[FieldTrip] Orientation of headmodel with respect to sensors poisition (Susmita Sen)
Susmita Sen
susmitasen.ece at gmail.com
Wed Oct 19 17:39:38 CEST 2016
Thanks a lot. I will try that.
Thanks and Regards,
Susmita Sen
Research Scholar
Audio and Bio Signal Processing Lab.
E & ECE Dept.
IIT Kharagpur
On Wed, Oct 19, 2016 at 4:01 PM, Paul Sowman <paul.sowman at mq.edu.au> wrote:
> 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 "Unlike other systems,
> the Yokogawa system software does not automatically analyze its
> sensorlocations relative to fiducial coils":- http://www.fieldtriptoolbox.
> org/getting_started/yokogawa
>
> 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.
>
> This may or may not be your problem. Good luck.
>
>
> Paul
>
>
> *Paul F Sowman*
>
> ARC DECRA Fellow
>
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> *From:* fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>
> on behalf of fieldtrip-request at science.ru.nl <
> fieldtrip-request at science.ru.nl>
> *Sent:* Wednesday, 19 October 2016 6:15 PM
> *To:* fieldtrip at science.ru.nl
> *Subject:* fieldtrip Digest, Vol 71, Issue 24
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> Today's Topics:
>
> 1. Re: error with ft_appenddata (Wong-Barnum, Mona)
> 2. Separating MEG/EEG data (Wong-Barnum, Mona)
> 3. Re: Separating MEG/EEG data (Tzvetan Popov)
> 4. Re: Separating MEG/EEG data (Stephen Whitmarsh)
> 5. Orientation of headmodel with respect to sensors poisition
> (Susmita Sen)
> 6. Re: Orientation of headmodel with respect to sensors
> poisition (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 18 Oct 2016 22:45:15 +0000
> From: "Wong-Barnum, Mona" <mona at sdsc.edu>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] error with ft_appenddata
> Message-ID: <DFD88583-7786-4F22-81C5-E6C8ACADF966 at mail.ucsd.edu>
> Content-Type: text/plain; charset="utf-8"
>
>
> Thanks Jan for your help!
>
> I ended up doing the following steps:
>
> addpath /path/to/fieldtrip
> ft_defaults
>
> cfg1 = [];
> cfg1.dataset = '1.fif';
> data1 = ft_preprocessing ( cfg1 );
>
> cfg2 = [];
> cfg2.dataset = '2.fif';
> data2 = ft_preprocessing ( cfg2 );
>
> cfg3 = [];
> cfg3.dataset = '3.fif';
> data3 = ft_preprocessing ( cfg3 );
>
> cfg=[];
> data = ft_appenddata ( cfg, data1, data2, data3 )
>
> save stitched.mat data -v7.3
>
>
> Which worked.
>
> If you see any other problem that I may have missed, please feel free to
> educate me.
>
> Thanks!
>
> Mona
>
>
> On Oct 5, 2016, at 5:21 PM, Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>> wrote:
>
> Hi Mona,
>
> 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?:
>
> cfg = [];
> cfg.dataset = ;somefiffile.fif?;
> data = ft_preprocessing(cfg);
>
> Best
>
> Jan-Mathijs
>
> On 05 Oct 2016, at 23:06, Wong-Barnum, Mona <mona at sdsc.edu<mailto:mona@
> sdsc.edu>> wrote:
>
>
> I?m getting a runtime error with ft_appenddata:
>
> data = ft_appenddata ( cfg, data1, data2, data3, data4, data5, data6,
> data7, data8, data9, data10, data11, data12, data13, data14 )
>
>
> Error using ft_checkdata (line 468) This function requires raw+comp or raw
> data as input.
>
> Error in ft_appenddata (line 80) varargin{i} = ft_checkdata(varargin{i},
> 'datatype', {'raw+comp', 'raw'}, 'feedback', 'no');
>
> 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 )
>
> Error in run (line 96) evalin('caller', [script ';']);
>
> I have Neuromag data and was able to read the files into data# using
> ft_read_data.
>
> In the documentation, it says cfg can be empty so I declared it by "cfg =
> ??;? before the ft_appenddata call; is that ok?
>
> Any help/suggstions/tips regarding the ft_appenddata error would be
> appreciated. Thanks!
>
> Mona
>
>
> *********************************************
> Mona Wong
> Web & iPad Application Developer
> San Diego Supercomputer Center
>
> "To handle yourself, use your head;
> to handle others, use your heart."
>
> -- Eleanor Roosevelt
> *********************************************
>
> _______________________________________________
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>
> *********************************************
> Mona Wong
> Web & iPad Application Developer
> San Diego Supercomputer Center
>
> "Strive not to be a success, but
> rather to be of value."
> --- Albert Einstein
> *********************************************
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 18 Oct 2016 23:17:15 +0000
> From: "Wong-Barnum, Mona" <mona at sdsc.edu>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Separating MEG/EEG data
> Message-ID: <5B37A434-D55B-4C44-A2F7-A1D0D0E8467A at mail.ucsd.edu>
> Content-Type: text/plain; charset="utf-8"
>
>
> 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)?
>
> I have been looking through the FieldTrip documentation but
> haven?t found what I need. All help is appreciated.
>
> thanks,
> Mona
>
>
> *********************************************
> Mona Wong
> Web & iPad Application Developer
> San Diego Supercomputer Center
>
> "Strive not to be a success, but
> rather to be of value."
> --- Albert Einstein
> *********************************************
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 19 Oct 2016 07:14:27 +0200
> From: Tzvetan Popov <tzvetan.popov at uni-konstanz.de>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Separating MEG/EEG data
> Message-ID: <37D50E5D-6836-48B1-8DCC-6BFD903CF21D at uni-konstanz.de>
> Content-Type: text/plain; charset=windows-1252
>
> Dear Mona,
>
> please have a look here: http://www.fieldtriptoolbox.org/tutorial/natmeg/
> dipolefitting
>
> 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.
> Good luck
> tzvetan
>
>
> Am 19.10.2016 um 01:17 schrieb Wong-Barnum, Mona <mona at sdsc.edu>:
>
> >
> > 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)?
> >
> > I have been looking through the FieldTrip documentation but
> haven?t found what I need. All help is appreciated.
> >
> > thanks,
> > Mona
> >
> >
> > *********************************************
> > Mona Wong
> > Web & iPad Application Developer
> > San Diego Supercomputer Center
> >
> > "Strive not to be a success, but
> > rather to be of value."
> > --- Albert Einstein
> > *********************************************
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 19 Oct 2016 07:22:17 +0200
> From: Stephen Whitmarsh <stephen.whitmarsh at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Separating MEG/EEG data
> Message-ID:
> <CAFrxm=zrLtX32DEiGY0kpd8vsTMNwu5iUzqz78K1CxnaHqNOCw at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Mona,
>
> To add to Tzvetan:
>
> - You can in many FieldTrip functions specify on which channels you want to
> work (cfg.channel), e.g. in ft_preprocessing.
> - You can also split the data later using ft_selectdata, e.g.:
>
> cfg = []
> cfg.channel = 'MEG';
> data_MEG = ft_selectdata(cfg,data_combined);
>
> cfg = []
> cfg.channel = 'EEG';
> data_EEG = ft_selectdata(cfg,data_combined);
>
> - To selecting magnetometers or gradiometers you can use:
> cfg.channel = 'MEG*1'
> cfg.channel = {'MEG*2', 'MEG*3'}
>
> Cheers,
> Stephen
>
>
> On 19 October 2016 at 01:17, Wong-Barnum, Mona <mona at sdsc.edu> wrote:
>
> >
> > 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)?
> >
> > I have been looking through the FieldTrip documentation but
> > haven?t found what I need. All help is appreciated.
> >
> > thanks,
> > Mona
> >
> >
> > *********************************************
> > Mona Wong
> > Web & iPad Application Developer
> > San Diego Supercomputer Center
> >
> > "Strive not to be a success, but
> > rather to be of value."
> > --- Albert Einstein
> > *********************************************
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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> ------------------------------
>
> Message: 5
> Date: Wed, 19 Oct 2016 11:32:25 +0530
> From: Susmita Sen <susmitasen.ece at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Orientation of headmodel with respect to sensors
> poisition
> Message-ID:
> <CAOD6VW90TygYzKfWMKwns+mxRG=Z_FspP2J_HYV52Z2WU_Hn_g at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear FieldTrip community,
>
> 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.
>
>
> load('standard_mri.mat')
>
> cfg = [];
> cfg.coordsys = 'yokogawa';
> cfg.viewresult = 'yes';
> cfg.snapshot = 'yes';
> cfg.fiducial.nas = mri.hdr.fiducial.mri.nas; %position of nasion
> cfg.fiducial.lpa = mri.hdr.fiducial.mri.lpa; %position of LPA
> cfg.fiducial.rpa = mri.hdr.fiducial.mri.rpa; %position of RPA
> cfg.fiducial.zpoint = [ 91 109 107];
> [mri_realigned] = ft_volumerealign(cfg,mri);
>
> %% SEGMENTATION
>
> cfg = [];
> cfg.output = 'brain';
> segmentedmri = ft_volumesegment(cfg, mri_realigned);
>
> %% create headmodel
>
> cfg = [];
> cfg.method='singleshell';
> vol = ft_prepare_headmodel(cfg, segmentedmri);
>
> %% visualize
>
> vol = ft_convert_units(vol,'cm');
> grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load
> grad
>
> figure
> ft_plot_sens(grad, 'style', '*b');
>
> hold on
> ft_plot_vol(vol);
>
> 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.
>
> [image: Inline image 1]
>
> [image: Inline image 2]
>
>
> Thanks and Regards,
> Susmita Sen
> Research Scholar
> Audio and Bio Signal Processing Lab.
> E & ECE Dept.
> IIT Kharagpur
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> ------------------------------
>
> Message: 6
> Date: Wed, 19 Oct 2016 07:15:34 +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] Orientation of headmodel with respect to
> sensors poisition
> Message-ID: <B8B40FFC-C8B6-47AA-B01F-B8A33CA31148 at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Susmita,
>
> 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 http://www.fieldtriptoolbox.
> org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined 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.
>
> 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 (
> http://www.fieldtriptoolbox.org/faq/how_are_the_different_
> head_and_mri_coordinate_systems_defined). 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.
>
> Good luck
>
> Jan-Mathijs
>
> J.M.Schoffelen
> Senior Researcher
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
>
>
> On 19 Oct 2016, at 08:02, Susmita Sen <susmitasen.ece at gmail.com<mailto:
> susmitasen.ece at gmail.com>> wrote:
>
> Dear FieldTrip community,
>
> 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.
>
>
> load('standard_mri.mat')
>
> cfg = [];
> cfg.coordsys = 'yokogawa';
> cfg.viewresult = 'yes';
> cfg.snapshot = 'yes';
> cfg.fiducial.nas = mri.hdr.fiducial.mri.nas; %position of nasion
> cfg.fiducial.lpa = mri.hdr.fiducial.mri.lpa; %position of LPA
> cfg.fiducial.rpa = mri.hdr.fiducial.mri.rpa; %position of RPA
> cfg.fiducial.zpoint = [ 91 109 107];
> [mri_realigned] = ft_volumerealign(cfg,mri);
>
> %% SEGMENTATION
>
> cfg = [];
> cfg.output = 'brain';
> segmentedmri = ft_volumesegment(cfg, mri_realigned);
>
> %% create headmodel
>
> cfg = [];
> cfg.method='singleshell';
> vol = ft_prepare_headmodel(cfg, segmentedmri);
>
> %% visualize
>
> vol = ft_convert_units(vol,'cm');
> grad = ft_read_sens('D:\Data\all\raw_preproc_data\raw\ari.con'); % load
> grad
>
> figure
> ft_plot_sens(grad, 'style', '*b');
>
> hold on
> ft_plot_vol(vol);
>
> 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.
>
> <Headmodel_sens1.jpg>
>
> <Headmodel_sens2.jpg>
>
>
> Thanks and Regards,
> Susmita Sen
> Research Scholar
> Audio and Bio Signal Processing Lab.
> E & ECE Dept.
> IIT Kharagpur
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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