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 *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. < DGREVE@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 CautionThanks 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated!
Thanks,
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu mailto:dcallow@gmail.com 443-254-6298 *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> wrote:
Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I /Volumes - R.On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow@umd.edu <mailto:dcallow@umd.edu>> wrote: External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --iVolumes/DANIEL/tutorial_data/diffusion_recons/${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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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