Akio, You should just run -autorecon2 instead of -subcortseg in order to get the subcortical segmentation.
Nick > Hi Freesurfer experts, > > After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test > -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error. > > Then, when I ran "recon-all -s test -subcortseg", I got the following > error: > > ========== > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg > --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --ctab > /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test > sysname Linux > hostname dhcp006 > machine x86_64 > user yamamoto > UseRobust 0 > atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) > MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): > could not open file > ========== > > I encountered this error in v5.2.0, and am still having the same error > in v5.3.0. > Is this a known issue? > > I attached the recon-all.log file. Any help is greatly appreciated. > > Best, > Akio > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
