New subject: mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.)

28 May 2021

      External Email - Use Caution
Dear Dear FreeSurfer Developers,
(We’re the message 3)
This happened to multiple subjects. Our computer got 16GB MHz DDR4 , We thought it met the requirements to run the module based on the documentation on  freesurfer wiki , or didn’t it? :(
Best regards,
Josephine
...
freesurfer-request@nmr.mgh.harvard.edu 於 2021年5月29日 上午12:03 寫道：
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Today's Topics:

(no subject) (Daniel Davidson Callow)
Hippocampal Subfield error (Daniel Davidson Callow)
Re: mri_hippocampal-subfields error: MATLAB existed for no
reason (Iglesias Gonzalez, Juan E.)
Re: Choosing projfrac/projdist and checking mri_vol2surf
output (M Pope)
Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.)
PVC to calculate myelin maps (Marina Fern?ndez)
Re: PVC to calculate myelin maps (Glasser, Matthew)
PVC to calculate myelin maps (Marina Fern?ndez)
Re: PVC to calculate myelin maps (Glasser, Matthew)
(no subject) (Francisca Ferreira)

Message: 1
Date: Fri, 28 May 2021 07:52:44 -0400
From: Daniel Davidson Callow dcallow@umd.edu
Subject: [Freesurfer] (no subject)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
   CAFMVdsfJ9Scx1sQ+CC6BMobLtKQT6501=vTR9KKxVA4OB_rOxg@mail.gmail.com
Content-Type: text/plain; charset="utf-8"
   External Email - Use Caution        

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/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oDU...
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
dcallow@umd.edu dcallow@gmail.com
443-254-6298

Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.)

#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux

Setting up environment variables

#1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux

Setting up environment variables