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<p>Dear Susmita, you may check that your sensor positions extracted from the .con file are in the same co-ordinate frame as the MRI. Using the KIT/Yokogawa system software to co-register the sensor locations and the headshape/mri might be a necessary first
step as "<span>Unlike other systems, the Yokogawa system software does not automatically analyze its sensorlocations relative to fiducial coils</span>":-
<a href="http://www.fieldtriptoolbox.org/getting_started/yokogawa" class="OWAAutoLink">
http://www.fieldtriptoolbox.org/getting_started/yokogawa</a><br>
</p>
<p>The way we deal with it is to first do coregistration in MEG160 - the KIT/Yokogawa software, and then export the sensor locations which are then in headspace. Then coregistration with the MRI brings sensors and MRI into alignment.</p>
<p>This may or may not be your problem. Good luck.<br>
</p>
<p><br>
</p>
<p>Paul</p>
<p><br>
</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> fieldtrip-bounces@science.ru.nl <fieldtrip-bounces@science.ru.nl> on behalf of fieldtrip-request@science.ru.nl <fieldtrip-request@science.ru.nl><br>
<b>Sent:</b> Wednesday, 19 October 2016 6:15 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> fieldtrip Digest, Vol 71, Issue 24</font>
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Today's Topics:<br>
<br>
1. Re: error with ft_appenddata (Wong-Barnum, Mona)<br>
2. Separating MEG/EEG data (Wong-Barnum, Mona)<br>
3. Re: Separating MEG/EEG data (Tzvetan Popov)<br>
4. Re: Separating MEG/EEG data (Stephen Whitmarsh)<br>
5. Orientation of headmodel with respect to sensors poisition<br>
(Susmita Sen)<br>
6. Re: Orientation of headmodel with respect to sensors<br>
poisition (Schoffelen, J.M. (Jan Mathijs))<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 18 Oct 2016 22:45:15 +0000<br>
From: "Wong-Barnum, Mona" <mona@sdsc.edu><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] error with ft_appenddata<br>
Message-ID: <DFD88583-7786-4F22-81C5-E6C8ACADF966@mail.ucsd.edu><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
Thanks Jan for your help!<br>
<br>
I ended up doing the following steps:<br>
<br>
addpath /path/to/fieldtrip<br>
ft_defaults<br>
<br>
cfg1 = [];<br>
cfg1.dataset = '1.fif';<br>
data1 = ft_preprocessing ( cfg1 );<br>
<br>
cfg2 = [];<br>
cfg2.dataset = '2.fif';<br>
data2 = ft_preprocessing ( cfg2 );<br>
<br>
cfg3 = [];<br>
cfg3.dataset = '3.fif';<br>
data3 = ft_preprocessing ( cfg3 );<br>
<br>
cfg=[];<br>
data = ft_appenddata ( cfg, data1, data2, data3 )<br>
<br>
save stitched.mat data -v7.3<br>
<br>
<br>
Which worked.<br>
<br>
If you see any other problem that I may have missed, please feel free to educate me.<br>
<br>
Thanks!<br>
<br>
Mona<br>
<br>
<br>
On Oct 5, 2016, at 5:21 PM, Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen@donders.ru.nl<mailto:jan.schoffelen@donders.ru.nl>> wrote:<br>
<br>
Hi Mona,<br>
<br>
If you directly use the output of ft_read_data as input into ft_appenddata, it won?t work. The reason is that ft_appenddata expects in the input (data#) matlab structures that are generated by ft_preprocessing. Ft_read_data outputs a numeric data matrix, which
is only part of the ft_preprocessing generated output. Have you something like this yet?:<br>
<br>
cfg = [];<br>
cfg.dataset = ;somefiffile.fif?;<br>
data = ft_preprocessing(cfg);<br>
<br>
Best<br>
<br>
Jan-Mathijs<br>
<br>
On 05 Oct 2016, at 23:06, Wong-Barnum, Mona <mona@sdsc.edu<mailto:mona@sdsc.edu>> wrote:<br>
<br>
<br>
I?m getting a runtime error with ft_appenddata:<br>
<br>
data = ft_appenddata ( cfg, data1, data2, data3, data4, data5, data6, data7, data8, data9, data10, data11, data12, data13, data14 )<br>
<br>
<br>
Error using ft_checkdata (line 468) This function requires raw+comp or raw data as input.<br>
<br>
Error in ft_appenddata (line 80) varargin{i} = ft_checkdata(varargin{i}, 'datatype', {'raw+comp', 'raw'}, 'feedback', 'no');<br>
<br>
Error in stitch (line 45) data = ft_appenddata ( cfg, data1, data2, data3, data4, data5, data6, data7, data8, data9, data10, data11, data12, data13, data14, data15, data16, data17, data18, data19, data20 )<br>
<br>
Error in run (line 96) evalin('caller', [script ';']);<br>
<br>
I have Neuromag data and was able to read the files into data# using ft_read_data.<br>
<br>
In the documentation, it says cfg can be empty so I declared it by "cfg = ??;? before the ft_appenddata call; is that ok?<br>
<br>
Any help/suggstions/tips regarding the ft_appenddata error would be appreciated. Thanks!<br>
<br>
Mona<br>
<br>
<br>
*********************************************<br>
Mona Wong<br>
Web & iPad Application Developer<br>
San Diego Supercomputer Center<br>
<br>
"To handle yourself, use your head;<br>
to handle others, use your heart."<br>
<br>
-- Eleanor Roosevelt<br>
*********************************************<br>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
fieldtrip@donders.ru.nl<mailto:fieldtrip@donders.ru.nl><br>
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<br>
_______________________________________________<br>
fieldtrip mailing list<br>
fieldtrip@donders.ru.nl<mailto:fieldtrip@donders.ru.nl><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
*********************************************<br>
Mona Wong<br>
Web & iPad Application Developer<br>
San Diego Supercomputer Center<br>
<br>
"Strive not to be a success, but<br>
rather to be of value."<br>
--- Albert Einstein<br>
*********************************************<br>
<br>
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<br>
Message: 2<br>
Date: Tue, 18 Oct 2016 23:17:15 +0000<br>
From: "Wong-Barnum, Mona" <mona@sdsc.edu><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] Separating MEG/EEG data<br>
Message-ID: <5B37A434-D55B-4C44-A2F7-A1D0D0E8467A@mail.ucsd.edu><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
I have Elekta Neuromag .fif files which contains MEG and EEG data. What steps do I need to do to separate the MEG from EEG and the 3 different MEG sensor data (magnetometer, 2 gradiometer)?<br>
<br>
I have been looking through the FieldTrip documentation but haven?t found what I need. All help is appreciated.<br>
<br>
thanks,<br>
Mona<br>
<br>
<br>
*********************************************<br>
Mona Wong<br>
Web & iPad Application Developer<br>
San Diego Supercomputer Center<br>
<br>
"Strive not to be a success, but<br>
rather to be of value."<br>
--- Albert Einstein<br>
*********************************************<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 19 Oct 2016 07:14:27 +0200<br>
From: Tzvetan Popov <tzvetan.popov@uni-konstanz.de><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Separating MEG/EEG data<br>
Message-ID: <37D50E5D-6836-48B1-8DCC-6BFD903CF21D@uni-konstanz.de><br>
Content-Type: text/plain; charset=windows-1252<br>
<br>
Dear Mona,<br>
<br>
please have a look here: <a href="http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting">
http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting</a><br>
<br>
In the section ?segment and read MEG data? there is a call to ft_rejectvisual for example where the different MEG sensors are separated. Further down the tutorial deals also with the EEG part of the analysis.<br>
Good luck<br>
tzvetan<br>
<br>
<br>
Am 19.10.2016 um 01:17 schrieb Wong-Barnum, Mona <mona@sdsc.edu>:<br>
<br>
> <br>
> I have Elekta Neuromag .fif files which contains MEG and EEG data. What steps do I need to do to separate the MEG from EEG and the 3 different MEG sensor data (magnetometer, 2 gradiometer)?<br>
> <br>
> I have been looking through the FieldTrip documentation but haven?t found what I need. All help is appreciated.<br>
> <br>
> thanks,<br>
> Mona<br>
> <br>
> <br>
> *********************************************<br>
> Mona Wong<br>
> Web & iPad Application Developer<br>
> San Diego Supercomputer Center<br>
> <br>
> "Strive not to be a success, but<br>
> rather to be of value."<br>
> --- Albert Einstein<br>
> *********************************************<br>
> <br>
> <br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> fieldtrip@donders.ru.nl<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Wed, 19 Oct 2016 07:22:17 +0200<br>
From: Stephen Whitmarsh <stephen.whitmarsh@gmail.com><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Separating MEG/EEG data<br>
Message-ID:<br>
<CAFrxm=zrLtX32DEiGY0kpd8vsTMNwu5iUzqz78K1CxnaHqNOCw@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Mona,<br>
<br>
To add to Tzvetan:<br>
<br>
- You can in many FieldTrip functions specify on which channels you want to<br>
work (cfg.channel), e.g. in ft_preprocessing.<br>
- You can also split the data later using ft_selectdata, e.g.:<br>
<br>
cfg = []<br>
cfg.channel = 'MEG';<br>
data_MEG = ft_selectdata(cfg,data_combined);<br>
<br>
cfg = []<br>
cfg.channel = 'EEG';<br>
data_EEG = ft_selectdata(cfg,data_combined);<br>
<br>
- To selecting magnetometers or gradiometers you can use:<br>
cfg.channel = 'MEG*1'<br>
cfg.channel = {'MEG*2', 'MEG*3'}<br>
<br>
Cheers,<br>
Stephen<br>
<br>
<br>
On 19 October 2016 at 01:17, Wong-Barnum, Mona <mona@sdsc.edu> wrote:<br>
<br>
><br>
> I have Elekta Neuromag .fif files which contains MEG and EEG<br>
> data. What steps do I need to do to separate the MEG from EEG and the 3<br>
> different MEG sensor data (magnetometer, 2 gradiometer)?<br>
><br>
> I have been looking through the FieldTrip documentation but<br>
> haven?t found what I need. All help is appreciated.<br>
><br>
> thanks,<br>
> Mona<br>
><br>
><br>
> *********************************************<br>
> Mona Wong<br>
> Web & iPad Application Developer<br>
> San Diego Supercomputer Center<br>
><br>
> "Strive not to be a success, but<br>
> rather to be of value."<br>
> --- Albert Einstein<br>
> *********************************************<br>
><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> fieldtrip@donders.ru.nl<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
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<br>
Message: 5<br>
Date: Wed, 19 Oct 2016 11:32:25 +0530<br>
From: Susmita Sen <susmitasen.ece@gmail.com><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: [FieldTrip] Orientation of headmodel with respect to sensors<br>
poisition<br>
Message-ID:<br>
<CAOD6VW90TygYzKfWMKwns+mxRG=Z_FspP2J_HYV52Z2WU_Hn_g@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear FieldTrip community,<br>
<br>
I am constructing headmodel using standard mri data. The meg data that I am<br>
working with is recorded using yokogawa system. I have used the following<br>
code.<br>
<br>
<br>
load('standard_mri.mat')<br>
<br>
cfg = [];<br>
cfg.coordsys = 'yokogawa';<br>
cfg.viewresult = 'yes';<br>
cfg.snapshot = 'yes';<br>
cfg.fiducial.nas = mri.hdr.fiducial.mri.nas; %position of nasion<br>
cfg.fiducial.lpa = mri.hdr.fiducial.mri.lpa; %position of LPA<br>
cfg.fiducial.rpa = mri.hdr.fiducial.mri.rpa; %position of RPA<br>
cfg.fiducial.zpoint = [ 91 109 107];<br>
[mri_realigned] = ft_volumerealign(cfg,mri);<br>
<br>
%% SEGMENTATION<br>
<br>
cfg = [];<br>
cfg.output = 'brain';<br>
segmentedmri = ft_volumesegment(cfg, mri_realigned);<br>
<br>
%% create headmodel<br>
<br>
cfg = [];<br>
cfg.method='singleshell';<br>
vol = ft_prepare_headmodel(cfg, segmentedmri);<br>
<br>
%% visualize<br>
<br>
vol = ft_convert_units(vol,'cm');<br>
grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load grad<br>
<br>
figure<br>
ft_plot_sens(grad, 'style', '*b');<br>
<br>
hold on<br>
ft_plot_vol(vol);<br>
<br>
However, I am facing a problem when I plotting headmodel with the sensors.<br>
I noticed that the orienations of headmodel and sensors are not aligned. I<br>
am attaching the figure with this mail. I would be very greatful if any<br>
could kindly give me suggestions how to align these two.<br>
<br>
[image: Inline image 1]<br>
<br>
[image: Inline image 2]<br>
<br>
<br>
Thanks and Regards,<br>
Susmita Sen<br>
Research Scholar<br>
Audio and Bio Signal Processing Lab.<br>
E & ECE Dept.<br>
IIT Kharagpur<br>
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<br>
Message: 6<br>
Date: Wed, 19 Oct 2016 07:15:34 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br>
To: FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] Orientation of headmodel with respect to<br>
sensors poisition<br>
Message-ID: <B8B40FFC-C8B6-47AA-B01F-B8A33CA31148@donders.ru.nl><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Susmita,<br>
<br>
It looks as if there is a discrepancy between the definition of the coordinate system according to fieldtrip (see ft_headcoordinates in fieldtrip/utilities, where it seems that an ALS axis system is imposed), when specifying cfg.coordsys = ?yokogawa?, and the
coordinate system of the sensors in your data file (which is probably RAS). I could not find any documentation about the ?yokogawa?-convention (which is probably the reason why the yokogawa-entry in the table on
<a href="http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined">
http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined</a> is empty). Perhaps one of the Yokogawa-users on this list could chime in to enlighten you, or you could check the system?s documentation to find out what the
expected.<br>
<br>
The easy solution would be to register the mri to an RAS-based coordinate system (e.g. use cfg.coordsys = ?neuromag? for ft_volumerealign), but I would recommend to get to the bottom of this, and provide a principled solution. Once you have found out about
the conventional coordinate system for yokogawa systems, it would be great if you could update the table on (<a href="http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined">http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined</a>).
Note, that if it turns out to be that there is no specific convention (e.g. site-specific ALS or RAS or so) it is worth documenting, too.<br>
<br>
Good luck<br>
<br>
Jan-Mathijs<br>
<br>
J.M.Schoffelen<br>
Senior Researcher<br>
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br>
<br>
<br>
<br>
On 19 Oct 2016, at 08:02, Susmita Sen <susmitasen.ece@gmail.com<mailto:susmitasen.ece@gmail.com>> wrote:<br>
<br>
Dear FieldTrip community,<br>
<br>
I am constructing headmodel using standard mri data. The meg data that I am working with is recorded using yokogawa system. I have used the following code.<br>
<br>
<br>
load('standard_mri.mat')<br>
<br>
cfg = [];<br>
cfg.coordsys = 'yokogawa';<br>
cfg.viewresult = 'yes';<br>
cfg.snapshot = 'yes';<br>
cfg.fiducial.nas = mri.hdr.fiducial.mri.nas; %position of nasion<br>
cfg.fiducial.lpa = mri.hdr.fiducial.mri.lpa; %position of LPA<br>
cfg.fiducial.rpa = mri.hdr.fiducial.mri.rpa; %position of RPA<br>
cfg.fiducial.zpoint = [ 91 109 107];<br>
[mri_realigned] = ft_volumerealign(cfg,mri);<br>
<br>
%% SEGMENTATION<br>
<br>
cfg = [];<br>
cfg.output = 'brain';<br>
segmentedmri = ft_volumesegment(cfg, mri_realigned);<br>
<br>
%% create headmodel<br>
<br>
cfg = [];<br>
cfg.method='singleshell';<br>
vol = ft_prepare_headmodel(cfg, segmentedmri);<br>
<br>
%% visualize<br>
<br>
vol = ft_convert_units(vol,'cm');<br>
grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load grad<br>
<br>
figure<br>
ft_plot_sens(grad, 'style', '*b');<br>
<br>
hold on<br>
ft_plot_vol(vol);<br>
<br>
However, I am facing a problem when I plotting headmodel with the sensors. I noticed that the orienations of headmodel and sensors are not aligned. I am attaching the figure with this mail. I would be very greatful if any could kindly give me suggestions how
to align these two.<br>
<br>
<Headmodel_sens1.jpg><br>
<br>
<Headmodel_sens2.jpg><br>
<br>
<br>
Thanks and Regards,<br>
Susmita Sen<br>
Research Scholar<br>
Audio and Bio Signal Processing Lab.<br>
E & ECE Dept.<br>
IIT Kharagpur<br>
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