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Sure, what is the best way to share it with you? and which folders/files should I send?

On Fri, May 28, 2021 at 3:28 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
It seems the linear registration is dying. Would you mind sharing the subject, please?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On May 28, 2021, at 12:20, Daniel Davidson Callow <dcallow@umd.edu> wrote:

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Hello Juan,

I am using data from the HCP aging dataset which has a T1 and a high-resolution hippocampal scan (T2). 

Yes, it does seem that the T2 and T1's are roughly aligned to each other. It seems like it has something to do with the creation of the  tmp/hippoSF_T1T2_v21_highres_left/ folder where the program is expecting something to be produced that is not there/hasn't been produced.

Again, here is an example of the code output/error.

@ linenum = 1
cd /data/bswift-1/dcallow/aging/freesurfer
set subj= ( HCA8587705_V1_MR )
rm: No match.
rm -rf /a/ha-nfs-2-ib/export/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/IsRunning.lh+rh
cd /data/bswift-1/dcallow/aging/freesurfer
echo HCA8587705_V1_MR
HCA8587705_V1_MR
segmentHA_T2.sh HCA8587705_V1_MR /data/bswift-1/dcallow/aging/imaging/HCA8587705_V1_MR/unprocessed/TSE_HiResHp/HCA8587705_V1_MR_TSE_HiResHp.nii.gz highres 1
#--------------------------------------------
#@# Hippocampal Subfields processing (T1+T2) left Fri May 28 12:05:35 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/bswif$Registering norm.mgz to additional volume
No more processes.
ERROR: could not open /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh for reading
ERROR: loading /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh as MGH
Warning: File '/data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/tmp/hippoSF_T1T2_v21_highres_left/41244773_norm__502687.mgh' not found.
[^H> In myMRIread at 64
  In segmentSubjectT1T2_autoEstimateAlveusML at 186]^H
Attempt to reference field of non-structure array.

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 188)
MATLAB:nonStrucReference
@#@FSTIME  2021:05:28:12:05:35 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 7.49 S 0.61 U 6.79 P 98% M 283156 F 0 R 84320 W 0 c 2392 w 9596 I 0 O 85080 L 5$@#@FSLOADPOST 2021:05:28:12:05:42 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 60.45 53.15 38.08
Linux compute-4-33.bswift.umd.edu 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux

T2 hippocampal subfields exited with ERRORS at Fri May 28 12:05:42 EDT 2021

For more details, see the log file /data/bswift-1/dcallow/aging/freesurfer/HCA8587705_V1_MR/scripts/hippocampal-subfields-T2.highres.log


Any ideas what might be causing this error. Again, it seems to be working for a small subset of participants however, the majority are failing with this error.
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298



On Fri, May 28, 2021 at 9:32 AM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Dear Daniel,

Are the T2s and T1s roughly aligned in RAS (physical coordinates)? In other words: do they (roughly) overlap when you open them together in Freeview?

Cheers,

/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
On May 28, 2021, at 07:53, Daniel Davidson Callow <dcallow@umd.edu> wrote:

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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
PROCESSID 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

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:
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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
443-254-6298

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Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298