OK, I just uploaded it via the FileDrop (and sent it to Zeke)... On Thu, Jan 12, 2017 at 4:02 AM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote:
> Could you please upload the a copy of the subject data and I'll take a > look early next week when I get back. Also, what Linux distribution are you > on? > > On Jan 12, 2017, at 1:55 AM, Jamie Hanson <jlhans...@wisc.edu> wrote: > > 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/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 >> >> <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 <(617)%20724-2358> >> > Fax: 617-726-7422 <(617)%20726-7422> >> > >> > 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/grev >> e/ >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >> >
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