Dear Bruce, Doug and all, Thanks for your suggestion, it helped a lot. (1) I load the fsaverage surface (lh.inflated) in tksurfer, and then load the fsaverage patch (lh.cortex.patch.flat). The flat map was shown for several seconds, and then an error occurred and tksurfer was shut down. The terminal said: ‘tksurfer.bin:tnl/t_vertex.c:407: update_input_ptrs: Assertion ‘a[j].inputstride == vptr-> stride’ failed. Abort(core dumped)’. Could you give me some advice? I use a 'CentOS release 6.2' system. The freesurfer is ‘freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0’.
(2) Indeed, I want to flatten all cortical thickness surfaces of 140 subjects onto the ‘lh.cortex.patch.flat’ of fsaverage. I just don’t understand your idea how to do this. After I load ‘lh.cortex.patch.flat’ of fsaverage, the tksurfer only shows this flat map (now it lasted for several seconds and crashed), so how can I ' load whatever overlay you want in the same way you would on the inflated surface’? Does it mean that I load the individual flat map on the individual inflated surface? But I haven’t got the individual flat map yet. (3) I am wondering if there are some table recording the transformation relationships between the fsaverage surface vertices and the flat map vertices? If so, then I think all I need to do is extracting the cortical thickness value of every vertex in individual inflated surface, and then putting into the corresponding vertex in the flat map. Thank you very much! Best regards, Qiongmin ------------------------------------------------------------------------------------------------------------------------------------------------- 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 > ______________________________
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