Hi Gunes
Just set it in your environment before calling mri_em_register. For example
setenv OMP_NUM_THREADS 1
in csh/tcsh or
export OMP_NUM_THREADS=1
in bash. I think you can also give -openmp 1 to recon-all (hopefully that will also work)
cheers Bruce From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of gunes Sent: Monday, February 8, 2021 6:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Number of threads in mri_em_register
External Email - Use Caution Dear freesurfer developers,
I'm using freesurfer v5.3.0 and having problems with the number of threads opened by `mri_em_register`. It automatically opens up as many threads as there are in the system, but I need to limit that.
I have seen this post with the same problem: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41604.htmlhttps://secure-web.cisco.com/19w3ZWmagO9QFaobk1ln0Z4sQQWaHjFCCO6n7ZqpGmL6VZAX0w21CCEAaa33RUpdWANy9uLXqTHg-0cjdlk5HCted7Gp7uDpg3tO3_DmxRhvJenYCKZQREEaLmxycNmE2D8Ox3UhspmsCAalRJv-l1c8vIoOqxQWsnBkHxmxAPQl7ByUL9_FboPsVaZwzquIDs-URt8xUqzTTSz4YTXd6Fcw92VFKXs_mUZDOxtaC2LORNpipqDBbkyVkRxeUsP-LMTSSuAGFNWOinnV1yjoM2g/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg41604.html
In the end, it seems to be solved by setting OMP_NUM_THREADS to 1 in the mri_em_register script, but it is a binary file. I don't know how to set it.
Kind regards, Gunes