Hi Nárlon,
Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix will make it into the next v7 patch. As you mentioned, this error occurs at random, so in the meantime, you can mitigate this by either:
- Rerunning recons until they don’t fail (not recommended) - Rerunning these failing recons without the parallel flag enabled - Patching your version of recon-all by commenting out or removing the following (line 4217) from $FREESURFER_HOME/bin/recon-all: if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel)
Hope that helps, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Boa Sorte Silva, Narlon" narlon.silva@ubc.ca Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, December 14, 2020 at 7:31 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!
External Email - Use Caution Hi there, Hope this finds you well
I have noticed the following error for some of my runs:
@# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64
recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020
Here are details of the computer and FS version I am using:
* OS: macOS Mojave (10.14.4) * FS: 7.1.1
It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem.
I was wondering if you guys would be able to help?
Thank you Nárlon Cássio
Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon
External Email - Use Caution
Thanks Andrew!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon
On Dec 16, 2020, at 7:18 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote:
[CAUTION: Non-UBC Email] Hi Nárlon,
Unfortunately, this is a known bug with parallel processing in FS 7.1.1. A fix will make it into the next v7 patch. As you mentioned, this error occurs at random, so in the meantime, you can mitigate this by either:
- Rerunning recons until they don’t fail (not recommended) - Rerunning these failing recons without the parallel flag enabled - Patching your version of recon-all by commenting out or removing the following (line 4217) from $FREESURFER_HOME/bin/recon-all: if($OMP_NUM_THREADS > 1) set cmd = ($cmd --parallel)
Hope that helps, Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva@ubc.camailto:narlon.silva@ubc.ca> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, December 14, 2020 at 7:31 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Recon-all error: MatrixMultiply: m1 is null!
External Email - Use Caution Hi there, Hope this finds you well
I have noticed the following error for some of my runs:
@# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64
recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020
Here are details of the computer and FS version I am using:
* OS: macOS Mojave (10.14.4) * FS: 7.1.1
It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem.
I was wondering if you guys would be able to help?
Thank you Nárlon Cássio
Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon
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Hoopes, Andrew