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) http://www.jeiglesias.com

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.

[cid:image001.png@01D62787.F791BD00]

Could you help me troubleshoot this problem?

Thank you! Soichi Hayashi