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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:
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 ? 2021?5?29? ??12:03 ??? Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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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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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-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
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
$@#@FSLOADPOST
2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 31.22 29.74 28.95 Linux compute-4-32.bswift.umd.edu <
http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzVa...
2.6.32-754.35.1.el6.x86_64 #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT
2021
I am also getting a matlab_crash_dump file
Segmentation violation detected at Thu May 27 21:51:52 2021
Configuration: Crash Decoding : Disabled Current Visual : None Default Encoding : US-ASCII GNU C Library : 2.12 stable MATLAB Architecture: glnxa64 MATLAB Root : /export/rel60_shadow/ glue.umd.edu/software/matlab/2014b/Linux MATLAB Version : 8.4.0.150421 (R2014b) Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 04:45:43 EDT 2020 x86_64 Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel Software OpenGL : 0 Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode Window System : No active display
Fault Count: 1
Abnormal termination: Segmentation violation
Stack Trace (from fault): [ 0] 0x00007f2b30f06213 /lib64/libpthread.so.0+00033299 pthread_join+00000035 [ 1] 0x00007f2a9f4d847d
/tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[
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