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 zkaufman@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 greve@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
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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: please include previous correspondence. we get a lot ofemails
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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 wassent
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 greve@nmr.mgh.harvard.edu mailto:greve@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 greve@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/
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