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:

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: 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

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

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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