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:
External Email - Use Caution
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
…
The information transmitted is intended only for the person or entity
to which it is addressed and may contain confidential and/or
privileged material. Any review, transmission, re-transmission,
dissemination or other use of, or taking of any action in reliance
upon this information by persons or entities other than the intended
recipient is prohibited. If you received this in error, please contact
the sender and delete the material from any computer.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
