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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 <fsbu...@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 <hjac...@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 <dgr...@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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