External Email - Use Caution
Here it is.
[hlhp-105:DANIEL/scripts/dti_freesurfer] 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 18:44:07 EST 2019
echo "" | & tee -a $LF
tee -a
echo
exit 1 ;
exit 1 [hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% *aniel 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 6:31 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
what happens when you run
ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
On 2/13/19 6:27 PM, Daniel Callow wrote:
External Email - Use CautionThe 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 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 18:26:16 EST 2019
echo "" | & tee -a $LF
tee -a
echo
exit 1 ;
exit 1
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <ddcc2442@gmail.com mailto:ddcc2442@gmail.com> wrote:
Is this what you mean by no variables?? dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>_ 443-254-6298 On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote: can you send the command line without the variables? On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > External Email - Use Caution > > Thanks for pointing that out! Unfortunately after making the change > > dt_recon --debug --i >/Volumes/DANIEL/tutorial_data/diffusion_recons/${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> <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 $LF > > tee -a > > echo > > > exit 1 ; > > exit 1 > > > Again the DICOM files are named image000001.dcm through > image000065.dcm. These were 64 gradient images acquired on a SIEMENS > scanner with 1 bo image. I assume there is an issue with how I am > naming the input volumes for dt_recon. Any advice on how I should > structure this command would be greatly appreciated! > > > Thanks, > > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> > 443-254-6298 > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com <mailto:fsbuild@contbay.com> > <mailto:fsbuild@contbay.com <mailto:fsbuild@contbay.com>>> wrote: > > Hello Daniel. > > It looks like you need a slash in front of Volumes for the path > after —I > /Volumes > > - R. > >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow >> <dcallow@umd.edu <mailto:dcallow@umd.edu> <mailto:dcallow@umd.edu <mailto:dcallow@umd.edu>>> wrote: >> >> External Email - Use Caution >> >> >> Hello, >> >> I am trying to run dt_recon on my dti data using the following >> script. >> >> dt_recon --debug --i >>Volumes/DANIEL/tutorial_data/diffusion_recons/${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@umd.edu> <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com>> >> 443-254-6298 >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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