data in fieldtrip. Do you know?ThanksBest regards
___________________________________________________ Leila Ayoubian 

 

      From: Anja Pflug <anja.pflug at musterkind.eu>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 1:06 PM
 Subject: [FieldTrip] Importing large edf data
   
 Hello Leila,
have you tried to import only one of your 51 channels?
If this works you  could cut the data or downsample it and then combine all channels in a later step.
Best,
Anja


fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
 <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
-------------- next part --------------
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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 61, Issue 14
*****************************************

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

  
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From jorn at artinis.com  Fri Dec 18 14:17:34 2015
From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=)
Date: Fri, 18 Dec 2015 14:17:34 +0100
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
Message-ID: <007301d13996$7573dc60$605b9520$@artinis.com>

Hi all,

 

I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension. 

 

Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.

 

Best of luck ;)

Jörn

--
Jörn M. Horschig, PhD, Software Engineer
 <http://www.artinis.com/> Artinis Medical Systems  |  +31 481 350 980 

 

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data

 

Hello Leila,

have you tried to import only one of your 51 channels?

If this works you  could cut the data or downsample it and then combine all channels in a later step.

Best,

Anja

 

 <mailto:fieldtrip-request at science.ru.nl> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


Send fieldtrip mailing list submissions to
fieldtrip at science.ru.nl <mailto: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 <mailto:fieldtrip-request at science.ru.nl> 

You can reach the person managing the list at
fieldtrip-owner at science.ru.nl <mailto: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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com <mailto:leilayou_54 at yahoo.com> >
To: "fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> " <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl> >
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com <mailto:807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com> >
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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From leilayou_54 at yahoo.com  Fri Dec 18 14:40:59 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
References: <CAJT2k_8Hpsite9e3NZ+Tfe72StXTin0oUu+2dmTf=_2EmcT80Q@mail.gmail.com>
Message-ID: <2054001626.533069.1450446059200.JavaMail.yahoo@mail.yahoo.com>

 Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.  Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same! 

So this is what I get: 


   hdr: [1x1 struct]
         label: {51x1 cell}
          time: {1x50710 cell}
         trial: {1x50710 cell}
       fsample: 1024
    sampleinfo: [50710x2 double]
           cfg: [1x1 struct]

so the actual data which is in data.trial  is this in both cases! 
size(data.trial)

ans =

           1       50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian 

 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing. 

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

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   1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
        <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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From leilayou_54 at yahoo.com  Fri Dec 18 14:55:18 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Fri, 18 Dec 2015 13:55:18 +0000 (UTC)
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <778201681.538338.1450446918121.JavaMail.yahoo@mail.yahoo.com>

Thanks Jorn. Appreciate your feedback.
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Jörn M. Horschig <jorn at artinis.com>
 To: 'FieldTrip discussion list' <fieldtrip at science.ru.nl> 
 Sent: Friday, December 18, 2015 1:17 PM
 Subject: Re: [FieldTrip] Importing large edf data
   
#yiv8769305188 #yiv8769305188 -- _filtered #yiv8769305188 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8769305188 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv8769305188 {font-family:Verdana;panose-1:2 11 6 4 3 5 4 4 2 4;}#yiv8769305188 #yiv8769305188 p.yiv8769305188MsoNormal, #yiv8769305188 li.yiv8769305188MsoNormal, #yiv8769305188 div.yiv8769305188MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:12.0pt;}#yiv8769305188 a:link, #yiv8769305188 span.yiv8769305188MsoHyperlink {color:#0563C1;text-decoration:underline;}#yiv8769305188 a:visited, #yiv8769305188 span.yiv8769305188MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv8769305188 p {margin-right:0in;margin-left:0in;font-size:12.0pt;}#yiv8769305188 span.yiv8769305188EmailStyle18 {color:#1F497D;}#yiv8769305188 .yiv8769305188MsoChpDefault {font-size:10.0pt;} _filtered #yiv8769305188 {margin:1.0in 1.0in 1.0in 1.0in;}#yiv8769305188 div.yiv8769305188WordSection1 {}#yiv8769305188 Hi all,  I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.   Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.  Best of luck ;)Jörn--
Jörn M. Horschig, PhD, Software Engineer
Artinis Medical Systems  |  +31 481 350 980   From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
Sent: Friday, December 18, 2015 14:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Importing large edf data  Hello Leila,have you tried to import only one of your 51 channels?If this works you  could cut the data or downsample it and then combine all channels in a later step.Best,Anja  
fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:


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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
<807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>> 

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance. 
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian 
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http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

End of fieldtrip Digest, Vol 61, Issue 14
*****************************************

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From a.stolk8 at gmail.com  Fri Dec 18 18:51:20 2015
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Fri, 18 Dec 2015 07:51:20 -1000
Subject: [FieldTrip] Importing large edf data
In-Reply-To: <007301d13996$7573dc60$605b9520$@artinis.com>
References: <mailman.9.1450436402.15840.fieldtrip@science.ru.nl>
 <232492090.41659.0b573584-8ef2-47e8-9557-3e16f95d6d1d.open-xchange@email.1und1.de>
 <007301d13996$7573dc60$605b9520$@artinis.com>
Message-ID: <81DC3EE6-21D4-4BB7-80B8-AF642B616768@gmail.com>

Hi all,

Perhaps this links helps:
http://www.fieldtriptoolbox.org/getting_started/edf

Arjen

> On Dec 18, 2015, at 3:17 AM, Jörn M. Horschig <jorn at artinis.com> wrote:
> 
> Hi all,
>  
> I am not expert in edf data, but it is indeed true that some dataformats allow for reading in single channels, while others do not, and some dataformats allow for reading in only specific time points while others do not. While the FT-end-user may specify these things always, independently of the data format, ‘behind the curtain’ FT may need to read in all data and/or channels and then throw away what the user did NOT ask for. So, while specifying only a second of data for the ft_ high level function, it might be that the specific low-level reading function (mostly written by the manufacturer) does return ALL samples anyways. Same might happen for the channel dimension.
>  
> Most dataformats allow for at least either the one or the other, few for both and few for none. So, if specifying shorter trial lengths does not work, it might be well worth to specify only a single channel (as Anja suggested). But again, I do not know the specifics of edf. I justed wanted to add that to the discussion for educational purposes.
>  
> Best of luck ;)
> Jörn
> --
> Jörn M. Horschig, PhD, Software Engineer
> Artinis Medical Systems  |  +31 481 350 980
>  
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Anja Pflug
> Sent: Friday, December 18, 2015 14:07
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Importing large edf data
>  
> Hello Leila,
> 
> have you tried to import only one of your 51 channels?
> 
> If this works you  could cut the data or downsample it and then combine all channels in a later step.
> 
> Best,
> 
> Anja
> 
>  
> 
> fieldtrip-request at science.ru.nl hat am 18. Dezember 2015 um 12:00 geschrieben:
> 
> 
> 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. importing large edf data (Leila Ayoubian)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
> 
> Error in ReadFedfiles (line 8)
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error. 
> 
> 
> I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100') 
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.
> 
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
> 
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
> 
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >> 
> 
> Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
> Thanks again for your support and assistance. 
> We appreciate your effort.
> Kind regards
> 
> ___________________________________________________ Dr. Leila Ayoubian 
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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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> *****************************************
> 
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Sat Dec 19 15:06:46 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Sat, 19 Dec 2015 14:06:46 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a
sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it
worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Friday, December 18, 2015 12:37 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
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> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
>
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From senakahks at gmail.com  Sun Dec 20 12:51:47 2015
From: senakahks at gmail.com (Senaka Amarakeerthi)
Date: Sun, 20 Dec 2015 17:21:47 +0530
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data structure.
Message-ID: <CA+si8qkXe5W7J=J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg@mail.gmail.com>

Dear all,

I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
The file I am trying to process is a single trial.

The code I tried is:

%% import data from testbench emotiv edf file

[hdr, data_eeg] = edfread('emotive.edf');



%% Rearrange data to match FieldTrip Format

% Remove unnecessary columns

data.trial = data_eeg([3:16,39], : );





% Cell-array containing strings, Nchan X 1

% Based on https://emotiv.com/forum/forum14/topic1817/messages/

data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6' 'F4'
'F8' 'AF4' 'MARKER'};



% Sampling frequency in Hz, single number

data.fsample = 128;



% Setting time

[x, filelength] = size(data.trial);

data.time{1} = [1:filelength]./data.fsample;

%% Using the rearranged data





% Set the trial column name and event value (what you enter to the last
column.

% here enter number 1 as the marker)

cfg.trialdef.eventtype = 'MARKER';

cfg.trialdef.eventvalue = 1;

cfg.trialdef.eventtype = '?';

ft_definetrial(cfg);


%% Preprocessing

 cfg = [];

 cfg.channel       = 'AF3';

 cfg.lpfilter      = 'yes';

 cfg.hpfilter      = 'yes';

 cfg.bsfilter      = 'yes';

 cfg.lpfreq        = 100;

 cfg.hpfreq        = 10;

 cfg.bsfreq        = [59 61];

 cfg.lpfiltord     = 4;

 cfg.hpfiltord     = 4;

 cfg.bpfiltord     = 4;

 cfg.lpfilttype    = 'but';

 cfg.hpfilttype    = 'but';

 ecog = ft_preprocessing(cfg,data);


When I run the script. I am getting the following error.

Error in ft_trialfun_general (line 78)
hdr = ft_read_header(cfg.headerfile, 'headerformat',
cfg.headerformat);

Do I need to set the header structure as well? Can somebody help me to get
this fixed. I am reading the documentation but it seems start is bit hard!

Appreciate your support
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From leilayou_54 at yahoo.com  Mon Dec 21 10:36:27 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
References: <CAJT2k_-ABLzL71MVwB9-C2-8wOSZ-JSVnSa=cw6BjrQ2RSgcjw@mail.gmail.com>
Message-ID: <1459455402.1301519.1450690587900.JavaMail.yahoo@mail.yahoo.com>

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first. 
But now I see thecfg2.trialdef.triallength = 1; 
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference? Thanks again.Kind regards
 __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x500 double]}
         trial: {[37x500 double]}
       fsample: 200
    sampleinfo: [1 500]
           cfg: [1x1 struct]

>> data_1000samples

data_1000samples = 

           hdr: [1x1 struct]
         label: {37x1 cell}
          time: {[1x1000 double]}
         trial: {[37x1000 double]}
       fsample: 200
    sampleinfo: [1 1000]
           cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/ 
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Friday, December 18, 2015 12:37 PM
 Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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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 stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:35:23 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:35:23 +0000
Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
	structure
Message-ID: <CAJT2k_-wZpxENz55hHhJDerN1RuBQH34j3dyKvhLoPHSEGfTbg@mail.gmail.com>

Hello Senaka,

I think you might be making your life more difficult by trying to directly
call edfread(), which is a low-level function. Have you tried just using
ft_preprocessing(), the high-level wrapper function, as described in the
tutorial on the fieldtrip wiki? In my experience, this function reads EDF
data straightforwardly.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 20 Dec 2015 17:21:47 +0530
> From: Senaka Amarakeerthi <senakahks at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Adjsting Emotive EEG data to FieldTrip data
>         structure.
> Message-ID:
>         <CA+si8qkXe5W7J=
> J-1ensqWCTreAGdsHovwSavJA5sAG6i1nDGg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I am new to FieldTrip and  trying to process offline Emotive Epoc EEG data.
> The file I am trying to process is a single trial.
>
> The code I tried is:
>
> %% import data from testbench emotiv edf file
>
> [hdr, data_eeg] = edfread('emotive.edf');
>
>
>
> %% Rearrange data to match FieldTrip Format
>
> % Remove unnecessary columns
>
> data.trial = data_eeg([3:16,39], : );
>
>
>
>
>
> % Cell-array containing strings, Nchan X 1
>
> % Based on https://emotiv.com/forum/forum14/topic1817/messages/
>
> data.label = {'AF3' 'F7' 'F3' 'FC5' 'T7' 'P7' 'O1' 'O2' 'P8' 'T8' 'FC6'
> 'F4'
> 'F8' 'AF4' 'MARKER'};
>
>
>
> % Sampling frequency in Hz, single number
>
> data.fsample = 128;
>
>
>
> % Setting time
>
> [x, filelength] = size(data.trial);
>
> data.time{1} = [1:filelength]./data.fsample;
>
> %% Using the rearranged data
>
>
>
>
>
> % Set the trial column name and event value (what you enter to the last
> column.
>
> % here enter number 1 as the marker)
>
> cfg.trialdef.eventtype = 'MARKER';
>
> cfg.trialdef.eventvalue = 1;
>
> cfg.trialdef.eventtype = '?';
>
> ft_definetrial(cfg);
>
>
> %% Preprocessing
>
>  cfg = [];
>
>  cfg.channel       = 'AF3';
>
>  cfg.lpfilter      = 'yes';
>
>  cfg.hpfilter      = 'yes';
>
>  cfg.bsfilter      = 'yes';
>
>  cfg.lpfreq        = 100;
>
>  cfg.hpfreq        = 10;
>
>  cfg.bsfreq        = [59 61];
>
>  cfg.lpfiltord     = 4;
>
>  cfg.hpfiltord     = 4;
>
>  cfg.bpfiltord     = 4;
>
>  cfg.lpfilttype    = 'but';
>
>  cfg.hpfilttype    = 'but';
>
>  ecog = ft_preprocessing(cfg,data);
>
>
> When I run the script. I am getting the following error.
>
> Error in ft_trialfun_general (line 78)
> hdr = ft_read_header(cfg.headerfile, 'headerformat',
> cfg.headerformat);
>
> Do I need to set the header structure as well? Can somebody help me to get
> this fixed. I am reading the documentation but it seems start is bit hard!
>
> Appreciate your support
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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Mon Dec 21 12:39:56 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Mon, 21 Dec 2015 11:39:56 +0000
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>

Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
needed if all you want to do is read a single segment of continuous data
based on predetermined latencies; you may notice that, in the sample code
snippets I sent in my last message, I did not use this function at all, I
just hard-coded the latency range in cfg.trl (and then passed this cfg
structure to ft_preprocessing() ). So, if this is all you need to do, there
is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into
one dataset (which is what you would accomplish by using
cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
it's not working for you at the moment; I would have to see your code to be
able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/



>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Saturday, December 19, 2015 2:06 PM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151218/6dfa7ce1/attachment-0001.html
> >
>
> ------------------------------
>
>
>
>
>
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From leilayou_54 at yahoo.com  Mon Dec 21 13:04:36 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:04:36 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <1581782628.1312312.1450699476132.JavaMail.yahoo@mail.yahoo.com>

 You are absolutely right. It is either using the fix cfg.trl to choose the begining and end of the samples or to choose the cfg2.trialdef.triallength =5. 
In your initial code you had them together, and that is why I was confused. So basically there are two ways to segment the file.
Thanks you very much. You have been very helpful.
My questions are endless. I have another one for you! Sorry!
When loading edf+ the events are lost. using cfg2.trialdef.eventtype  = '?' gives me no events detected.
Any idea how I could go about it?
Thanks again for your help. I really appreciate it.Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <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. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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------------------------------





 
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From leilayou_54 at yahoo.com  Mon Dec 21 13:59:38 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
Subject: [FieldTrip] importing large edf data
In-Reply-To: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
References: <CAJT2k_95xRbwuaC_3LXfNUmrvDzYKESCSCB+QPsvQJKCdERF-w@mail.gmail.com>
Message-ID: <916358647.1306232.1450702778200.JavaMail.yahoo@mail.yahoo.com>

Dear Steve,I have shared my data file in drop box with you. 
I am trying to read the events in this file and I get 0 events. cfg2.trialdef.eventtype  = '?'
Could you please help me out?
Thanks __________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 


 

      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl 
 Sent: Monday, December 21, 2015 11:39 AM
 Subject: Re: [FieldTrip] importing large edf data
   
Hi Leila,

cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not needed if all you want to do is read a single segment of continuous data based on predetermined latencies; you may notice that, in the sample code snippets I sent in my last message, I did not use this function at all, I just hard-coded the latency range in cfg.trl (and then passed this cfg structure to ft_preprocessing() ). So, if this is all you need to do, there is no need to worry about these additional parameters.

If you are trying to read multiple segments of data as separate epochs into one dataset (which is what you would accomplish by using cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why it's not working for you at the moment; I would have to see your code to be able to diagnose what might be going on.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
 

Message: 2
Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
        <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I got a different result at first.
But now I see thecfg2.trialdef.triallength = 1;?
there is no difference in the way data is loaded once I change the number to let's say 5! Where should I see that difference??Thanks again.Kind regards
?__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London





      From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
 To: fieldtrip at science.ru.nl
 Sent: Saturday, December 19, 2015 2:06 PM
 Subject: Re: [FieldTrip] importing large edf data

Hi Leila,

I'm not sure why it didn't work for you. I tried the following code (on a sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and it worked perfectly for me:


cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 500 0];
cfg.continuous = 'yes';
data_500samples = ft_preprocessing(cfg);

cfg = [];
cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
cfg.trl = [1 1000 0];
cfg.continuous = 'yes';
data_1000samples = ft_preprocessing(cfg);



Here's the output:
>> data_500samples

data_500samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x500 double]}
???????? trial: {[37x500 double]}
?????? fsample: 200
??? sampleinfo: [1 500]
?????????? cfg: [1x1 struct]

>> data_1000samples

data_1000samples =

?????????? hdr: [1x1 struct]
???????? label: {37x1 cell}
????????? time: {[1x1000 double]}
???????? trial: {[37x1000 double]}
?????? fsample: 200
??? sampleinfo: [1 1000]
?????????? cfg: [1x1 struct]


Best,
Steve




---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/?
------------------------------

Message: 5
Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

?Thanks Steve for your reply.I think your code for segmenting the data is the way to go for me ! :) And I do appreciate you gave me an example.? Thanks
However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl = [1 10000 0]; to see the results, and it looked the same!

So this is what I get:


?? hdr: [1x1 struct]
???????? label: {51x1 cell}
????????? time: {1x50710 cell}
???????? trial: {1x50710 cell}
?????? fsample: 1024
??? sampleinfo: [50710x2 double]
?????????? cfg: [1x1 struct]

so the actual data which is in data.trial? is this in both cases!
size(data.trial)

ans =

?????????? 1?????? 50710

How could that happen if you are segmenting it in two different chunks?
Best regards

___________________________________________________ Leila Ayoubian



? ? ? From: Stephen Politzer-Ahles <stephen.politzer-ahles at ling-phil.ox.ac.uk>
?To: fieldtrip at science.ru.nl
?Sent: Friday, December 18, 2015 12:37 PM
?Subject: Re: [FieldTrip] importing large edf data

Hello Leila,

I think there are a few possible options for you. If you're not interested in analyzing high frequencies, then you could import the data one sample at a time, downsampling each channel, and then concatenate the channels into one structure, as described in http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory. I don't know what your sampling rate was, but if your sampling rate was extremely high then this can save you a lot of space. For example, if you're only interested in frequencies up to high gamma (around 90-100 Hz), then your data only need to be sampled at around 250 Hz (per the Nyquist theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500 Hz (which our EDF system does by default) or 5000 Hz then you have way more samples than necessary; downsampling like this will greatly reduce your array size.



If that is not an option, then you can read in a segment of data as a 'trial'. ft_preprocessing understands trial start and end times from cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to read, and the columns are the start sample for each trial, the end sample for each trial, and the trigger value associated with the trial; you could just put 0 if there's no trigger). So let's say you want to read the first through thousandth sample of the recording, then you would set up your cfg as normal, then add:

cfg.trl = [1 1000 0];

and then use ft_preprocessing.

By way of example, here is code that reads in raw data as a series of 1-second "trials":

cfg = [];
cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for an explanation of these parameters
cfg.trialdef.ntrials = Inf;
cfg = ft_definetrial( cfg );

cfg.continuous = 'yes';
data = ft_preprocessing(cfg);

After doing whatever you need to these trials, you could concatenate them back into continuous data (see http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html for details).

Best,
Steve

---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/
On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:

Send fieldtrip mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:

? ?1. importing large edf data (Leila Ayoubian)


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

Message: 1
Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
From: Leila Ayoubian <leilayou_54 at yahoo.com>
To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
Subject: [FieldTrip] importing large edf data
Message-ID:
? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi:Thanks for providing us with this amazing toolbox.
I am new to fieldtrip. I am trying to import EEG data in the format of *.edf for the purpose of seizure detection for epileptic patients. I can't break up the data as you understand the detection has to have continuous data. However I could load section of the data at a time and clear what is already used and reload again.?
So trying to load the data like this:
cfg.dataset= ('mydata.edf');
rawdata=ft_preprocessing(cfg);
This is the error message I get :
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a long time
and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ft_preprocessing (line 566)
????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);

Error in ReadFedfiles (line 8)
rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I tried the ft_redefinetrial, but since the input to this file is the output from ft-PREPROCESSING it gives me the same error.


I also tried to use ft_read_data to choose the samples I want to load :?filename???? = 'mydata.edf'
?hdr?? = ft_read_header(filename);
?sample.start=1
?sample.end=100
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
and here is again the error message:
Error using zeros
Requested 51x51927040 (19.7GB) array exceeds maximum array size preference. Creation of arrays greater than this limit may take a
long time and cause MATLAB to become unresponsive. See array size limit or preference panel for more information.

Error in read_edf (line 403)
? dat = zeros(length(chanindx),nepochs*epochlength);

Error in ft_read_data (line 622)
??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);

Error in ReadFedfiles (line 31)
dat = ft_read_data(filename,'sample.start','1','sample.end','100')
?
>>

Could you please direct me as to which functions and in which order I should be using the functions to load data in smaller samples.Some examples would be useful.
Thanks again for your support and assistance.
We appreciate your effort.
Kind regards

___________________________________________________ Dr. Leila Ayoubian
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------------------------------





 
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
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From leilayou_54 at yahoo.com  Mon Dec 21 16:49:12 2015
From: leilayou_54 at yahoo.com (Leila Ayoubian)
Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
Subject: [FieldTrip] EDF+ annotations
References: <782532884.1387709.1450712952642.JavaMail.yahoo.ref@mail.yahoo.com>
Message-ID: <782532884.1387709.1450712952642.JavaMail.yahoo@mail.yahoo.com>

Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab and read the events/annotations. These annotations are usually seizure, or spikes....
The files are EEG data from nicollet one, lengthy data for epileptic patients.
This is how I try to look at the events:

cfg2 = [];

cfg2.dataset = 'For leila.edf';
cfg2.trialdef.eventtype  = '?'
cfg2 = ft_definetrial( cfg2 );


cfg2.continuous = 'yes';
data2 = ft_preprocessing(cfg2);
However the output for events are always empty.Does anyone have an idea how I could extract the events/annotation on these files? 

 Thanks in advance for your assistance.
Best regards
__________________________________________________ Leila Ayoubian, PhD.
Institute of Psychiatry, Psychology and Neuroscience
King's College London
 

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From weston.pack at yale.edu  Mon Dec 21 18:56:11 2015
From: weston.pack at yale.edu (Pack, Weston)
Date: Mon, 21 Dec 2015 17:56:11 +0000
Subject: [FieldTrip] How to implement the .pl2 patch for Plexon data
Message-ID: <46289A1970E74F4888AA0D7E75AAB1E6210097A4@x10-mbx13.yu.yale.edu>

Greetings FieldTrip community,

I am new to using FieldTrip, but am well versed in Matlab. I would like to use FieldTrip to analyze Plexon data from LFP recordings and am working with the .pl2 format. I have read through the current documentation (very short) about the patch for loading .pl2 files, but I still have no idea how to install and use the patch as this is not documented (that I can find). The following is provided but with no explanation of how to implement it:

“ (filetype = plexon_plx_v2) “

I have added the path of the Plexon SDK folder using:
“ addpath ('E:\MatlabOfflineFilesSDK')”

I have download the .diff patch file as well as the .zip folder “ft_plexon” but I don’t know where to put them. Does the “plexon” folder inside go in the main FieldTrip directory, the main Plexon SDK directory (currently listed above), or somewhere else? The same question applies to the .diff file.
Thank you in advance for your assistance. Once I get FieldTrip figured out, I intend to create a thorough, novice-friendly tutorial with step-by-step instructions how to work with .pl2 files for LFP analysis. I’ve spent the better part a week fumbling through the tutorials and I’m certain I can write a novice-friendly tutorial on the wiki that will only take a few hours at most for beginners to master. My goal is first to understand how to utilize FieldTrip, at which point I can document my struggles and successes so that future users (especially my lab-mates) can obtain competency with far more efficiency.

Thanks again in advance. I hope to contribute significantly to the community. Happy Holidays!

Weston Pack, PhD

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From jochem.rieger at uni-oldenburg.de  Mon Dec 21 20:00:15 2015
From: jochem.rieger at uni-oldenburg.de (Jochem Rieger)
Date: Mon, 21 Dec 2015 20:00:15 +0100
Subject: [FieldTrip] Job vacancies: MEG-physicist/engineer and
 MRI-physicist/engineer at Oldenburg University, Germany
Message-ID: <56784C3F.4050501@uni-oldenburg.de>

The newly founded Neuroimaging Center at the University of Oldenburg,
Germany,
offers the following two positions


*1. MEG-Physicist/Engineer (E13/TV-L, initially 3 years) *

* *

*2. MRI-Physicist/Engineer (E13/TV-L, initially 3 years)*

 

The positions are suitable for part-time work.

 

The Neuroimaging Center hosts a state of the art magnetoencephalograph
(ElektaTriux)
and a magnetic resonance tomograph (Siemens Prisma 3T) and is embedded
in an
excellent interdisciplinary scientific environment with a strong
research focus on
neurosensory, neurocognitive, and medical research. 

 

We seek for highly motivated post-doctoral candidates  (with PhD) with
an academic university degree in physics, engineering or related fields,
with documented research experience in magnetoencephalography (position
1) or magnetic resonance imaging (position 2). For both positions,
fluency in English is necessary. German and experience in the design of
neurocognitive experiments are desirable.

 

Successful candidates will be responsible for the operation and
administration of the
MEG-system and MRI-system respectively, their infrastructure, the
development and
improvement of measurement and analyses techniques and user consultancy.

 

The University of Oldenburg is rapidly growing and offers a vibrant
scientific environment with strong foci on cognitive and sensory
neuroscience and a new medical school. The European Medical School is a
cooperation project between the Universities of Oldenburg and Groningen
and three local hospitals. Oldenburg is an attractive city in Germany's
northwest with excellent quality of life. It is close to Bremen,
Hamburg, Groningen, and approx. 1 h from the north sea.

 

The University of Oldenburg is dedicated to increasing the percentage of
women in science. Therefore, female candidates are particularly
encouraged to apply and will be given preference in cases of equal
qualification. Handicapped applicants will be given preference if
equally qualified.

 

Electronic applications (one pdf file) are preferred and can be send to:
Professor Dr. JochemRieger: Jochem.rieger at uni-oldenburg.de
<mailto:Jochem.rieger at uni-oldenburg.de> 

Applications by mail should be sent to

Prof. Jochem Rieger

Universität Oldenburg

Kuepkersweg 74 (W30)

26129 Oldenburg

Germany

 

The application process is open until January 31st 2016. Applications
should include
your CV, a list of most recent publications, and a statement (max. 3
pages).
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From plyons at udel.edu  Mon Dec 21 20:39:59 2015
From: plyons at udel.edu (Peter Lyons)
Date: Mon, 21 Dec 2015 14:39:59 -0500
Subject: [FieldTrip] Clarification on plotting WPLI
Message-ID: <CALq-V2q-ubebB0u1S_wa_RFpfW4gAFXntNb4C+SC8uHT2QpPzw@mail.gmail.com>

Hello Everyone,

I have a question regarding the interpretation of negative values in the
debiased wPLI. Although the reference page on the debiased wPLI notes that
estimates are computed by squaring the wPLI values, I and others have
noticed that some of the values in the debiased wPLI spectrum are negative.
How should these negative values be interpreted in reference to 0?

To view the results of the debiased wPLI connectivity analysis
(ft_connectivity analysis with cfg.method = 'wpli_debiased'), I've been
using the ft_topoplotER function. However, I'm concerned that the default
scaling (zlim = 'maxmin') of the plot does not seem to register the
negative values in the debiased wPLI spectrum. That is, the negative values
are not being plotted. It is curious, however, that the ft_topoplotER
does register the negative values in the *non-debiased *wPLI spectrum.

Is there a reason why the ft_topoplotER function is treating the negative
values from the debiased vs. non-debiased wPLI spectrums differently? Is
there perhaps a more appropriate plotting function I should be using to
view the debiased wPLI output?

I would greatly appreciate any guidance in this.

Thank you!

Peter
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From shlomitbeker at gmail.com  Tue Dec 22 07:42:31 2015
From: shlomitbeker at gmail.com (Shlomit Beker)
Date: Tue, 22 Dec 2015 06:42:31 +0000
Subject: [FieldTrip] Please remove me from mailing list
Message-ID: <7fa9847a19964083a25ceb552d18577f@EXPRD01.hosting.ru.nl>




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From stephen.politzer-ahles at ling-phil.ox.ac.uk  Tue Dec 22 18:48:01 2015
From: stephen.politzer-ahles at ling-phil.ox.ac.uk (Stephen Politzer-Ahles)
Date: Tue, 22 Dec 2015 12:48:01 -0500
Subject: [FieldTrip] importing large edf data
Message-ID: <CAJT2k__yFvF-Khymgo7fVLyZnCUdsb9htcC-kFGqDZ1JM=1Akg@mail.gmail.com>

Hi Leila,

According to the warning messages that pop up, the annotation channel is
not being read because it is at a different sampling rate than the data.
>From what I can tell, this appears to be a common problem.
http://www.fieldtriptoolbox.org/getting_started/edf explains a workaround;
have you tried this?

Alternatively, you could consider trying some other toolboxes---I believe
mne-python is capable of handling this issue with EDF triggers
straightforwardly, or you could use one of the softwares that is
specifically made for EDF (such as EDFViewer or EDFBrowser) to export your
annotations into a format that is more easily readable and then use that to
create your cfg.trl structure for Fieldtrip.

Best,
Steve



---
Stephen Politzer-Ahles
University of Oxford
Language and Brain Lab
Faculty of Linguistics, Phonetics & Philology
http://users.ox.ac.uk/~cpgl0080/


>
> Message: 4
> Date: Mon, 21 Dec 2015 12:59:38 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
>         <916358647.1306232.1450702778200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Steve,I have shared my data file in drop box with you.
> I am trying to read the events in this file and I get 0 events.
> cfg2.trialdef.eventtype? = '?'
> Could you please help me out?
> Thanks?__________________________________________________ Leila Ayoubian,
> PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
>       From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
>  To: fieldtrip at science.ru.nl
>  Sent: Monday, December 21, 2015 11:39 AM
>  Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> cfg.trialdef.triallength is a parameter for ft_definetrial(), which is not
> needed if all you want to do is read a single segment of continuous data
> based on predetermined latencies; you may notice that, in the sample code
> snippets I sent in my last message, I did not use this function at all, I
> just hard-coded the latency range in cfg.trl (and then passed this cfg
> structure to ft_preprocessing() ). So, if this is all you need to do, there
> is no need to worry about these additional parameters.
>
> If you are trying to read multiple segments of data as separate epochs
> into one dataset (which is what you would accomplish by using
> cfg.trialdef.triallength = 1 and ft_definetrial() ), then I'm not sure why
> it's not working for you at the moment; I would have to see your code to be
> able to diagnose what might be going on.
>
> Best,
> Steve
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> ?
>
> Message: 2
> Date: Mon, 21 Dec 2015 09:36:27 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <1459455402.1301519.1450690587900.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Steve,Thanks for checking for me. You are indeed right. Not sure why I
> got a different result at first.
> But now I see thecfg2.trialdef.triallength = 1;?
> there is no difference in the way data is loaded once I change the number
> to let's say 5! Where should I see that difference??Thanks again.Kind
> regards
> ?__________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Saturday, December 19, 2015 2:06 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hi Leila,
>
> I'm not sure why it didn't work for you. I tried the following code (on a
> sample EDF file I found at http://www.teuniz.net/edf_bdf_testfiles/) and
> it worked perfectly for me:
>
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 500 0];
> cfg.continuous = 'yes';
> data_500samples = ft_preprocessing(cfg);
>
> cfg = [];
> cfg.dataset = 'C:\Users\Spolitzerahles\Desktop\ma0844az_1-1+.edf';
> cfg.trl = [1 1000 0];
> cfg.continuous = 'yes';
> data_1000samples = ft_preprocessing(cfg);
>
>
>
> Here's the output:
> >> data_500samples
>
> data_500samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x500 double]}
> ???????? trial: {[37x500 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 500]
> ?????????? cfg: [1x1 struct]
>
> >> data_1000samples
>
> data_1000samples =
>
> ?????????? hdr: [1x1 struct]
> ???????? label: {37x1 cell}
> ????????? time: {[1x1000 double]}
> ???????? trial: {[37x1000 double]}
> ?????? fsample: 200
> ??? sampleinfo: [1 1000]
> ?????????? cfg: [1x1 struct]
>
>
> Best,
> Steve
>
>
>
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/?
> ------------------------------
>
> Message: 5
> Date: Fri, 18 Dec 2015 13:40:59 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <2054001626.533069.1450446059200.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> ?Thanks Steve for your reply.I think your code for segmenting the data is
> the way to go for me ! :) And I do appreciate you gave me an example.?
> Thanks
> However I tried it with two different cfg.trl = [1 1000 0]; and cfg.trl =
> [1 10000 0]; to see the results, and it looked the same!
>
> So this is what I get:
>
>
> ?? hdr: [1x1 struct]
> ???????? label: {51x1 cell}
> ????????? time: {1x50710 cell}
> ???????? trial: {1x50710 cell}
> ?????? fsample: 1024
> ??? sampleinfo: [50710x2 double]
> ?????????? cfg: [1x1 struct]
>
> so the actual data which is in data.trial? is this in both cases!
> size(data.trial)
>
> ans =
>
> ?????????? 1?????? 50710
>
> How could that happen if you are segmenting it in two different chunks?
> Best regards
>
> ___________________________________________________ Leila Ayoubian
>
>
>
> ? ? ? From: Stephen Politzer-Ahles <
> stephen.politzer-ahles at ling-phil.ox.ac.uk>
> ?To: fieldtrip at science.ru.nl
> ?Sent: Friday, December 18, 2015 12:37 PM
> ?Subject: Re: [FieldTrip] importing large edf data
>
> Hello Leila,
>
> I think there are a few possible options for you. If you're not interested
> in analyzing high frequencies, then you could import the data one sample at
> a time, downsampling each channel, and then concatenate the channels into
> one structure, as described in
> http://www.fieldtriptoolbox.org/faq/how_can_i_preprocess_a_dataset_that_is_too_large_to_fit_into_memory.
> I don't know what your sampling rate was, but if your sampling rate was
> extremely high then this can save you a lot of space. For example, if
> you're only interested in frequencies up to high gamma (around 90-100 Hz),
> then your data only need to be sampled at around 250 Hz (per the Nyquist
> theorem, plus a little extra wiggle room), so if you sampled at e.g. 2500
> Hz (which our EDF system does by default) or 5000 Hz then you have way more
> samples than necessary; downsampling like this will greatly reduce your
> array size.
>
>
>
> If that is not an option, then you can read in a segment of data as a
> 'trial'. ft_preprocessing understands trial start and end times from
> cfg.trl, which minimally is an Nx3 matrix (N is the number of trials to
> read, and the columns are the start sample for each trial, the end sample
> for each trial, and the trigger value associated with the trial; you could
> just put 0 if there's no trigger). So let's say you want to read the first
> through thousandth sample of the recording, then you would set up your cfg
> as normal, then add:
>
> cfg.trl = [1 1000 0];
>
> and then use ft_preprocessing.
>
> By way of example, here is code that reads in raw data as a series of
> 1-second "trials":
>
> cfg = [];
> cfg.dataset = 'C:\Users\Steve\Desktop\subj2.vhdr';
> cfg.trialdef.triallength = 1; % see documentation for ft_definetrial for
> an explanation of these parameters
> cfg.trialdef.ntrials = Inf;
> cfg = ft_definetrial( cfg );
>
> cfg.continuous = 'yes';
> data = ft_preprocessing(cfg);
>
> After doing whatever you need to these trials, you could concatenate them
> back into continuous data (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-June/003971.html
> for details).
>
> Best,
> Steve
>
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab
> Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/
> On Fri, Dec 18, 2015 at 11:00 AM, <fieldtrip-request at science.ru.nl> wrote:
>
> Send fieldtrip mailing list submissions to
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> You can reach the person managing the list at
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> Today's Topics:
>
> ? ?1. importing large edf data (Leila Ayoubian)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 18 Dec 2015 09:43:43 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] importing large edf data
> Message-ID:
> ? ? ? ? <807603762.476165.1450431823359.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi:Thanks for providing us with this amazing toolbox.
> I am new to fieldtrip. I am trying to import EEG data in the format of
> *.edf for the purpose of seizure detection for epileptic patients. I can't
> break up the data as you understand the detection has to have continuous
> data. However I could load section of the data at a time and clear what is
> already used and reload again.?
> So trying to load the data like this:
> cfg.dataset= ('mydata.edf');
> rawdata=ft_preprocessing(cfg);
> This is the error message I get :
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a long time
> and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ft_preprocessing (line 566)
> ????? dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample',
> begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',
> ????? strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat);
>
> Error in ReadFedfiles (line 8)
>
> rawdata=ft_preprocessing(cfg);%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I tried the ft_redefinetrial, but since the input to this file is the
> output from ft-PREPROCESSING it gives me the same error.
>
>
> I also tried to use ft_read_data to choose the samples I want to load
> :?filename???? = 'mydata.edf'
> ?hdr?? = ft_read_header(filename);
> ?sample.start=1
> ?sample.end=100
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> and here is again the error message:
> Error using zeros
> Requested 51x51927040 (19.7GB) array exceeds maximum array size
> preference. Creation of arrays greater than this limit may take a
> long time and cause MATLAB to become unresponsive. See array size limit or
> preference panel for more information.
>
> Error in read_edf (line 403)
> ? dat = zeros(length(chanindx),nepochs*epochlength);
>
> Error in ft_read_data (line 622)
> ??? dat = read_edf(filename, hdr, begsample, endsample, chanindx);
>
> Error in ReadFedfiles (line 31)
> dat = ft_read_data(filename,'sample.start','1','sample.end','100')
> ?
> >>
>
> Could you please direct me as to which functions and in which order I
> should be using the functions to load data in smaller samples.Some examples
> would be useful.
> Thanks again for your support and assistance.
> We appreciate your effort.
> Kind regards
>
> ___________________________________________________ Dr. Leila Ayoubian
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>
>
>
> ?
> _______________________________________________
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> ------------------------------
>
> Message: 5
> Date: Mon, 21 Dec 2015 15:49:12 +0000 (UTC)
> From: Leila Ayoubian <leilayou_54 at yahoo.com>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] EDF+ annotations
> Message-ID:
>         <782532884.1387709.1450712952642.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,I am new to fieldtrip .I am trying to load some edf+ file to Matlab
> and read the events/annotations. These annotations are usually seizure, or
> spikes....
> The files are EEG data from nicollet one, lengthy data for epileptic
> patients.
> This is how I try to look at the events:
>
> cfg2 = [];
>
> cfg2.dataset = 'For leila.edf';
> cfg2.trialdef.eventtype? = '?'
> cfg2 = ft_definetrial( cfg2 );
>
>
> cfg2.continuous = 'yes';
> data2 = ft_preprocessing(cfg2);
> However the output for events are always empty.Does anyone have an idea
> how I could extract the events/annotation on these files?
>
>  Thanks in advance for your assistance.
> Best regards
> __________________________________________________ Leila Ayoubian, PhD.
> Institute of Psychiatry, Psychology and Neuroscience
> King's College London
>
>
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From fanshine at yeah.net  Wed Dec 23 09:55:28 2015
From: fanshine at yeah.net (Hanson)
Date: Wed, 23 Dec 2015 16:55:28 +0800 (CST)
Subject: [FieldTrip] Make a custom layout
Message-ID: <7af7ec0c.1eaf.151ce0cdf79.Coremail.fanshine@yeah.net>

Dear all,

I am new to FieldTrip and  trying to  do the time-frequency analysis of my eeg data , however it seems that no suitable layout. And I use ft_prepare_layout function to make a custom layout(electrode_position32.mat).
%% Time-frequency analysis 
cfg              = [];
cfg.output       = 'pow';
cfg.channel      = 'EEG';
cfg.method       = 'mtmconvol';
cfg.taper        = 'hanning';
cfg.foi          = 2:2:30;                           
cfg.t_ftimwin    = ones(length(cfg.foi),1).*0.5;   
cfg.toi          = -0.5:0.05:1.5;                   
TFRhann = ft_freqanalysis(cfg, data);


cfg = [];       
cfg.showlabels   = 'yes';
cfg.layout       = 'electrode_position32.mat';
figure 
ft_multiplotTFR(cfg, TFRhann);


cfg = [];
cfg.channel      = 'C4';
figure 
ft_singleplotTFR(cfg, TFRhann);


cfg = [];
cfg.layout = 'electrode_position32.mat';
figure 
ft_topoplotTFR(cfg, TFRhann);


When I run the script. I am getting the following error.


Warning: (one of the) axis is/are not evenly spaced, but plots are made as if axis are linear 
> In ft_multiplotTFR at 405
  In TFanalysis_zhs_2 at 52 
the call to "ft_multiplotTFR" took 0 seconds
the call to "ft_singleplotTFR" took 0 seconds
reading layout from file electrode_position32.mat
the call to "ft_prepare_layout" took 0 seconds
Warning: Some points fall outside the outline, please consider using another layout 
> In ft_plot_topo at 171
  In fieldtrip\private\topoplot_common at 731
  In ft_topoplotTFR at 192
  In TFanalysis_zhs_2 at 62 
Index exceeds matrix dimensions.


Error in ft_plot_topo (line 182)
    mask{i}(end+1, :) = mask{i}(1, :);                   % force them to be closed


Error in topoplot_common (line 731)
  ft_plot_topo(chanX,chanY,datavector,opt{:});


Error in ft_topoplotTFR (line 192)
[cfg] = topoplot_common(cfg, varargin{:});


Error in TFanalysis_zhs_2 (line 62)
ft_topoplotTFR(cfg, TFRhann);


Do you have any suggestion about it?
Thank you very much for your attention.


Kind Regards,
Hanson
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