Hello,
I am running into errors when running
segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1
Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is an output from the error log.
------------------------------
USER dcallow
HOST
compute-4-32.bswift.umd.eduPROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux
compute-4-32.bswift.umd.edu 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
------------------------------
#--------------------------------------------
#@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT 2021
------------------------------------------
Setting up environment variables
---
INFO: error loading libraries in default configuration, trying with MCR libraries only
LD_LIBRARY_PATH is .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering norm.mgz to additional volume
makeIsotropic WARNING: not different enough, won't reslice!
No more processes.
ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh for reading
ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh as MGH
Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' not found.
[^H> In myMRIread at 64
In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H
Attempt to reference field of non-structure array.
Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211)
MATLAB:nonStrucReference
@#@FSTIME 2021:05:27:21:39:51 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U 8.61 P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L $@#@FSLOADPOST 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 31.22 29.74 28.95
Linux
compute-4-32.bswift.umd.edu 2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
I am also getting a matlab_crash_dump file
------------------------------------------------------------------------
Segmentation violation detected at Thu May 27 21:51:52 2021
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : US-ASCII
GNU C Library : 2.12 stable
MATLAB Architecture: glnxa64
MATLAB Root : /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64
Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
Software OpenGL : 0
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Any insight or help you can provide is greatly appreciated.
Daniel CallowPhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298