14 Feb
2019
14 Feb
'19
11:45 a.m.
what happens when you run
ls -l /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
On 2/13/19 6:45 PM, Daniel Callow wrote:
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 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 18:44:07 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 mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto: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 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 <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 18:26:16 EST 2019 > > echo "" | & tee -a $LF > > tee -a > > echo > > > exit 1 ; > > exit 1 > * > * > * > * > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>> wrote: > > > Is this what you mean by no variables?? > > dt_recon --debug --i > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > can you send the command line without the variables? > > > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > > > External Email - Use Caution > > > > Thanks for pointing that out! Unfortunately after making the > change > > > > dt_recon --debug --i > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/${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> > <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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > <mailto: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>> > > <mailto: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>> > <mailto: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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > >> <mailto: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> > <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> > <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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