Totally fine. I will try to check in then.
On Wed, Jan 11, 2017 at 5:15 PM, Douglas N Greve <[email protected]> wrote: > 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/201 >> 6-September/047734.html> >> <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/201 >> 6-September/047734.html >> <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/201 >> 6-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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> 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 >> [email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> 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.e >> du/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 >> [email protected] <mailto:[email protected]> >> 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 > [email protected] > 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/ > >
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