Dear Allison,
The error happened in the old hippocampal subfield module. I would recommend that you used the new hippocampal subfield code in FreeSurfer 6.0. Having said that, if you really
want to run the 5.3 subfield version, Koen Van Leemput maybe knows what the problem might have been.
Kind regards,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Chen, Allison" <allisonchen@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 22 August 2017 at 21:06
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FW: CNDA update: Processing failed for SD10013_1
Hello Team,
I have run ”recon-all args -qcache -all -hippo-subfields” command, but there are some errors.
I used freesurfer 5.3 on CNDA:
Attached and below are the error information. There is no any problem with our image. Could you give me any suggestions?
Thanks a lot!
Allison
From: cnda-ops@nrg.wustl.edu [mailto:cnda-ops@nrg.wustl.edu]
Sent: Thursday, August 17, 2017 9:21 PM
To: Chen, Allison; cnda-ops@nrg.wustl.edu
Subject: CNDA update: Processing failed for SD10013_1
The pipeline Freesurfer 5.3 encountered an error.
The CNDA technical team is aware of the issue and will notify you when it has been resolved.
We appreciate your patience. Please contact cnda-ops@nrg.wustl.edu with questions or concerns.
The stdout and stderr log files are attached.
|
qc_rating |
1 |
|
workdir |
builddir/SD10013_1 |
|
logdir |
workdir/LOGS |
|
XNAT_CSRF |
7790fecf-8edf-41cc-8b26-caadb8150e06 |
|
email_csv_in |
|
|
freesurfer_subjectdir |
workdir/PROCESSED/SD10013_1 |
|
rawdir |
workdir/RAW |
|
id |
CNDA_E162884 |
|
paramsFile |
workdir/LOGS/SD10013_1.bashparams |
|
tempdir |
workdir/temp |
|
qc_rating_scale |
' |
|
scan_ids |
[3] |
|
recon_all_args |
-qcache -all -hippo-subfields |
|
freesurferdir |
workdir/PROCESSED |
|
adminemail |
|
|
host |
|
|
relaunch |
false |
|
use_manual_qc |
0 |
|
assessorId |
CNDA_E162884_freesurfer_20170817112729 |
|
label |
SD10013_1 |
|
format |
DICOM |
|
workflowid |
6438524 |
|
freesurfer_tempdir |
workdir/PROCESSED/temp |
|
project |
MEDEX |
|
builddir |
/data/CNDA/build/MEDEX/20170817_112717/restlaunch |
|
u |
2be260df-0fcb-4dda-9cdc-1ae13d9f02bd |
|
pwd |
******** |
|
environment |
LOCAL |
|
useremail |
|
|
xnatserver |
CNDA |
|
datestamp |
20170817112729 |
|
user |
2be260df-0fcb-4dda-9cdc-1ae13d9f02bd |
|
mailhost |
mail.nrg.wustl.edu |
|
userfullname |
g.chen |
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Level 2 Warning in ../include/gmm/gmm_precond_diagonal.h, line 57: The matrix has a zero on its diagonal
Time taken to solve the Levenberg-Marquardt system of equations: 0.09901
...done!
maximalDeformation: 67.1108
Transforming mesh
Done transforming mesh
Rasterizing Levenberg-Marquardt...
numberOfEntries: 24131
/nrgpackages/tools/freesurfer53-patch/bin/kvlSegmentHippocampalSubfields.sh: line 18: 400668 Segmentation fault (core dumped) kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt
Linux nrglab08.nrg.mir 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Jan 11 20:56:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SD10013_1 exited with ERRORS at Thu Aug 17 21:20:53 CDT 2017
For more details, see the log file /data/CNDA/build/MEDEX/20170817_112717/restlaunch/SD10013_1/PROCESSED/SD10013_1/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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+ die 'recon-all failed'
+ echo 'recon-all failed'
recon-all failed
+ exit 1
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