External Email - Use Caution
Is this what you mean by no variables??
dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the change
> >
> > dt_recon --debug --i
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> > --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >
> >
> > I still get the error.
> >
> >
> > ./dt_recon.sh
> >
> > mkdir: tutorial_data: File exists
> >
> > mkdir: diffusion_recons: File exists
> >
> > subj =AES101 , cond =Ex
> >
> > mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File
> > exists
> >
> > set echo = 1 ;
> >
> > breaksw
> >
> > breaksw
> >
> > end
> >
> > end
> >
> > while ( $#argv != 0 )
> >
> > while ( 6 != 0 )
> >
> >
> > set flag = $argv[1] ; shift ;
> >
> > set flag = --i
> >
> > shift
> >
> >
> > switch ( $flag )
> >
> > switch ( --i )
> >
> > if ( $#argv < 1 ) goto arg1err ;
> >
> > if ( 5 < 1 ) goto arg1err
> >
> > set InputVol = "$argv[1]" ; shift ;
> >
> > set InputVol =
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > shift
> >
> > if ( ! -e "$InputVol" ) then
> >
> > if ( ! -e
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ) then
> >
> > echo "ERROR: cannot find $InputVol"
> >
> > echo ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > ERROR: cannot find
> > Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >
> > goto error_exit ;
> >
> > goto error_exit
> >
> > uname -a | tee -a $LF
> >
> > uname -a
> >
> > tee -a
> >
> > Darwin hlhp-105.umd.edu <http://hlhp-105.umd.edu> 16.7.0 Darwin Kernel
> > Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018;
> > root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > echo "dt_recon exited with ERRORS at `date`" | & tee -a $LF
> >
> > tee -a
> >
> > echo dt_recon exited with ERRORS at `date`
> >
> > date
> >
> > dt_recon exited with ERRORS at Wed Feb 13 17:12:30 EST 2019
> >
> > echo "" | & tee -a $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> >
> >
> > Again the DICOM files are named image000001.dcm through
> > image000065.dcm. These were 64 gradient images acquired on a SIEMENS
> > scanner with 1 bo image. I assume there is an issue with how I am
> > naming the input volumes for dt_recon. Any advice on how I should
> > structure this command would be greatly appreciated!
> >
> >
> > Thanks,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu <mailto:dcal...@gmail.com>
> > 443-254-6298
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbu...@contbay.com
> > <mailto:fsbu...@contbay.com>> wrote:
> >
> > Hello Daniel.
> >
> > It looks like you need a slash in front of Volumes for the path
> > after —I
> > /Volumes
> >
> > - R.
> >
> >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
> >> <dcal...@umd.edu <mailto:dcal...@umd.edu>> wrote:
> >>
> >> External Email - Use Caution
> >>
> >>
> >> Hello,
> >>
> >> I am trying to run dt_recon on my dti data using the following
> >> script.
> >>
> >> dt_recon --debug --i
> >>
> Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm
> >> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
> >>
> >>
> >> with the following error
> >>
> >> echo "ERROR: cannot find $InputVol"
> >> echo ERROR: cannot find
> >> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >> ERROR: cannot find
> >> Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> >> goto error_exit ;
> >>
> >> the DICOM files are named image000001.dcm through image000065.dcm
> >>
> >> These were 64 gradient images acquired on a SIEMENS scanner with
> >> 1 bo image. Any advice on how I should structure this command
> >> would be greatly appreciated!
> >>
> >> *Daniel Callow*
> >> /PhD Student, Neuroscience and Cognitive Science/
> >> Exercise for Brain Health Lab
> >> University of Maryland, College Park
> >> dcal...@umd.edu <mailto:dcal...@gmail.com>
> >> 443-254-6298
> >>
> >> _______________________________________________
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> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > _______________________________________________
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>
>
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