New subject: mri_hippocampal-subfields error: MATLAB exited for no reason

8 Jun 2021

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Dear Developer and Eugenio,
Huge thanks for your help in the previous emails. We finally completed the
analysis. However, when we run the code to gather the volumes, it shows no
error but we can't find the path of the file either in FreeSurfer root
(/application/freesurfer/subjects) or in the subject data
direction(/data/S013). I'm wondering if there is any way to set the writing
path for this process. Could you provide some advice? Thank you!
*The terminal looks like this:*
*[root@2981d0ea233a data]# quantifyHAsubregions.sh hippoSf T1 results.txt
/data/S013Gathering results from subjects in:    /data/S013 Using the
prefix name:    hippoSfUsing the suffix name:    T1And writing them to:
 results.txt *
Best regards,
Josephine
freesurfer-request@nmr.mgh.harvard.edu 於 2021年5月29日 週六 下午3:26寫道：
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Today's Topics:

Re: mri_hippocampal-subfields error: MATLAB exited        for     no
reason (Iglesias Gonzalez, Juan E.) (Iglesias Gonzalez, Juan E.)
Re: Hippocampal Subfield error (Daniel Davidson Callow)
Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.)
Re: Hippocampal Subfield error (Daniel Davidson Callow)
mri_glmfit-sim with grf (ERROR: need --csd with   --csd-out)
(Di?genes Bispo)
Group comparison with MD (Antti Cajanus)

Message: 1
Date: Fri, 28 May 2021 19:29:14 +0000
From: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu
Subject: Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB
        exited  for     no reason (Iglesias Gonzalez, Juan E.)
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID: 7A66B3DD-56D6-4754-B9B5-84A215B1F480@mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Multiple subjects or all of them?
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1GdciW0unJf79By6yzNdaCZgdWfXJEeLsraM57FUyfY3trPR...
...
On May 28, 2021, at 12:26, ??? ytlin923@g.ntu.edu.tw wrote:
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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 ? 2021?5?29? ??12:03 ???
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or, via email, send a message with subject or body 'help' to
  freesurfer-request@nmr.mgh.harvard.edu
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When replying, please edit your Subject line so it is more specific
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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"
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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-8zCzVa...
...
...
PROCESSID 4033
PROCESSOR x86_64
OS Linux
Linux compute-4-32.bswift.umd.edu
<
http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVa...
...
...
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
...
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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
...
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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
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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-8zCzVa...
...
...
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

the majority fail to execute. Here is an output from the error log.

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

2021

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

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

Setting up environment variables

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.

#@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 EDT 2021

Setting up environment variables

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

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