Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-12 Thread Jamie Hanson 
OK, I just uploaded it via the FileDrop (and sent it to Zeke)...

On Thu, Jan 12, 2017 at 4:02 AM, Z K  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  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 de

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-12 Thread Z K 
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  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-al

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Jamie Hanson 
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  wrote:

> Hello Jamie,
>
> Are you a

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Jamie Hanson 
Totally fine.
I will try to check in then.


On Wed, Jan 11, 2017 at 5:15 PM, Douglas N Greve 
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
>> 
>> > >
>>
>> 
>>
>> 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
>> > 6-September/047734.html>
>> > 6-September/047734.html
>> > 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 
>> 
>>
>>
>> On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Douglas N Greve 
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
> 
>  >
>
> 
>
> 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
> 
> 
> 
>  
> >).
> 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 
> 
>
>
> On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> please include previous correspondence. we get a lot of emails
> here and can't remember the context o

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Jamie Hanson 
> 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/P
>> ardini_Projects/K_award/10007/scripts/recon-all.log
>> To report a problem, see http://surfer.nmr.mgh.harvard.
>> edu/fswiki/BugReporting > .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.e
>> du/pipermail///freesurfer/2016-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 
>>
>>
>> On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve <
>> 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 
>> 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/
>> 
>>
>>
>>
>> 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://

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Douglas N Greve 
Is it happening on all subjects or just some 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 
> 
>
> 
>
> 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
>  
> ).
>  
> 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 
>
>
> On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve 
> 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 
> 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/
> 
>
>
>
> 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 pat

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Jamie Hanson 
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/P
ardini_Projects/K_award/10007/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harv
ard.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.h
arvard.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


On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve 
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
> 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/
>
>
>
> 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.
>
___
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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.

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Douglas N Greve 
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
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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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.

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-11 Thread Jamie Hanson 
I'm seeing it for multiple subjects, same issue. I can't get passed the
autorecon1 steps. Any thoughts?
___
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Freesurfer@nmr.mgh.harvard.edu
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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.

Re: [Freesurfer] autorecon1 crash (with nu_correct).

2017-01-10 Thread Douglas N Greve 
Is this happening on all your subjects or just this one? If just this 
one, have you looked at the image to see if it looks ok?


On 01/10/2017 01:09 PM, Jamie Hanson wrote:
> 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 
> 
>
> 
>
> 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
>  
> ).
>  
> 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 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
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[Freesurfer] autorecon1 crash (with nu_correct).

2017-01-10 Thread Jamie Hanson 
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



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). 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
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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.