Hi all I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag (e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippocampal-subfieldsT1.log indicated the following: "Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf" (see below for the full content of hippocampal-subfieldsT1.log). I tried to run only the hippocampal subfield recon-all again (e.g. "recon-all -s recon-all -all -subjid SPS01-1910_pre_lazar hippocampal-subfields-T1") and received the same error message. I tried to look in the indicated folder ("/autofs/cluster/freesurfer/centos6_x86_64/dev/bin") and found a file named segmentSubjectT1_autoEstimateAlveusML (without the ctf extension). I do not know if this is the source of the problem.
My FREESURFER_HOME directory is /autofs/cluster/freesurfer/centos6_x86_64/stable6/. My SUBJECTS_DIR is /autofs/cluster/lazar/Projects/jonathan-miracle/unpacking-dicoms/SUBJECTS_DIR/.
Any suggestions? (full hippocampal-subfieldsT1.log below) Thank you! Jonathan
hippocampal-subfieldsT1.log content:
#-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jun 16 09:58:23 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Thu Jun 16 09:58:26 EDT 2016 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/stable6/MCRv80/runtime/glnxa64:/usr/local/freesurfer/stable6/MCRv80/bin/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/stable6/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf