Uuummm this is funny. A directory “hippoSF_T1_v21_left” should have been created under tmp, but it isn’t there. Are you sure you have writing permissions for the subject directory?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Soichi Hayashi <hayashis@iu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, May 8, 2020 at 21:53
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T1.sh outputs "Error using myMRIread (line 16)"
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.
Could you help me troubleshoot this problem?
Thank you!
Soichi Hayashi