External Email - Use Caution
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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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="$FS_53/mni/share/perl5"
Hope that helps, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tobias, Malcolm mtobias@wustl.edu Date: Monday, March 8, 2021 at 10:48 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
External Email - Use Caution
External Email - Use Caution
All,
We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP). We're hitting a perl error which appears to be a known issue with newer versions of Perl:
[mtobias@login02 mri]$ 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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
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
* External Email - Caution *
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="$FS_53/mni/share/perl5"
Hope that helps,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tobias, Malcolm mtobias@wustl.edu Date: Monday, March 8, 2021 at 10:48 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
External Email - Use Caution
External Email - Use Caution
All,
We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer versions of Perl:
[mtobias@login02 mri]$ 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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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
External Email - Use Caution
External Email - Use Caution
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
* External Email - Caution *
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="$FS_53/mni/share/perl5"
Hope that helps,
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tobias, Malcolm mtobias@wustl.edu Date: Monday, March 8, 2021 at 10:48 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Supporting older versions of FreeSurfer (5.3) on newer OSs
External Email - Use Caution
External Email - Use Caution
All,
We're setting up a new cluster (based on CentOS 8) but have many users that still want to run older versions of FreeSurfer (5.3 and 5.3-HCP).
We're hitting a perl error which appears to be a known issue with newer versions of Perl:
[mtobias@login02 mri]$ 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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Tobias, Malcolm