Dear Soichi,
Can you please double check that you’ve got writing permissions on your 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: Monday, May 4, 2020 at 09:24
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T1.sh fails with "Error in myMRIread: temporary directory does not exist"
External Email - Use Caution
Hello.
I am trying to run segmentHA_T1.sh right after successfully completing recon-all -all
I have a freesurfer output directory under my currently working directory inside ./output. So I ran this command.
$ segmentHA_T1.sh output .
When I do I run into the following error message.
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Mon May 4 09:16:43 EDT 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 elogin2 4.4.180-94.103-default #1 SMP Mon Aug 19 15:06:57 UTC 2019 (62f4295) x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Mon May 4 09:16:58 EDT 2020
For more details, see the log file ./output/scripts/hippocampal-subfields-T1.log
How can I correct this problem?
Soichi