Dear Ferdi, It is really hard for us to know why you‘re getting such a weird error (segfault of kvlAutoCrop) in a submitted job when you don’t get it in an interactive session … You will have to look into the peculiarities of the submission system to see what is changing from one setting to the other (maybe some permissions?). What version of FreeSurfer are you exactly using? Kind regards, /Eugenio

Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 11 Jan 2017, at 07:49, Ferdi van de Kamp <ferdivdkamp@gmail.commailto:ferdivdkamp@gmail.com> wrote:

Hi all,

I'm trying to perform the longitudinal hippocampal subfields processing on a cluster.

When I simply access a core on the cluster directly and use it to run the hippocampal subfields it will run, but if I try to submit the process to the cluster, it will either throw errors as I have pasted below or stop after some registration steps.

The recon-all steps have run on the cluster (submitted) without problems.

Some notes: As I'm testing things, the data is not in the original folder, so the path names in recon-all log are not correct, but if that is the problem I'd imagine it would be a problem for both submitting and direct processing.

Matlab runtime is installed, though in a separate folder, linking it in the way described on the Freesurfer website.

The problem persists no matter how much memory I allocate to the process (20GB RAM was the highest I tried).

Kind regards,

Ferdi van de Kamp

#-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) left Wed Jan 4 03:06:40 CET 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/ Warning: Unable to open display 'localhost:10.0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG of Base Point /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop: line 3: 65931 Segmentation fault (core dumped) kvlAutoCrop.bin "$@" /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask.mgz 6 >/dev/null: Segmentation fault gzip: /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in SegmentSubfieldsT1Longitudinal (line 228)

MATLAB:badSwitchExpression @#@FSTIME 2017:01:04:03:06:40 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 e 12.17 S 0.80 U 3.63 P 36% M 680932 F 530 R 118193 W 0 c 10055 w 5994 I 439360 O 194448 L 4.58 4.59 4.59 @#@FSLOADPOST 2017:01:04:03:06:52 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 4.72 4.62 4.60 #-------------------------------------------- #@# Longitudinal Hippocampal Subfields processing (T1) right Wed Jan 4 03:06:52 CET 2017 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/ Warning: Unable to open display 'localhost:10.0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG of Base Point /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop: line 3: 66086 Segmentation fault (core dumped) kvlAutoCrop.bin "$@" /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_right//hippoAmygBinaryMask.mgz 6 >/dev/null: Segmentation fault gzip: /exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)

Error in myMRIread>myMRIread_aux (line 92)

Error in myMRIread (line 63)

Error in SegmentSubfieldsT1Longitudinal (line 228)

MATLAB:badSwitchExpression @#@FSTIME 2017:01:04:03:06:52 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 e 6.50 S 0.64 U 3.59 P 65% M 678904 F 1 R 119401 W 0 c 3877 w 3509 I 65600 O 194416 L 4.72 4.62 4.60 @#@FSLOADPOST 2017:01:04:03:06:58 /usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh N 8 4.84 4.65 4.61

If you have used results from this software for a publication, please cite:

Iglesias J.E., Van Leemput K., Augustinack J., Insausti R., Fischl B., Reuter M., Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases, Neuroimage, in press. http://dx.doi.org/10.1016/j.neuroimage.2016.07.020

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