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 -- 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.
