I’m not sure. How long do these runs usually take Eugenio? I’m noticing that
the process only used 9% of the cpu, which is odd since it ran for 10+ hours
Andrew
From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
Date: Tuesday, May 8, 2018 at 4:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem
External Email - Use Caution
Is it possible that it ran out of memory? Andrew, what do you think?
--
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-boun...@nmr.mgh.harvard.edu> on behalf of Tamir Eisenstein
<tami...@mail.tau.ac.il>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 6 May 2018 at 08:22
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem
External Email - Use Caution
Hi FreeSurfer experts,
I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time
points on FS 6.0, and it seemed working well while running.
However, after about 10 hours of processing it "ended" with the following
message, and no files have been created in any of the subject's /mri folders:
Applying LTAtransformInterp (resample_type 0)
writing to discreteLabelsResampledT1_tp_1.mgz...
numberOfLabels: 25
Rasterizing mesh...here: 25
/usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45:
103248 Killed "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args
@#@FSTIME 2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N
7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280
w 377770 I 48432510 O 1579840 L 5.28 3.10 2.20
@#@FSLOADPOST 2018:05:06:07:37:57
/usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49
With appreciation for your help,
Best,
Tamir
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