[FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace

[Ion Lavado]

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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>> > > fieldtrip at donders.ru.nl
>> > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
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>> >
>
>
> >
>
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