On 15 Mar 2016, at 16:30, Douglas N Greve <greve@nmr.mgh.harvard.edu> 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 <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> 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
<http://nig.ioppn.kcl.ac.uk/><http://nig.ioppn.kcl.ac.uk
<http://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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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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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