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/P ardini_Projects/K_award/10007/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harv ard.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.h arvard.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 On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve <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 > 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/ > > > > 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. >
_______________________________________________ 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.
