Hi Phoebe,
there is no corresponding volume, as the averaging is intrinsically surface-based.
cheers, Bruce
On Tue, 5 Apr 2005 orphoebe@polyu.edu.hk wrote:
Hi,
I used the following script in the old post to do the subject averaging of the surfaces. However, the 'T1' and 'orig' sub-directory under 'mri' of the 'average' are empty. Is there any way that I can convert the surface file (e.g. rh.orig) into CORs so that I can view the corresponding brain volume using TkMedit?
Thanks, Phoebe.
#!/bin/tcsh -ef
set SUBJECTS = (031204_wwk 031204_yts 040115_llk 040219_wly) # set SUBJECTS=($SUBJECTS) set average_subject=average if (-e $SUBJECTS_DIR/${average_subject} == 0) then mksubjdirs $SUBJECTS_DIR/${average_subject} else mkdir -p $SUBJECTS_DIR/${average_subject}/surf endif foreach hemi (lh rh) foreach s (orig white pial inflated) set echo=1 mris_make_average_surface -i 7 -o $s $hemi ${s}_avg sphere.reg ${average_subject} $SUBJECTS unset echo end cd $SUBJECTS_DIR/${average_subject}/surf pwd mris_smooth -n 5 ./${hemi}.white_avg ./$hemi.smoothwm mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_curvature -a 10 -w ./${hemi}.white_avg cp ${hemi}.white_avg.H ${hemi}.curv cp $CSURF_DIR/average/$hemi.sphere.reg . ln -s -f $hemi.sphere.reg $hemi.sphere set echo=1 mris_average_curvature -o $average_subject curv $hemi sphere.reg $SUBJECTS ./${hemi}.curv mris_average_curvature -o $average_subject sulc $hemi sphere.reg $SUBJECTS ./${hemi}.sulc mris_average_curvature -o $average_subject thickness $hemi sphere.reg $SUBJECTS ./${hemi}.thickness end cp $SUBJECTS_DIR/$SUBJECTS[1]/mri/T1/COR-.info $SUBJECTS_DIR/${average_subject}/mri/T1
Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer