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Hello R.
Thank you!
I just set the FREESURFER_HOME directory in the same way, and that worked!
Thank you.
But unfortunately, it does not solve the issue with mri_sclimbic_seg: it is
still giving me this weird error (see below).
Any thoughts?
Thank you
Heidi
[schopenhauer:LC_HYP] (nmr-dev-env) setenv FREESURFER_HOME
/usr/local/freesurfer/7.4.1
[schopenhauer:LC_HYP] (nmr-dev-env) source $FREESURFER_HOME/SetUpFreeSurfer.csh
-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.4.1
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:LC_HYP] (nmr-dev-env) mri_sclimbic_seg --s HAB_008_CST_2.4
/usr/local/freesurfer/7.4.1/python/scripts/mri_sclimbic_seg --s HAB_008_CST_2.4
Excluding seg [853]
Using CPU
Illegal instruction (core dumped)
From: fsbuild <fsbu...@contbay.com>
Date: Sunday, 20 August 2023 at 20:39
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
You should be able to use either of the paths below for FREESURFER_HOME to run
the freesurfer CentOS7 7.4.1 release. You should see the same output using
either path. If one of these commands does not work, then it means that path
is not mounted/available on your machine (so don’t use that one).
% cat /usr/local/freesurfer/7.4.1/build-stamp.txt
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
% cat /autofs/cluster/freesurfer/centos7_x86_64/7.4.1/build-stamp.txt
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
Both commands work on my test machine, so I will use the first one. Using csh
to setup the environment,
% setenv FREESURFER_HOME /usr/local/freesurfer/7.4.1
% source $FREESURFER_HOME/SetUpFreeSurfer.csh
-------- freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/7.4.1
FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects
MNI_DIR /usr/local/freesurfer/7.4.1/mni
FSL_DIR /usr/pubsw/packages/fsl/current
But your posted output from the source command does not match the output above.
It is fine to change SUBJECTS_DIR to a different path *after* you run the
“source” command above, in order to process your own data, e.g.,
% setenv SUBJECTS_DIR /autofs/space/locus_001/users/mv1048/LC_HYP/FS6
I’m wondering if something was added into your shell initialization file in
your home directory to set FREESURFER_HOME, etc. to be different. For csh,
that would be your “.cshrc" file. I would check that file and either change or
comment out setting FREESURFER_HOME there, etc. But you should get the same
output listed above from the source command (apart from changing SUBJECTS_DIR).
- R.
On Aug 20, 2023, at 18:12, Jacobs, Heidi I.,PHD <hjac...@mgh.harvard.edu> wrote:
/autofs/space/locus_001/users/mv1048/LC_HYP/FS6
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