you do not need to run recon-all -all on the tutorial subjects, as is stated in the tutorial. its already been processed.
On Tue, 2012-05-08 at 19:16 +0000, Natacha Beck, Ms wrote:
Thank you for your reply,
I try to run the first command
"recon-all -subjid OAS2_0001_MR1 -all"
and I receive the following trace:
Tue May 08 user1 /Applications/freesurfer/subjects/long-tutorial =>recon-all -subjid OAS2_0001_MR1 -all INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-v5.1.0-20110517 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/long-tutorial Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 user1 admin 390840 Jun 24 2011 /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/scripts/recon-all.log Darwin host.ca 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer/ Previous: /space/freesurfer/centos4.0_x86_64/stable5 #-------------------------------------------- #@# MotionCor Tue May 8 15:02:39 EDT 2012 Found 2 runs /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/001.mgz /Applications/freesurfer/subjects/long-tutorial/OAS2_0001_MR1/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... if: Expression Syntax.
Seems like FreeSurfer has a problem with the inputs 001.mgz and 002.mgz because it can't reach them.
Natacha