Dear Eugenio,
I am writing because I am getting a mkdir error when I try to run the FreeSurfer 6.0 hippocampal subfields segmentation. I tried moving my installation of freesurfer to a local directory where I have write permission and I also made sure I had write permission in my subject's directory. Do you have any idea what might be causing the error? Thanks in advance!
Command and error pasted below: recon-all -s 1001 -sd . -hippocampal-subfields-T1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 Actual FREESURFER_HOME /opt/freesurfer6 -rw-rw-r-- 1 rolsen buchsbaum_lab 549732 Feb 3 09:35 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/recon-all.log Linux gateway.neuroinfo.rri 2.6.32-279.9.1.el6.x86_64 #1 SMP Tue Sep 25 21:43:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Wed Feb 3 09:35:59 EST 2016
/opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 left
See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied
Error in segmentSubjectT1_autoEstimateAlveusML (line 113)
MATLAB:MKDIR:OSError #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Wed Feb 3 09:36:07 EST 2016
/opt/freesurfer6/bin/segmentSF_T1.sh /opt/freesurfer6/MCRv80 /opt/freesurfer6 1001 /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0 right
See log file: /scratch/buchsbaum_lab/rolsen/FaceRepfMRIYoungers/FS_Version6.0/1001/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/opt/freesurfer6/MCRv80/runtime/glnxa64:/opt/freesurfer6/MCRv80/bin/glnxa64:/opt/freesurfer6/MCRv80/sys/os/glnxa64:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/opt/freesurfer6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/opt/lib.exported Warning: application is running on a locale different from the original platform locale. Error using mkdir Permission denied
Error in segmentSubjectT1_autoEstimateAlveusML (line 113)
MATLAB:MKDIR:OSError
#------------------------------------------
Started at Wed Feb 3 09:35:56 EST 2016 Ended at Wed Feb 3 09:36:14 EST 2016 #@#%# recon-all-run-time-hours 0.005 recon-all -s 1001 finished without error at Wed Feb 3 09:36:15 EST 2016 done