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.
* User: achenmailto:allisonchen@wustl.edu * Project: MEDEX * Experiment: SD10013_1 * Pipeline Step: RUN_FS
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.
PIPELINE PARAMETERS qc_rating
1
workdir
builddir/SD10013_1
logdir
workdir/LOGS
XNAT_CSRF
7790fecf-8edf-41cc-8b26-caadb8150e06
email_csv_in
cnda-ops@nrg.wustl.edumailto:cnda-ops@nrg.wustl.edu
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
cnda-ops@nrg.wustl.edumailto:cnda-ops@nrg.wustl.edu
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
allisonchen@wustl.edumailto:allisonchen@wustl.edu
xnatserver
CNDA
datestamp
20170817112729
user
2be260df-0fcb-4dda-9cdc-1ae13d9f02bd
mailhost
mail.nrg.wustl.edu
userfullname
g.chen
TAIL stdout
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 TAIL stderr
rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. rm: No match. + die 'recon-all failed' + echo 'recon-all failed' recon-all failed + exit 1
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