Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50
When I executed the command separately I got below error message:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/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
Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani
What version of freesurfer are you using? My guess is 5.3 or earlier?
With pre v6.0 versions of freesurfer, the Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and newer versions of perl. The issue has been fixed in version 6.0.
On 04/05/2017 05:12 PM, Das S. wrote:
Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50
When I executed the command separately I got below error message:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/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
Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I had the same problem with one server. The freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. The system is openSUSE13.2 for both servers. But one works well (A), while another one showed this problem (B). I found the kernel is somehow different, though I am not sure whether this is the point. kernel for A is 3.16.7-35-desktop, while kernel for B is 3.16.6-2-desktop. They have the same verion of perl, v5.20.1.
Hope this case would be helpful for fixing the issue.
Best, Xiangzhen
On Tue, Apr 11, 2017 at 8:12 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
What version of freesurfer are you using? My guess is 5.3 or earlier?
With pre v6.0 versions of freesurfer, the Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and newer versions of perl. The issue has been fixed in version 6.0.
On 04/05/2017 05:12 PM, Das S. wrote:
Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an
error. When I checked I found the error was coming while executing the below command:
nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc
./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50
When I executed the command separately I got below error message:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?)
at /usr/local/freesurfer/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
Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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