External Email - Use Caution Hi Douglas,
I was unsure if the emails I had been replying with were going through. They did not seem to come up on the mailing list so I wasn’t sure if they had reached you. I recently responded to your question about the ls -l path output and the —debug output after fixing the path to the input Volumes. I wonder if you have any idea why this might still produce the same error? Is it an issue with the setenv or the naming of the DICOM files?. Sorry for any questions. Any help is greatly appreciated! On Wed, Feb 13, 2019 at 6:30 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Yes. Can you run it with --debug with the slash in front of "Volumes"? > > On 2/13/19 6:25 PM, Daniel Callow wrote: > > > > External Email - Use Caution > > > > > > 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 -- *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
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