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 *ddcc2...@gmail.com <ddcc2...@gmail.com>* 443-254-6298 On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. < 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> 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 $LF > > > > tee -a > > > > echo > > > > > > exit 1 ; > > > > exit 1 > > * > > * > > * > > * > > *Daniel Callow* > > /PhD Student, Neuroscience and Cognitive Science/ > > Exercise for Brain Health Lab > > University of Maryland, College Park > > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_ > > 443-254-6298 > > > > > > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <ddcc2...@gmail.com > > <mailto:ddcc2...@gmail.com>> wrote: > > > > > > Is this what you mean by no variables?? > > > > dt_recon --debug --i > > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > > --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > > > *Daniel Callow* > > /PhD Student, Neuroscience and Cognitive Science/ > > Exercise for Brain Health Lab > > University of Maryland, College Park > > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>_ > > 443-254-6298 > > > > > > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > can you send the command line without the variables? > > > > > > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > > > > > External Email - Use Caution > > > > > > Thanks for pointing that out! Unfortunately after making the > > change > > > > > > dt_recon --debug --i > > > > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/${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 $LF > > > > > > tee -a > > > > > > echo > > > > > > > > > exit 1 ; > > > > > > exit 1 > > > > > > > > > Again the DICOM files are named image000001.dcm through > > > image000065.dcm. These were 64 gradient images acquired on a > > SIEMENS > > > scanner with 1 bo image. I assume there is an issue with how > > I am > > > naming the input volumes for dt_recon. Any advice on how I > > should > > > structure this command would be greatly appreciated! > > > > > > > > > Thanks, > > > > > > *Daniel Callow* > > > /PhD Student, Neuroscience and Cognitive Science/ > > > Exercise for Brain Health Lab > > > University of Maryland, College Park > > > dcal...@umd.edu <mailto:dcal...@umd.edu> > > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>> > > > 443-254-6298 > > > *Daniel Callow* > > > /PhD Student, Neuroscience and Cognitive Science/ > > > Exercise for Brain Health Lab > > > University of Maryland, College Park > > > _ddcc2...@gmail.com <mailto:ddcc2...@gmail.com> > > <mailto:ddcc2...@gmail.com <mailto:ddcc2...@gmail.com>>_ > > > 443-254-6298 > > > > > > > > > On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbu...@contbay.com > > <mailto:fsbu...@contbay.com> > > > <mailto:fsbu...@contbay.com <mailto:fsbu...@contbay.com>>> > > wrote: > > > > > > Hello Daniel. > > > > > > It looks like you need a slash in front of Volumes for > > the path > > > after —I > > > /Volumes > > > > > > - R. > > > > > >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow > > >> <dcal...@umd.edu <mailto:dcal...@umd.edu> > > <mailto:dcal...@umd.edu <mailto:dcal...@umd.edu>>> wrote: > > >> > > >> External Email - Use Caution > > >> > > >> > > >> Hello, > > >> > > >> I am trying to run dt_recon on my dti data using the > > following > > >> script. > > >> > > >> dt_recon --debug --i > > >> > > > Volumes/DANIEL/tutorial_data/diffusion_recons/${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...@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>> > > >> 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
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