Hi Zach,

Just to double check: your directory structure is:

FStests/CDN0001_MSB/CDN0001

So the following directory:

FStests/CDN0001_MSB/CDN0001/tmp

exists and is writable? For example, this command:

echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt

will create the file:

FStests/CDN0001_MSB/CDN0001/tmp/test.txt

Cheers,

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

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From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zachary Miller <mill5076@umn.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, December 21, 2020 at 12:14
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T1.sh Error

 

        External Email - Use Caution        

Hello,

 

I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below.

 

Thank you,

Zach

 

Command:

segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB

 

 

Output:

#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020

------------------------------------------

Setting up environment variables

---

LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64

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)

 

 

 

 

@#@FSTIME  2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64

@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35

Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

 

T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020

 

 

 

--

Zachary Miller

Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu

University of Minnesota | umn.edu

mill5076@umn.edu

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