Yes, I was just going to follow up with this disclaimer. It’s a slightly newer version of nu_correct, so it’s possible the result will differ very slightly. The problem is that the FS 5.3 version of MNI/nu_correct uses a perl version that reached end-of-life in 2008! So it would be quite difficult to rebuild a local package for centos8. Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tobias, Malcolm mtobias@wustl.edu Date: Monday, March 8, 2021 at 3:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
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Andrew,
That's a great suggestion, thanks.
Any idea whether using the MNI from FS6 has an impact on the results?
Cheers, Malcolm ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Monday, March 8, 2021 2:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
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Hi Malcolm,
Yes, this is an unfortunate bug, but I've been playing around with a few options and the following seems to be the best patch. This assumes you also have FS v6 installed and, in this case, FS_53 and FS_60 point to the respective freesurfer base directories:
rm -rf $FS_53/mni
cp -r $FS_60/mni $FS_53/
Then, customize the 5.3 SetUpFreeSurfer.sh (or whatever you use to source FS) to ensure that the following variables are set in a 5.3 environment:
export PERL5LIB="$FS_53/mni/share/perl5"
export MNI_PERL5LIB="$FS_53/mni/share/perl5"
Hope that helps,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tobias, Malcolm mtobias@wustl.edu Date: Monday, March 8, 2021 at 10:48 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
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All,
We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer versions of Perl:
[mtobias@login02 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
/mnt/beegfs/scratch/mtobias/mri
/export/freesurfer/freesurfer-5.3.0-HCP/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
...
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /export/freesurfer/freesurfer-5.3.0-HCP/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
ERROR: nu_correct
One fix suggested for Ubuntu users is to install an older version of Perl. While we've tried that on our system, it seems the perl scripts are hard-wired to use /usr/bin/perl:
[root@mgt bin]# head -1 nu_estimate_np_and_em
#!/usr/bin/perl -w
So without replacing the system perl on every system in the cluster, is anyone aware of any other work-arounds for this issue?
Cheers,
Malcolm
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