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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.edu
<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
PROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux compute-4-32.bswift.umd.edu
<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-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 $@#@FSLOADPOST
2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17
31.22 29.74 28.95
Linux compute-4-32.bswift.umd.edu
<http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVaVM-bCkayzZxY9xDU_KpcZcFWAPDqh90GDmfaCegId3XT6PKwKdcFIZXP27qvAGlubWjMrtSWPUClEYijiXXbemw4pG8RKDOZj6DPjOltVe5yMFHmf90ukT3OUKeqf7sTx70vaHCRaffDJe-yRzF5oO2Dnqy3JYjPkwjI1FW999MJQXWT6pjT1rnDxOkwbjKhl9FNrKXzV8OI9YJB12uI0m5B759UFLn4F9vrPog/http%3A%2F%2Fcompute-4-32.bswift.umd.edu>
2.6.32-754.35.1.el6.x86_64
#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT 2021
I am also getting a matlab_crash_dump file
------------------------------------------------------------------------
Segmentation violation detected at Thu May 27 21:51:52 2021
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Current Visual : None
Default Encoding : US-ASCII
GNU C Library : 2.12 stable
MATLAB Architecture: glnxa64
MATLAB Root : /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29
04:45:43 EDT 2020 x86_64
Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel
Software OpenGL : 0
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java
HotSpot(TM) 64-Bit Server VM mixed mode
Window System : No active display
Fault Count: 1
Abnormal termination:
Segmentation violation
Stack Trace (from fault):
[ 0] 0x00007f2b30f06213
/lib64/libpthread.so.0+00033299 pthread_join+00000035
[ 1] 0x00007f2a9f4d847d
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
2] 0x00007f2a9f4d8cac
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
3] 0x00007f2a9f5cae63
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
4] 0x00007f2a9f5af896
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
5] 0x00007f2a9f5a6b8d
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
6] 0x00007f2a9f5a6fd0
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
7] 0x00007f2a9f5aad00
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
8] 0x00007f2a9f5a5c3c
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
9] 0x00007f2a9f44fb03
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
10] 0x00007f2a9f42b9cc
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
11] 0x00007f2a9f42b132
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
12] 0x00007f2b21dcfc0a /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538
mexRunMexFile+00000090
[ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644
[ 14] 0x00007f2b21dcd414 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308
[ 15] 0x00007f2b232ff329 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
_ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70
/export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
[ 17] 0x00007f2b225bfe02 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
[ 18] 0x00007f2b225c2022 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
[ 19] 0x00007f2b225c7f87 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
[ 20] 0x00007f2b225c36ff /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
[ 21] 0x00007f2b225c4334 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
[ 22] 0x00007f2b2263952e /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
[ 23] 0x00007f2b232ff329 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
_ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70
/export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04053872
[ 25] 0x00007f2b225bfe02 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03726850
[ 26] 0x00007f2b225c2022 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03735586
[ 27] 0x00007f2b225c7f87 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03760007
[ 28] 0x00007f2b225c36ff /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03741439
[ 29] 0x00007f2b225c4334 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03744564
[ 30] 0x00007f2b2263952e /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+04224302
[ 31] 0x00007f2b232ff329 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+00791337
_ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0
/export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03910640
[ 33] 0x00007f2b225ec449 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03908681
[ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03137494
inCallFcnWithTrap+00000086
[ 35] 0x00007f2b225b3c0b /export/rel60_shadow/
glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+03677195
This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.
If this problem is reproducible, please submit a Service Request via:
http://secure-web.cisco.com/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oDUsy9FhA7GwO0ghIRuurPZncG6-zhlFrAY4VY2aJReGfBN8RZTuIOU6wmDTUghXHEP5BkbyHc8_vtCBJp-zOs_fNVzEV9sMAPfYeLzVn8oHPd9KBxN7WKzCC_d6TDceaO7Lp0-BGJpb2LlY2YFIup8Is3JddKjHfPknqA7Iw6cl6zmiNI9nmeOCX8z2z7AWJIPYKzlwUwhEs6EapI5BOlXjCbd034xSGJ57pwJmrw/http%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcontact_us%2F
A technical support engineer might contact you with further information.
Any insight or help you can provide is greatly appreciated.
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu <dcal...@gmail.com>
443-254-6298
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