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 >>>> 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 >>> >>> -- >>> 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 >>> 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/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 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
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