[FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace
Stolk, A.
a.stolk at fcdonders.ru.nl
Fri Jan 27 10:10:37 CET 2012
Hi Ion,
Thanks for providing the details. I cannot test run these commands myself as they point to your private dataset and not the example 'Subject01'. However, scanning through the text , it seems to me you have used the correct lines of code. Perhaps something may have gone wrong with the interactive volumealignment procedures, 3 times in total. Did you manually press the l, r, and n buttons when selecting the left and right ear, and nasion in the first and third interactive alignment steps? And, in contrast, did you press the a, p, and z buttons when selecting the anterior and posterior commi su res and an inter hemispheric point (see link in previous mail) in the second alignment step? This is the 'realign to talairach' part of the code.
Best regards,
Arjen
----- "Ion Lavado" <lavado at gmail.com> schreef:
> Van: "Ion Lavado" <lavado at gmail.com>
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Verzonden: Vrijdag 27 januari 2012 09:33:10
> Onderwerp: Re: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace
>
> Ok, thank you for your time Arjen. This is what i've done:
> %READ AND REALINGN
> mri = ft_read_mri('C:\Users\ilavado\Desktop\31_CW1AFMRI_ESG_ENDIKA_SANCHEZ_GOMEZ\1_028_t1_mpr_tra_p2_iso_20110314\31_CW1AFMRI_ESG_ENDIKA_SANCHEZ_GOMEZ_20110314_001_028_t1_mpr_tra_p2_iso.img');
> cfg = [];
> cfg.interactive = 'yes';
> cfg.coordsys = 'neuromag';
> mri_other = ft_volumerealign(cfg,mri);
> %RESLICING
> cfg = [];
> cfg.resolution=1;
> cfg.dim=[256 256 256];
> mrirs = ft_volumereslice(cfg, mri_other);
> save mrirs;
> %SEGMENTATION
> load mrirs;
> cfg = [];
> cfg.coordsys = 'neuromag';
> cfg.output={'skullstrip' 'brain'};
> seg = ft_volumesegment(cfg, mrirs)
> save seg seg;
> %REALING TO TALAIRACH
> load mrirs;
> cfg=[];
> cfg.method='interactive';
> cfg.coordsys = 'neuromag';
> mri_tal=ft_volumerealign(cfg,mrirs); %mrirs o mri_other???
> save mri_tal mri_tal
> seg.transform = mri_tal.transform;
> cfg = [];
> cfg.filename = 'Subject29_mri_freesurfer2';
> cfg.filetype = 'mgz';
> cfg.parameter = 'anatomy';
> ft_volumewrite(cfg, mri_tal);
> cfg.filename = 'Subject29masked2';
> ft_volumewrite(cfg, seg);
> THE I CREATE ALL THE FILES (WITH THE TUTORIAL COMMANDS) WITH FREESURFER with "Subject29masked2.mgz" and "Subject29_mri_freesurfer2.mgz"
> AND HERE IN THE SOURCE MODEL IS WHERE I GET THE PROBLEM.
>
> %CREATE THE MESH
>
bnd = ft_read_headshape('29_mri-oct-6-src.fif', 'format', 'mne_source');
figure;ft_plot_mesh(bnd);
>
%CO-REGISTRATION
>
mri_norm = ft_read_mri('/home/mlizarazu/public/Exchange/Mikel/Subject29/mri/orig-nomask.mgz');
cfg = [];
cfg.method = 'interactive';
mri_norm_ctf = ft_volumerealign(cfg, mri_norm);
>
>
mri_norm_ctf = ft_convert_units(mri_norm_ctf, 'cm');
T = mri_norm_ctf.transform*inv(mri_norm_ctf.transformorig);
bnd = ft_read_headshape('29_mri-oct-6-src.fif', 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
sourcespace = ft_transform_geometry(T, sourcespace);
> %VOLUME MODEL
> cfg = [];
> cfg.coordsys = 'spm';
> cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_norm);
> cfg = [];
> vol = ft_prepare_singleshell(cfg,seg);
> vol.bnd = ft_transform_geometry(T, vol.bnd);
> %PLOT
> figure;hold on;
> ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;
> ft_plot_mesh(sourcespace_ctf, 'edgecolor', 'none'); camlight
> When plotting i have the problem that you see in the photos... Hope we can solve this.
>
> Thank you.
> Best whises
> Ion
>
> 2012/1/26 Stolk, A. < a.stolk at fcdonders.ru.nl >
>
>
Hi Ion,
Could you specify some more details so we can reproduce your bug. Preferably by including a small test script with the same operations applied to the testdata (as in the tutorial).
Best regards,
Arjen
>
> ----- "Ion Lavado" < lavado at gmail.com > schreef:
> > Van: "Ion Lavado" < lavado at gmail.com >
> > Aan: "Email discussion list for the FieldTrip project" < fieldtrip at donders.ru.nl >
> > Verzonden: Donderdag 26 januari 2012 13:39:41
> > Onderwerp: Re: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace
>
> >
> > Thank you for your help. I realigned it to Tailarach prior to freesurfer processing. Any idea?
>
> >
Ion
> >
> > 2012/1/19 Stolk, A. < a.stolk at fcdonders.ru.nl >
> >
> >
Hi Ion,
Did you realign your anatomical image to Talairach space (and not accidentally to MNI space) prior to the processing with Freesurfer?
http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures
Best regards,
Arjen
> > ----- "Ion Lavado" < lavado at gmail.com > schreef:
> > > Van: "Ion Lavado" < lavado at gmail.com >
> > > Aan: fieldtrip at donders.ru.nl
> > > Verzonden: Donderdag 19 januari 2012 09:25:16
> > > Onderwerp: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace
>
> > >
> > > Hello, i'm trying a source reconstruction of event related fields using minimun-norm estimates and i get a problem with vol and sourcespace. When plot them together the vol doesn't fit the sourcespace. I adjunted in the mail two images where you can see what i get. It looks like that there isn't any problem of coordinate system also the units seem to be ok. I also procesed all the file with freesurfer so i suppose there is no problem with the orig-nomask.mgz.
>
Hope anyone can help me. Thank you very much.
> > >
Ion
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