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 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These
were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I
assume there is an issue with how I am naming the input volumes for
dt_recon. Any advice on how I should structure this command would be
greatly appreciated!
Thanks,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu <dcal...@gmail.com>
443-254-6298
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbu...@contbay.com> wrote:
> Hello Daniel.
>
> It looks like you need a slash in front of Volumes for the path after —I
> /Volumes
>
> - R.
>
> On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcal...@umd.edu> wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to run dt_recon on my dti data using the following script.
>
> dt_recon --debug --i
> Volumes/DANIEL/tutorial_data/diffusion_recons/${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 <dcal...@gmail.com>
> 443-254-6298
>
> _______________________________________________
> Freesurfer mailing list
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