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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 $args @#@FSTIME 2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 w 377770 I 48432510 O 1579840 L 5.28 3.10 2.20 @#@FSLOADPOST 2018:05:06:07:37:57 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49
With appreciation for your help, Best, Tamir
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Is it possible that it ran out of memory? Andrew, what do you think?
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tamir Eisenstein tamire1@mail.tau.ac.il Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, 6 May 2018 at 08:22 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem
External Email - Use Caution Hi FreeSurfer experts,
I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time points on FS 6.0, and it seemed working well while running. However, after about 10 hours of processing it "ended" with the following message, and no files have been created in any of the subject's /mri folders:
Applying LTAtransformInterp (resample_type 0) writing to discreteLabelsResampledT1_tp_1.mgz... numberOfLabels: 25 Rasterizing mesh...here: 25 /usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 103248 Killed "${exe_dir}"/SegmentSubfieldsT1Longitudinal $args @#@FSTIME 2018:05:05:21:24:27 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 e 36809.26 S 113.13 U 3327.28 P 9% M 1402760 F 150217 R 19897260 W 0 c 213280 w 377770 I 48432510 O 1579840 L 5.28 3.10 2.20 @#@FSLOADPOST 2018:05:06:07:37:57 /usr/local/freesurfer/bin/segmentSF_T1_long.sh N 7 6.10 6.21 4.49
With appreciation for your help, Best, Tamir
I’m not sure. How long do these runs usually take Eugenio? I’m noticing that the process only used 9% of the cpu, which is odd since it ran for 10+ hours Andrew
From: "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk Date: Tuesday, May 8, 2018 at 4:18 AM To: FS Help freesurfer@nmr.mgh.harvard.edu Cc: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem
External Email - Use Caution Is it possible that it ran out of memory? Andrew, what do you think?
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tamir Eisenstein tamire1@mail.tau.ac.il Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, 6 May 2018 at 08:22 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Longitudinal hippocampal subfields analysis problem
External Email - Use Caution Hi FreeSurfer experts,
I've tried running the longHippoSubfieldsT1.sh command on a subject with 2 time points on FS 6.0, and it seemed working well while running. However, after about 10 hours of processing it "ended" with the following message, and no files have been created in any of the subject's /mri folders:
Applying LTAtransformInterp (resample_type 0) writing to discreteLabelsResampledT1_tp_1.mgz... numberOfLabels: 25 Rasterizing mesh...here: 25 /usr/local/freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh: line 45: 103248 Killed "${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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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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Hoopes, Andrew -
Iglesias Gonzalez, Eugenio -
Tamir Eisenstein