Hello Zeke, I included the terminal output error for the stable version of Freesurfer, but get the same error with the dev version. Here's an example, pasted below:
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 INFO: SUBJECTS_DIR is /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award Actual FREESURFER_HOME /usr/local/pkg/freesurfer-dev 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 '/usr/local/pkg/freesurfer-dev/bin/recon-all' -> '/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Wed Jan 11 20:49:48 EST 2017 Found 1 runs /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107 mri_convert /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz --conform mri_convert.bin /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -0.971961, -0.235142) j_ras = (0, -0.235142, 0.971961) k_ras = (1, -1.11022e-16, -1.66533e-16) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz... mri_add_xform_to_header -c /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/transforms/talairach.xfm /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jan 11 20:50:00 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/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 Wed Jan 11 20:50:00 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.130158 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.130158/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, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.130158/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 11 20:50:03 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.130158/nu0.mnc ./tmp.mri_nu_correct.mni.130158/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.130158/0/ -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 10107 exited with ERRORS at Wed Jan 11 20:50:03 EST 2017 For more details, see the log file /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ===== The MNI tools are from 2010, but as noted at the start, the Freesurfer version is "Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1" (which I believe is the most recent dev version). Other thoughts or things to work on? Thanks much! Best, Jamie. On Wed, Jan 11, 2017 at 6:28 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > Hello Jamie, > > Are you absolutely sure your using the dev version of freeseurfer? It > looks like from the output you pasted below their is possibly some mixing > of the old and new versions (it says MNI was built in 2010 - should be much > more recent than that). Try starting with a fresh terminal window and > sourcing freesurfer and see what happens. If the problem persists I will > look deeper into the issue upon my return. > > > On Jan 11, 2017, at 10:15 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > 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/ > 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 > > > > > >
_______________________________________________ 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.
