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 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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