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-boun...@nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva,
Narlon" <narlon.si...@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
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