External Email - Use Caution Hello. I am testing freesurfer 7.0.0 with segmentHA processing.
I've run recon-all successfully, and now I am trying to run "segmentHA_T1.sh". When I do, it generates the following error message. $ segmentHA_T1.sh output . > ------------------------------ > USER user > HOST slurm3-compute2 > PROCESSID 14892 > PROCESSOR x86_64 > OS Linux > ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > ------------------------------ > > freesurfer-linux-centos7_x86_64-7.0.0-20200429-3a03ebd > > setenv SUBJECTS_DIR . > cd /export/prod/5eb5c3986d02b3164bd1ad8b/5eb5c8506d02b3677ed1add8 > /usr/local/freesurfer/bin/segmentHA_T1.sh output . > #-------------------------------------------- > #@# Hippocampal Subfields processing (T1) left Sat May 9 00:23:06 UTC 2020 > ------------------------------------------ > Setting up environment variables > --- > LD_LIBRARY_PATH is > .:/lib64:/usr/local/freesurfer/MCRv84//runtime/glnxa64:/usr/local/freesurfer/MCRv84//bin/glnxa64:/usr/local/freesurfer/MCRv84//sys/os/glnxa64:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/.singularity.d/libs > Registering imageDump.mgz to hippocampal mask from ASEG > Error using myMRIread (line 16) > Error in myMRIread: temporary directory does not exist > Error in segmentSubjectT1_autoEstimateAlveusML (line 157) > Linux slurm3-compute2 4.15.0-99-generic #100-Ubuntu SMP Wed Apr 22 > 20:32:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux > T1 hippocampal subfields exited with ERRORS at Sat May 9 00:23:16 UTC 2020 I am not sure what it means by "temporary directory does not exist", but I see that it's written some files under my freesurfer subject output directory. [image: image.png] Could you help me troubleshoot this problem? Thank you! Soichi Hayashi
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