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: <[email protected]> on behalf of "Chen, Allison" <[email protected]> Reply-To: Freesurfer support list <[email protected]> Date: Tuesday, 22 August 2017 at 21:06 To: "[email protected]" <[email protected]> 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: https://cnda.wustl.edu 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: [email protected] [mailto:[email protected]] Sent: Thursday, August 17, 2017 9:21 PM To: Chen, Allison; [email protected] Subject: CNDA update: Processing failed for SD10013_1 The pipeline Freesurfer 5.3 encountered an error. * User: achen<mailto:[email protected]> * 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 [email protected] 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 [email protected]<mailto:[email protected]> 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 [email protected]<mailto:[email protected]> host https://cnda.wustl.edu/ 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 [email protected]<mailto:[email protected]> 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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