It depends heavily on the number of time points… I’d say ~20 mins per time point and side.

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Date: Tuesday, 8 May 2018 at 16:27
To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

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.iglesias@ucl.ac.uk>
Date: Tuesday, May 8, 2018 at 4:18 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Hoopes, Andrew" <AHOOPES@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-bounces@nmr.mgh.harvard.edu> on behalf of Tamir Eisenstein <tamire1@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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