External Email - Use Caution
Sorry, scratch that. Apparently it just didn’t realise that my subjects were in
a subdirectory in the subjects directory.
Running now.
Note to self: “Think before you click send”
Kind regards,
FREDA SCHEFFLER
Research Assistant / PhD Candidate
[email.jpg]
MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika
Tel: +27 21 938 9771
Email | E-pos: fre...@sun.ac.za
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Scheffler, F, Mev
[fre...@sun.ac.za]" <fre...@sun.ac.za>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 26 October 2018 at 18:24
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Error in segmentHA_T1.sh
External Email - Use Caution
Dear Freesurfer Developers
I’ve run recon-all -all on a batch of 20 subjects on a linux based high
performance computing setup and am now trying to run the segmentHA_T1 on them
as well.
It sets up the environment and then complains about myMRIread and Error in
segmentSubjectT1_autoEstimateAlveusML (line 157)
Here is the command line output:
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Fri Oct 26 18:06:27 SAST 2018
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is
<redacted, because I’m paranoid>
Error using myMRIread (line 16)
Error in myMRIread: temporary directory does not exist
Error in segmentSubjectT1_autoEstimateAlveusML (line 157)
@#@FSTIME 2018:10:26:18:06:27 run_segmentSubjectT1_autoEstimateAlveusML.sh N
13 e 107.33 S 6.58 U 8.77 P 14% M 145072 F 14363 R 298922 W 0 c 179 w 32314 I
33416 O 0 L 0.02 5.50 14.86
@#@FSLOADPOST 2018:10:26:18:08:14 run_segmentSubjectT1_autoEstimateAlveusML.sh
N 13 0.78 4.16 13.38
Linux cnode0070 3.10.0-514.6.1.el7.x86_64 #1 SMP Wed Jan 18 13:06:36 UTC 2017
x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Fri Oct 26 18:08:15 SAST 2018
What am I doing wrong here?
Thanks very much.
Kind regards,
FREDA SCHEFFLER
Research Assistant / PhD Candidate
[email.jpg]
MA Research Psychology
Faculty of Medicine and Health Sciences
Fakulteit Geneeskunde en Gesondheidswetenskappe
Universiteit Stellenbosch University
PO Box | Posbus 241, Cape Town | Kaapstad, 8000
Francie van Zijl Drive | -rylaan, Tygerberg, 7505
South Africa | Suid-Afrika
Tel: +27 21 938 9771
Email | E-pos: fre...@sun.ac.za
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