On Thu, Jan 12, 2017 at 4:02 AM, Z K <zkaufman@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 <jlhanson5@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 <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 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
>> <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 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>>
>> 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
>> 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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