Hi Anita mris_anatomical_stats isn't a flag to recon-all. It is it's own binary that you should call directly from the command line.
For the znzTAGskip error, this was a bug we briefly had but hasn't been around in a long time. Can you try downloading a new version? What version did you use to create the wm.mgz? That might be the problem cheers Bruce On Fri, 21 Mar 2014, Anita van Loenhoud wrote: > Hi Bruce, > > See below. Thank you! > > Anita > > First I tried: > > aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/ > 0050$ mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a > label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial > > INFO: assuming MGZ format for volumes. > computing statistics for each annotation in label/lh.aparc.annot. > reading volume > /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/mri/wm.mgz... > znzTAGskip: tag=1818326118, failed to calloc 541878272 bytes! > > Cannot allocate memory > > Then I tried the following: > > aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/ > 0050$ recon-all -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f > stats/lh.aparc.stats -b -a label/lh.aparc.annot -c label/aparc.annot.ctab > 0050 lh pial > > ERROR: Flag mris_anatomical_stats unrecognized. > -autorecon3 -subjid 0050 mris_anatomical_stats -mgz -f stats/lh.aparc.stats > -b -a label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial > Linux somerenserver.herseninstituut.knaw.nl 2.6.32-431.5.1.el6.x86_64 #1 SMP > Wed Feb 12 00:41:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 0050 exited with ERRORS at Fri Mar 21 14:49:53 CET 2014 > > > > > _______________________________________________ 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.
