External Email - Use Caution        

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 <fsbuild@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" <HJACOBS@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 <HJACOBS@mgh.harvard.edu> wrote:

 

/autofs/space/locus_001/users/mv1048/LC_HYP/FS6