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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
