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:
<mailto:greve@nmr.mgh.harvard.
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
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >edu
<mailto:greve@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
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 >>
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<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.htm l
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/grev e/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/ flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >>ve/
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 >
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<http://www.partners.org/complianceline >> . If the e-mail was sent
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-- 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/grev e/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre >ve/
--
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/grev e/