Re: [Freesurfer] error - mri_nu_correct.mni

2016-03-19 Thread Flavia Niccolini new 
Hi Douglas,

I have done this but I got the following error:

[hwilson@nig05 ~]$ cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
[hwilson@nig05 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
--no-rescale --i orig.mgz --o orig_nu.mgz
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux nig05.nig.ioppn.kcl.ac.uk 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 
14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
Wed 16 Mar 10:09:44 GMT 2016
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.13997
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13997/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13997/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 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.13997/nu0.mnc...
 

Iteration 1 Wed 16 Mar 10:09:47 GMT 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.13997/nu0.mnc 
./tmp.mri_nu_correct.mni.13997/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.13997/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct
[hwilson@nig05 mri]$ 


any suggestions?

Many Thanks

With Best Wishes

Flavia




> On 15 Mar 2016, at 16:30, Douglas N Greve  wrote:
> 
> It should all be on one line
> 
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
> --i orig.mgz --o orig_nu.mgz
> 
> 
> 
> On 03/14/2016 05:43 AM, Flavia Niccolini new wrote:
>> Hi Douglas,
>> 
>> I have done this and I got the following message:
>> 
>> “cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>> hwilson@nig05 mri]$   mri_nu_correct.mni --n 1 --proto-iters 1000 
>> --distance 50 --no-rescale
>> ERROR: must specify an input volume
>> hwilson@nig05 mri]$ --i orig.mgz --o orig_nu.mgz “
>> 
>> 
>> Many Thanks
>> 
>> With Best Wishes
>> 
>> Flavia
>> 
>> 
>> 
>> 
>>> On 7 Mar 2016, at 23:51, Douglas N Greve >> > wrote:
>>> 
>>> what happens when you run the following?
>>> 
>>> cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>>> --i orig.mgz --o orig_nu.mgz
>>> 
>>> 
>>> 
>>> On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
 Hello,
 
 I was wondering whether you could help with this error:
 
 #
 #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
 Found 1 runs
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/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
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
 
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
 
 mri_convert
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
 --conform
 
 mri_convert
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
 --conform
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-1, 0, 0)
 j_ras = (0, 1, 0)
 k_ras = (-0, -0, 1)
 Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
 Data is conformed to 1 mm size and 256 voxels for all directions
 changing data type from float to uchar (noscale = 0)...
 MRIchangeType: Building histogram
 Reslicing using trilinear interpolation
 writing to
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
 
 mri_add_xform_to_header -c
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
 
 INFO: extension is mgz
 #
 #@# Talairach Thu Mar  3 11:35:59 GMT 2016
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
 
 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
 --no-rescale --i orig.mgz

Re: [Freesurfer] error - mri_nu_correct.mni

2016-03-15 Thread Douglas N Greve 
It should all be on one line

  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
--i orig.mgz --o orig_nu.mgz



On 03/14/2016 05:43 AM, Flavia Niccolini new wrote:
> Hi Douglas,
>
> I have done this and I got the following message:
>
> “cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
> hwilson@nig05 mri]$   mri_nu_correct.mni --n 1 --proto-iters 1000 
> --distance 50 --no-rescale
> ERROR: must specify an input volume
> hwilson@nig05 mri]$ --i orig.mgz --o orig_nu.mgz “
>
>
> Many Thanks
>
> With Best Wishes
>
> Flavia
>
>
>
>
>> On 7 Mar 2016, at 23:51, Douglas N Greve > > wrote:
>>
>> what happens when you run the following?
>>
>> cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o orig_nu.mgz
>>
>>
>>
>> On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
>>> Hello,
>>>
>>> I was wondering whether you could help with this error:
>>>
>>> #
>>> #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
>>> Found 1 runs
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/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
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>>
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
>>>
>>> mri_convert
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> --conform
>>>
>>> mri_convert
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> --conform
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 1, 0)
>>> k_ras = (-0, -0, 1)
>>> Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
>>> Data is conformed to 1 mm size and 256 voxels for all directions
>>> changing data type from float to uchar (noscale = 0)...
>>> MRIchangeType: Building histogram
>>> Reslicing using trilinear interpolation
>>> writing to
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
>>>
>>> mri_add_xform_to_header -c
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>>
>>> INFO: extension is mgz
>>> #
>>> #@# Talairach Thu Mar  3 11:35:59 GMT 2016
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>>>
>>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>>> --no-rescale --i orig.mgz --o orig_nu.mgz
>>>
>>> Linux nig05.nig.ioppn.kcl.ac.uk 
>>> >> >
>>> 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64
>>> x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016
>>>
>>>
>>> Many Thanks
>>>
>>> With Best Wishes
>>>
>>> Flavia
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> 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 
>> 
>> 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/
>>
>> ___
>> Freesurfer mailing list
>> 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 proper

Re: [Freesurfer] error - mri_nu_correct.mni

2016-03-14 Thread Flavia Niccolini new 
Hi Douglas,

I have done this and I got the following message:

“cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
hwilson@nig05 mri]$   mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
--no-rescale 
ERROR: must specify an input volume
hwilson@nig05 mri]$ --i orig.mgz --o orig_nu.mgz “


Many Thanks

With Best Wishes

Flavia




> On 7 Mar 2016, at 23:51, Douglas N Greve  wrote:
> 
> what happens when you run the following?
> 
> cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
> --i orig.mgz --o orig_nu.mgz
> 
> 
> 
> On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
>> Hello,
>> 
>> I was wondering whether you could help with this error:
>> 
>> #
>> #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
>> Found 1 runs
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/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 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>> 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
>> 
>> mri_convert 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
>> --conform
>> 
>> mri_convert 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
>> --conform
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 1, 0)
>> k_ras = (-0, -0, 1)
>> Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
>> Data is conformed to 1 mm size and 256 voxels for all directions
>> changing data type from float to uchar (noscale = 0)...
>> MRIchangeType: Building histogram
>> Reslicing using trilinear interpolation
>> writing to 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
>> 
>> mri_add_xform_to_header -c 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
>>  
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>> 
>> INFO: extension is mgz
>> #
>> #@# Talairach Thu Mar  3 11:35:59 GMT 2016
>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>> 
>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
>> --no-rescale --i orig.mgz --o orig_nu.mgz
>> 
>> Linux nig05.nig.ioppn.kcl.ac.uk  
>> > 
>> 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 
>> x86_64 x86_64 GNU/Linux
>> 
>> recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016
>> 
>> 
>> Many Thanks
>> 
>> With Best Wishes
>> 
>> Flavia
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> 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 
> 
> 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/ 
> 
> 
> ___
> Freesurfer mailing list
> 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] error - mri_nu_correct.mni

2016-03-07 Thread Douglas N Greve 
what happens when you run the following?

cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
--i orig.mgz --o orig_nu.mgz



On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
> Hello,
>
> I was wondering whether you could help with this error:
>
> #
> #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
> Found 1 runs
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/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 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
>
>  mri_convert 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> --conform
>
> mri_convert 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> --conform
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 1, 0)
> k_ras = (-0, -0, 1)
> Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from float to uchar (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
>
>  mri_add_xform_to_header -c 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
>  
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>
> INFO: extension is mgz
> #
> #@# Talairach Thu Mar  3 11:35:59 GMT 2016
> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
> --no-rescale --i orig.mgz --o orig_nu.mgz
>
> Linux nig05.nig.ioppn.kcl.ac.uk  
> 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64 
> x86_64 x86_64 GNU/Linux
>
> recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016
>
>
> Many Thanks
>
> With Best Wishes
>
> Flavia
>
>
>
>
>
>
> ___
> 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
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/

___
Freesurfer mailing list
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.

[Freesurfer] error - mri_nu_correct.mni

2016-03-07 Thread Flavia Niccolini new 
Hello,

I was wondering whether you could help with this error:

#
#@# MotionCor Thu Mar  3 11:35:51 GMT 2016
Found 1 runs
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/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 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 

/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1

 mri_convert 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform 

mri_convert /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (-0, -0, 1)
Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...

 mri_add_xform_to_header -c 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
 /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz 

INFO: extension is mgz
#
#@# Talairach Thu Mar  3 11:35:59 GMT 2016
/data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz 

Linux nig05.nig.ioppn.kcl.ac.uk 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 
14:09:15 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016


Many Thanks

With Best Wishes

Flavia




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