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 $LF
>
> tee -a
>
> echo
>
>
> exit 1 ;
>
> exit 1
>
>
> Again the DICOM files are named image000001.dcm through
> image000065.dcm. These were 64 gradient images acquired on a SIEMENS
> scanner with 1 bo image. I assume there is an issue with how I am
> naming the input volumes for dt_recon. Any advice on how I should
> structure this command would be greatly appreciated!
>
>
> Thanks,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcallow@umd.edu <mailto:dcallow@gmail.com>
> 443-254-6298
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>_
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com
> <mailto:fsbuild@contbay.com>> wrote:
>
>     Hello Daniel.
>
>     It looks like you need a slash in front of Volumes for the path
>     after —I
>     /Volumes
>
>     - R.
>
>>     On Feb 13, 2019, at 14:44, Daniel Davidson Callow
>>     <dcallow@umd.edu <mailto:dcallow@umd.edu>> wrote:
>>
>>             External Email - Use Caution
>>
>>
>>     Hello,
>>
>>     I am trying to run dt_recon on my dti data using the following
>>     script.
>>
>>     dt_recon --debug --i
>>     Volumes/DANIEL/tutorial_data/diffusion_recons/${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
>>     dcallow@umd.edu <mailto:dcallow@gmail.com>
>>     443-254-6298
>>
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>
>
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