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.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> > > > 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 > <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.
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