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 <zkauf...@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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- ----------------------------------------------------------------------------------------- Kong Xiangzhen State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China, 100875.
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