Load the fsaverage surface in tksurfer (say lh.inflated) then load the patch we distribute with fsaverage (I think it's called something like lh.cortex.patch.flat) with file->load patch. Then load whatever overlay you want in the same way you would on the inflated surface
Cheers Bruce > On May 19, 2014, at 10:06 PM, Caka <qiongmin...@gmail.com> wrote: > > > Hi Doug, > Thanks for your suggestion on tksurfer, it works. > I would like to map all the subjects into a flat map because I am curious > about the 2-D thickness patterns between different groups. I think there will > be some distinctions. > But if I flatten fsaverage, how can I map everyone?s 3D surface onto the > fsaverage?s 2D map? Is there a command? > > Best, > Qiongmin > > > > >> On 05/13/2014 11:19 PM, Caka wrote: >> Dear Doug and all, I have already done two things: (1) 'recon-all? to >> the segmentation for 140 subjects; (2) surface registration to >> fsaverage template for 1 subject using: mri_surf2surf --hemi lh >> --srcsubject sub001 --srcsurfval thickness --src_type curv >> --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I >> have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) >> Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How >> can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, >> but a dark scene was shown, nothing can be found. I also used >> ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz >> $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred >> like ?ERROR: number of vertices in >> /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match >> surface (163842, 132230)?. > Try tksurfer fsaverage lh inflated -aparc -overlay > sub001-thickness-lh.mgz -fminmax .01 4 >> (2) After the registration, I want to flatten the surface of curvature >> or thickness into a full plane. The wiki says we should first specify >> 5 vertices and cut the whole area without the midline region, then >> ?kris_flatten? can be used. Indeed, this procedure requires quite a >> lot manually operation. I am wondering if there are some automatically >> commands that can do this flatten projects for 140 subject? Any reply >> would be really appreciated! Qiongmin >> _______________________________________________ Freesurfer mailing >> list Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > I don't think so, though I think bruce was working on something. You > could just flatten fsaverage and then map everyone to fsaverage (as you > have already done). Why do you want to map everyone to a flat map? > > doug > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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