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)’. (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 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.
