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