Multiple subjects or all of them?
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
On May 28, 2021, at 12:26, 林鈺庭 ytlin923@g.ntu.edu.tw wrote:
External Email - Use CautionDear 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： Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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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 CautionHello,
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