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Thank you! I just tried setting it to version 7.4.1, however, upon checking it is still referring to the dev version. Here is the output (se is my shortcut for set subjects dir):
[schopenhauer:FS6] (nmr-dev-env) source /autofs/cluster/freesurfer/centos7_x86_64/7.4.1/SetUpFreeSurfer.csh -------- freesurfer-linux-centos7_x86_64-dev-20230820-df385b4 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /autofs/space/locus_001/users/mv1048/LC_HYP/FS6 MNI_DIR /usr/local/freesurfer/dev/mni FSL_DIR /usr/pubsw/packages/fsl/current [schopenhauer:FS6] (nmr-dev-env) se [schopenhauer:FS6] (nmr-dev-env) echo $FREESURFER_HOME /usr/local/freesurfer/dev [schopenhauer:FS6] (nmr-dev-env) echo $SUBJECTS_DIR /autofs/space/locus_001/users/mv1048/LC_HYP/FS6 [schopenhauer:FS6] (nmr-dev-env) mri_sclimbic_seg --s HAB_008_CST_2.4 /usr/local/freesurfer/dev/python/scripts/mri_sclimbic_seg -s HAB_008_CST_2.4 Excluding seg [853] Using CPU Illegal instruction (core dumped)
Thank you Heidi
________________________________ From: fsbuild fsbuild@contbay.com Sent: Sunday, August 20, 2023 5:56 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Jacobs, Heidi I.,PHD HJACOBS@mgh.harvard.edu Subject: Re: [Freesurfer] ScLimbic issue
External Email - Use Caution
…. to do that, you can set FREESURFER_HOME to
/autofs/cluster/freesurfer/centos7_x86_64/7.4.1
On Aug 20, 2023, at 17:52, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use Caution
Can you try the 7.4.1 version? Can you also send your full command line and terminal output?
On 8/20/2023 2:57 PM, Jacobs, Heidi I.,PHD wrote:
External Email - Use Caution
Hello FreeSurfer team,
I am trying to run the sclimbic tool on our FreeSurfer processed images (from the Martinos center). For some unknown reason I keep getting the same problem: Excluding seg [853] Using CPU Illegal instruction (core dumped)
Not sure what this means? I have sourced /usr/local/freesurfer/nmr-dev-env and set the SUBJECTS_DIR correctly. I tried with the - - s option referring to the FreeSurfer processed subject as well as the - - i option, referring to the orig.mgz image. Using the nifti image or the mgz image doesn’t make a difference either.
Any suggestions on what the problem may be or how to resolve this?
Thank you All the best Heidi
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