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) 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: 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