[FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace
Magyari, Lilla
Lilla.Magyari at mpi.nl
Fri Jan 27 15:17:34 CET 2012
hi Ion,
yes, the tutorial script was written and tested in the following way:
you have to align your volume to the ctf coordinate system (doesn't
matter what was its original coordinate system),
then reslice this re-aligned volume, then segment the resliced volume,
then re-align to talairach the resliced volume (that has been re-aligned
to ctf before).
I hope it will work out.
Lilla
Ion Lavado wrote:
> I think the problem is in the first steps, where i used neuromag
> coordinates... and i have to work in CTF and then to Talairach... i'll
> try it againg.
>
> 2012/1/27 Ion Lavado <lavado at gmail.com <mailto:lavado at gmail.com>>
>
> 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
> <mailto: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 <mailto:lavado at gmail.com>>
> schreef:
> > Van: "Ion Lavado" <lavado at gmail.com <mailto:lavado at gmail.com>>
> > Aan: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl <mailto: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
> <mailto: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
> <mailto:lavado at gmail.com>> schreef:
> > > Van: "Ion Lavado" <lavado at gmail.com
> <mailto:lavado at gmail.com>>
> > > Aan: fieldtrip at donders.ru.nl
> <mailto: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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>
>
> >
>
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