It looks like it is only using one thread, though you have correctly specified 10. I often run it with more than 1, and it certainly uses as many as I give it. It is possible that it is not allowed to have that many threads. Have you been able to run other programs with multiple threads? You can try re-running it adding --debug as the 1st argument. Also run it through fs_time, eg,
fs_time mri_coreg ...
Capture all the terminal output.
fs_time will print out something in the end to indicate the amount of CPU it is using.

On 11/25/2024 4:32 PM, Hemond, Christopher wrote:

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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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