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Hi Bruce,

That did the trick! Thank you very much.

Fischl, Bruce BFISCHL@mgh.harvard.edu, 8 Şub 2021 Pzt, 23:23 tarihinde şunu yazdı:

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

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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://secure-web.cisco.com/11tdaInnqYtUWRkjKA3OhISAx7uqCwtpHf_YlHq0sFkLrxP... https://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1eDktoIdfGbGmm0m5Dv6McNft3kvF825zFnb15LaPR2JR7Q...