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 When you setup the freesurfer 7.4.1 environment from the terminal, check you see the output below when running bash shell from the terminal.  If you see all the same output, then it should at least work to get the help info from the command… $ bash

$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 ————     <—- MAKE SURE YOU SEE THIS EXACT LINESetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.4.1FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjectsMNI_DIR           /usr/local/freesurfer/7.4.1/mniFSL_DIR           /usr/pubsw/packages/fsl/current … then check you see this output ... $ which mri_easyreg/usr/local/freesurfer/7.4.1/bin/mri_easyreg$ file `which mri_easyreg`/usr/local/freesurfer/7.4.1/bin/mri_easyreg: Bourne-Again shell script, ASCII text executable$ which fspython/usr/local/freesurfer/7.4.1/bin/fspython$ fspython --versionPython 3.8.13 … now the help option should work … $ mri_easyreg —help … you may see some warning messages before the help text if your machine does not support cuda for tensorflow … usage: mri_easyreg [-h] [—ref REF] [--ref_seg REF_SEG] [--flo FLO] [--flo_seg FLO_SEG] [--ref_reg REF_REG] [--flo_reg FLO_REG] [--fwd_field FWD_FIELD] [--bak_field BAK_FIELD] [--affine_only]                   [--threads THREADS] EasyReg: deep learning registration simple and easy optional arguments:  -h, --help            show this help message and exit  --ref REF             Reference image .  --ref_seg REF_SEG     Reference SynthSeg segmentation (will be created if it does not exist).  --flo FLO             Floating image.  --flo_seg FLO_SEG     Floating SynthSeg segmentation (will be created if it does not exist).  --ref_reg REF_REG     (optional) Registered referenced.  --flo_reg FLO_REG     (optional) Registetred floating images (in space of reference).  --fwd_field FWD_FIELD                        (optional) Forward field  --bak_field BAK_FIELD                        (optional) Inverse field  --affine_only         (optional) Skips nonlinear part  --threads THREADS     (optional) Number of cores to be used. Default is 1. You can use -1 to use all available cores If you see all the above, then maybe some command options/parameters are causing mri_easyreg to fail.  I’ve asked the mri_easyreg developer to look at your command. - R. On Aug 15, 2024, at 10:23, Sara Ponticorvo <ponti045@umn..edu> wrote:        External Email - Use Caution        Hello,so the command I used is: mri_easyreg --ref MP2RAGE_uni_resampled_2mm.nii.gz --flo sub017_ute_anat.nii.gz --ref_seg mprage_seg.nii --flo_seg ute_seg.nii  The output I get is:Illegal instruction

I also tried putting the absolute path to the files, but I get the same output. And, I also tried to get the help (but I'm not sure if there is one) by typing mri_easyreg --h and mri_easyreg --help, but I get the same Illegal instruction output..I'm running it on CentOS Linux 7 server. The output from cat /etc/redhat-releaseCentOS Linux release 7.9.2009 (Core) Thank you for your help!SaraOn Thu, Aug 15, 2024 at 12:45 AM fsbuild <fsbuild@contbay.com> wrote:

Hello Sara, Please send along the terminal output from running the command so we can see the error. Maybe you could also let us know what version of CentOS you are running, e.g., also include the output from, $ cat /etc/redhat-release

- R.

On Aug 14, 2024, at 15:32, Sara Ponticorvo <ponti045@umn.edu> wrote:         External Email - Use Caution         Hi Freesurfer experts!I am trying to use mri_easyreg. I've installed freesurfer v7.4.1 on my centos machine but when I try to run mri_easyreg I've "Illegal instruction" message. Do you have any suggestion on how to solve it? Thank you,Sara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh..harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Sara Ponticorvo, PhDCenter for Magnetic Resonance ResearchUniversity of Minnesota2021 6th St. S.E.Minneapolis MN 55455 (USA)phone: +1 612 626 2001 (front-desk)e-mail: ponti045@umn.edu _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer