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