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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
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