I'm suspecting that there is an error or incompatibility in the MNI software (where we get nu_correct). Unforutnately, the person who would handle this (Zeke) is away until next Wed. Can it wait until then?
On 01/11/2017 04:58 PM, Jamie Hanson wrote: > > Is it happening on all subjects or just some of them? > > > all of them... > > > > > > On 01/11/2017 03:45 PM, Jamie Hanson wrote: > > Apologies my email must have clipped it out. > I pasted it below. > > > > ======= > > Hello Freesurfer List, > > I was running into issues processing subjects, with errors > just getting through the autorecon1 step of the pipeline. My > terminal outputs the following: > > ==== > > /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri > /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni > --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters > 1000 --distance 50 > nIters 1 > $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ > Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 > UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > Tue Jan 10 12:53:44 EST 2017 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by nicks@minerva > (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 > /usr/bin/bc > tmpdir is ./tmp.mri_nu_correct.mni.129237 > /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc > -odt float > mri_convert.bin orig.mgz > ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from orig.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, -1.32349e-23, -1.32349e-23) > j_ras = (0, 1.49012e-08, -1) > k_ras = (0, 1, 1.49012e-08) > changing data type from uchar to float (noscale = 0)... > writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Tue Jan 10 12:53:47 EST 2017 > nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc > ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50 > Can't use 'defined(@array)' (Maybe you should just omit the > defined()?) at > /usr/local/pkg/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 > Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 > UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 > EST 2017 > > For more details, see the log file > > /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > ==== > > Searching the FS list, I saw that I originally thought this > was an incompatibility with the current stable Freesurfer > version and the most recent MNI tools. To troubleshoot that > issue, I installed the dev version of Freesurfer (as noted by > this thread: > > https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html > > <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html> > > <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html > > <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html>>). > The error however still persists (even using the dev version). > Anyone else run into this issue or have thoughts about > troubleshooting it? Thanks much! > > Best, > Jamie. > > -- > Jamie Hanson > Assistant Professor, Psychology > Research Scientist, Learning Research and Development Center > University of Pittsburgh > Personal website: jamiehanson.org <http://jamiehanson.org> > <http://jamiehanson.org/> > > > On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > please include previous correspondence. we get a lot of emails > here and can't remember the context of each one. > > thanks > > > On 01/11/2017 03:17 PM, Jamie Hanson wrote: > > > I'm seeing it for multiple subjects, same issue. I > can't get > passed the autorecon1 steps. Any thoughts? > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > 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 > <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline > <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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
