Re: [Freesurfer] error - mri_nu_correct.mni
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 <gr...@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 <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@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 >>>
Re: [Freesurfer] error - mri_nu_correct.mni
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 <gr...@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 >> >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 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/> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.h
[Freesurfer] error - mri_nu_correct.mni
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 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.
