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 > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@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 $LF > > > > tee -a > > > > echo > > > > > > exit 1 ; > > > > exit 1 > > * > > * > > * > > * > > *Daniel Callow* > > /PhD Student, Neuroscience and Cognitive Science/ > > Exercise for Brain Health Lab > > University of Maryland, College Park > > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com> > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>>_ > > 443-254-6298 > > > > > > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow > <ddcc2...@gmail.com <mailto:ddcc2...@gmail.com> > > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>>> wrote: > > > > > > Is this what you mean by no variables?? > > > > dt_recon --debug --i > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > > > *Daniel Callow* > > /PhD Student, Neuroscience and Cognitive Science/ > > Exercise for Brain Health Lab > > University of Maryland, College Park > > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com> > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>>_ > > 443-254-6298 > > > > > > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>> > wrote: > > > > can you send the command line without the variables? > > > > > > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > > > > > External Email - Use Caution > > > > > > Thanks for pointing that out! Unfortunately after > making the > > change > > > > > > dt_recon --debug --i > > > > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/${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> > <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 > > > dcal...@umd.edu <mailto:dcal...@umd.edu> > <mailto:dcal...@umd.edu <mailto:dcal...@umd.edu>> > > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com> > <mailto:dcal...@gmail.com <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> > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>> > > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com> > <mailto: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> > > <mailto:fsbu...@contbay.com <mailto:fsbu...@contbay.com>> > > > <mailto:fsbu...@contbay.com > <mailto:fsbu...@contbay.com> <mailto: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> > <mailto:dcal...@umd.edu <mailto:dcal...@umd.edu>> > > <mailto:dcal...@umd.edu <mailto:dcal...@umd.edu> > <mailto: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...@umd.edu> > <mailto:dcal...@umd.edu <mailto:dcal...@umd.edu>> > > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com> > <mailto:dcal...@gmail.com <mailto:dcal...@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
