[FieldTrip] Source Reconstruction
Sarang S. Dalal
sarang at cfin.au.dk
Wed Mar 8 11:34:03 CET 2017
Hi Ainsley,
You might consider realigning your MEG to your MRI, rather than the
other way around. Our group typically does it this way to also simplify
some other aspects of our pipeline, in particular, to simplify (re-)use
of BEM head models and plotting the final source maps on the
participant's own MRI or the MNI template.
You can find examples of our scripts on github:
https://github.com/meeg-cfin/nemolab
Check out basics/nemo_mriproc.m -- you may need to add your particular
yokogawa system to line 45. (Note that I've tested this procedure on
Elekta, CTF, and 4D/BTi data, but not yet Yokogawa.)
An example of how to put it all the pipeline pieces together for a
basic LCMV source analysis and visulization of ERF data is given in:
basics/nemo_sourcelocER.m
Best wishes,
Sarang
On Wed, 2017-03-08 at 08:15 +0000, Schoffelen, J.M. (Jan Mathijs)
wrote:
> Hi Ainsley,
>
> I have never worked with ‘yokogawa’ data myself, so I can’t be of
> much help. The documentation you point to is already several years
> old, and appears not to have been actively maintained. Most likely
> the error you get is caused by incompatibility between the current
> version of the FieldTrip code, and the example code provided. Perhaps
> someone that has recently done coregistration between anatomical data
> and yokogawa data can chime in?
>
> Best wishes,
> Jan-Mathijs
>
>
> > On 08 Mar 2017, at 09:03, Ainsley Temudo <ainsley.temudo at nyu.edu>
> > wrote:
> >
> > Hi Jan-Mathijs
> > Thanks for getting back to me so quickly. I originally used
> > Ft_sensoralign, but I got the error messages one of which said
> > 'FT_SENSORREALIGN is deprecated, please use FT_ELECTRODEREALIGN
> > instead' so thats why I used electrode realign instead, even though
> > it's MEG data.
> >
> > I've been following this page to do the realignment.
> >
> > http://www.fieldtriptoolbox.org/getting_started/yokogawa?s[]=yokoga
> > wa
> >
> > if I use sensorrealign how should I deal with these error
> > messages?
> >
> > Undefined function or variable 'lab'.
> >
> > Error in channelposition (line 314)
> > n = size(lab,2);
> >
> > Error in ft_datatype_sens (line 328)
> > [chanpos, chanori, lab] = channelposition(sens);
> >
> > Error in ft_sensorrealign (line 212)
> > elec_original = ft_datatype_sens(elec_original); % ensure up-to-
> > date sensor description (Oct 2011)
> >
> >
> > is there another way to realign my anatomical with my MEG sensors
> > without using ft_sensorrealign?
> >
> > Thanks,
> > Ainsley
> >
> > On Wed, Mar 8, 2017 at 11:26 AM, Schoffelen, J.M. (Jan Mathijs) <ja
> > n.schoffelen at donders.ru.nl> wrote:
> > > Hi Ainsley,
> > >
> > > Why would you want to use sensorrealign/electroderealign since
> > > you have MEG-data? The former functions may be needed for EEG
> > > electrodes, not for MEG sensors.
> > >
> > > Best wishes,
> > > Jan-Mathijs
> > >
> > >
> > > J.M.Schoffelen, MD PhD
> > > Senior Researcher, VIDI-fellow - PI, language in interaction
> > > Telephone: +31-24-3614793
> > > Physical location: room 00.028
> > > Donders Centre for Cognitive Neuroimaging, Nijmegen,
> > > The Netherlands
> > >
> > >
> > > > On 08 Mar 2017, at 07:52, Ainsley Temudo <ainsley.temudo at nyu.ed
> > > > u> wrote:
> > > >
> > > > Hi FieldTrip Experts,
> > > >
> > > > I am trying to perform source reconstruction, and I am having
> > > > trouble with coregistering my anatomical with the sensors. The
> > > > MEG system we're using is Yokogawa and the anatomical is a
> > > > NIFTI file. I get some errors when using ft_sensorrealign and
> > > > ft_electroderealign. I will go through the steps I took before
> > > > getting to this stage, as maybe I have done something wrong.
> > > >
> > > > first I read in my MRI and determine the coordinate system
> > > > which is LPS.
> > > >
> > > > mriunknown = ft_read_mri('WMCP1011+22+t1mprage.nii');
> > > > mri = ft_determine_coordsys(mriunknown, 'interactive','yes')
> > > >
> > > > next I realign to the CTF coordinate system by marking the NAS
> > > > LPA, RPA
> > > >
> > > > cfg = [];
> > > > cfg.method = 'interactive';
> > > > cfg.coordsys = 'ctf';
> > > > mri_ctf = ft_volumerealign(cfg, mir);
> > > >
> > > > I read in the sensor information and added in the coordinates
> > > > for the marker positions. we have five marker positions, the
> > > > three I picked were the left and right ear markers and the
> > > > middle forehead marker.
> > > >
> > > > grad=ft_read_sens('srcLocTest01_FT_01.con');
> > > >
> > > >
> > > > grad.fid.pnt(1,:) = [96.07 3.11 -5.32]./10;
> > > > grad.fid.pnt(2,:) = [11.13 75.50 -78.23]./10;
> > > > grad.fid.pnt(3,:) = [8.50 -75.09 -64.60]./10;
> > > >
> > > > grad.fid.label = {'NAS' 'LPA' 'RPA'};
> > > >
> > > > I then put the template marker point cordinates into
> > > > the configuration which were taken from the mri_ctf
> > > >
> > > > cfg = [];
> > > > cfg.method = 'fiducial';
> > > > cfg.target.pnt(1,:) = [91.1 3.0 49.2]./10;
> > > > cfg.target.pnt(2,:) = [-0.1 70.5 0.0]./10;
> > > > cfg.target.pnt(3,:) = [0.1 -70.5 0.0]./10;
> > > >
> > > > cfg.target.label = {'NAS' 'LPA' 'RPA'};
> > > >
> > > > grad_aligned = ft_sensorrealign(cfg, grad);
> > > >
> > > > when I use ft_sensorrealign I get the following errors :
> > > >
> > > > Undefined function or variable 'lab'.
> > > >
> > > > Error in channelposition (line 314)
> > > > n = size(lab,2);
> > > >
> > > > Error in ft_datatype_sens (line 328)
> > > > [chanpos, chanori, lab] = channelposition(sens);
> > > >
> > > > Error in ft_sensorrealign (line 212)
> > > > elec_original = ft_datatype_sens(elec_original); % ensure up-
> > > > to-date sensor description (Oct 2011)
> > > >
> > > >
> > > > when I use ft_electroderealign I get the following errors:
> > > >
> > > > Error using ft_fetch_sens (line 192)
> > > > no electrodes or gradiometers specified.
> > > >
> > > > Error in ft_electroderealign (line 195)
> > > > elec_original = ft_fetch_sens(cfg);
> > > >
> > > >
> > > > Hope you can help me figure out why I'm getting these errors.
> > > > Thanks,
> > > > Ainsley
> > > > _______________________________________________
> > > > fieldtrip mailing list
> > > > fieldtrip at donders.ru.nl
> > > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> > >
> > >
> > > J.M.Schoffelen, MD PhD
> > > Senior Researcher, VIDI-fellow - PI, language in interaction
> > > Telephone: +31-24-3614793
> > > Physical location: room 00.028
> > > Donders Centre for Cognitive Neuroimaging, Nijmegen,
> > > The Netherlands
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> >
> >
> >
> > --
> > Ainsley Temudo
> > Research Assistant
> > Sreenivasan Lab
> > NYU Abu Dhabi
> > Office Tel (UAE): +971 2 628 4764
> > Mobile (UAE): +971 56 664 6952
> >
> > NYU Abu Dhabi, Saadiyat Campus
> > P.O. Box 129188
> > Abu Dhabi, United Arab Emirates
> > _______________________________________________
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> > fieldtrip at donders.ru.nl
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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