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
It sounds like you just want to do a standard group analysis. Look in the wiki for instructions and tutorials. Basically, you use mris_preproc to create a stack of your subjects thickenss maps, then use mri_surf2surf to smooth, then mri_glmfit to do the group analysis
doug
On 05/15/2014 09:55 PM, Caka 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 mailto: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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Caka -
Douglas N Greve