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Many thanks for your assistance. Very helpful to know it is not a general
problem with ARM or Mac. I tried exporting OMP_NUM_THREADS=4 but unfortunately
nothing changed; following running mri_coreg, nthreads is still listed as 1 and
the processing time remains the same. I really appreciate all the help — seems
like maybe this is something idiosyncratic about my system. I’ll find another
system to try this on to see if this is specific to my environment.
From: fsbuild <fsbu...@contbay.com>
Date: Tuesday, December 3, 2024 at 5:40 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] mri_coreg threads parallel processing
clarification
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You could try setting the environment variable OMP_NUM_THREADS, e.g., in
zsh/bash shell, on a machine with 4 performance cores,
$ export OMP_NUM_THREADS=4
The test command I ran did not take long to run, but it looks like it used 3 of
the 4 performance cores on an M1 Mac with OMP_NUM_THREADS=4. See attached
screenshot, mri_coreg_omp_num_threads.png
- R.
On Dec 3, 2024, at 17:06, Hemond, Christopher
<christopher.hem...@umassmemorial.org> wrote:
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Dear Doug and team,
Thanks very much for your support. I’ve tried multiple different thread
numbers between 1 and 10 with no effect. I can successfully use multithreading
to accelerate other applications like mri_synthseg.
I tried adding combinations of both ‘fs_time’ as well as ‘--debug’ to the
command, but I do not see any difference in final output, nor any CPU
load/usage readout at the end of the command…. Just the usual “mri_coreg
RunTimeSec <X> sec”.
Could this be related to the ARM processor in Mac? It seems to cause many
other issues, especially with some SPM commands including processing
specification.
Many thanks,
Chris
From: Hemond, Christopher
<christopher.hem...@umassmemorial.org<mailto:christopher.hem...@umassmemorial.org>>
Date: Monday, November 25, 2024 at 4:32 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: mri_coreg threads parallel processing clarification
Dear experts,
Thanks in advance for any help you can provide. I’m using “mri_coreg” and
trying to accelerate it with the “--threads” (and/or “--nthreads”) flags.
However in the subsequent command feedback it looks like it is still using just
one thread (see output below, “nthreads 1”; and also it is no faster). Am I
doing something obviously wrong? There are no errors and it executes
successfully… Not sure if relevant but I’m using this for nifty (.nii.gz)
files, my command is:
“mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg
<path/to/registration.lta> --threads 10”
I’m on MacOS running a recent dev download
(freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7.4.1 with
no success either.
…
INFO: using NIfTI-1 sform (sform_code=1)
Setting cras translation parameters to align volume centers
Init matrix params -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 1.0000
1.0000 1.0000 0.0000 0.0000 0.0000
Initial Matrix (RAS2RAS)
1.00000 0.00000 0.00000 0.45535;
0.00000 1.00000 0.00000 6.31235;
0.00000 0.00000 1.00000 -39.44280;
0.00000 0.00000 0.00000 1.00000;
Initial parameters to be opt -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000
Creating random numbers for coordinate dithering
Performing intensity dithering
Performing intensity dithering on mov with computed dither
Separation list (2): 4 2 min = 2
DoSmoothing 1
DoCoordDither 1
DoIntensityDither 1
nitersmax 4
ftol 1.000e-07
linmintol 1.000e-03
SatPct 99.990000
Hist FWHM 7.000000 7.000000
nthreads 1
movsat = 3917.0000
mov gstd 0.9539 0.9539 0.7422
Smoothing mov
…
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