External Email - Use Caution
The error output that accompanies the command.
administrator% dt_recon --debug --i
/Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
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 18:26:16 EST 2019
echo "" | & tee -a $LF
tee -a
echo
exit 1 ;
exit 1
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com <ddcc2...@gmail.com>*
443-254-6298
On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <ddcc2...@gmail.com> wrote:
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s
> AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com <ddcc2...@gmail.com>*
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> can you send the command line without the variables?
>>
>>
>> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for pointing that out! Unfortunately after making the change
>> >
>> > dt_recon --debug --i
>> > /Volumes/DANIEL/tutorial_data/diffusion_recons/${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
>> >>
>> >> _______________________________________________
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
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>>
>>
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