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
External Email - Use Caution
Hi there,
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
Running hemis in parallel
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?
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