you can only give it one dicom file from the series, it will find the rest.
On 2/14/19 4:11 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> As you can see the folder has 65 DICOM images labeled
> images000001.dcm-images000065.dcm.
>
> I tried
>
> dt_recon --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/*.dcm
> --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> and got this error.
>
>
> ./dt_recon.sh
>
> subj =AES101 , cond =Ex
>
> ERROR: Flag
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000002.dcm
> unrecognized.
>
> --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000002.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000003.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000004.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000005.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000006.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000007.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000008.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000009.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000010.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000011.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000012.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000013.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000014.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000015.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000016.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000017.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000018.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000019.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000020.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000021.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000022.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000023.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000024.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000025.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000026.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000027.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000028.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000029.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000030.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000031.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000032.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000033.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000034.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000035.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000036.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000037.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000038.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000039.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000040.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000041.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000042.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000043.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000044.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000045.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000046.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000047.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000048.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000049.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000050.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000051.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000052.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000053.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000054.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000055.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000056.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000057.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000058.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000059.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000060.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000061.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000062.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000063.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000064.dcm
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000065.dcm
> --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> 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
>
>
> dt_recon exited with ERRORS at Thu Feb 14 16:09:17 EST 2019
>
>
>
> I am unsure why it is not reading these DICOM volumes in? They should
> be in the path I specify? Is it something to do with the way I am
> naming the files?
>
> *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 Thu, Feb 14, 2019 at 4:03 PM Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
>
> You are trying to pass dt_recon the file 1-65.dcm but this does not
> exist in that folder
>
> On 2/14/19 3:41 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Oh sorry, for some reason the emails I am sending are not going
> > through to the listserv then. I have been sending them to
> > freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > and for some reason, they seem to have stopped going through?
> >
> > Anyways this is what I got when running the ls -l
> >
> > administrator% ls -l
> > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/
> >
> > total 172928
> >
> > -rwxrwxrwx1 administratorstaff1276058 Feb 13 17:13 image000001.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276462 Feb 13 17:13 image000002.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276462 Feb 13 17:13 image000003.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276470 Feb 13 17:13 image000004.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000005.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000006.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000007.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000008.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000009.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000010.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000011.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000012.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000013.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000014.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000015.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276478 Feb 13 17:13 image000016.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000017.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000018.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000019.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000020.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000021.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000022.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000023.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000024.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000025.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000026.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000027.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000028.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000029.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000030.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000031.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000032.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000033.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000034.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000035.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000036.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000037.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000038.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000039.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000040.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000041.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000042.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000043.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000044.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000045.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000046.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276482 Feb 13 17:13 image000047.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000048.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000049.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000050.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000051.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276474 Feb 13 17:13 image000052.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000053.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276486 Feb 13 17:13 image000054.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000055.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276488 Feb 13 17:13 image000056.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000057.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000058.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000059.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276472 Feb 13 17:13 image000060.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276480 Feb 13 17:13 image000061.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276484 Feb 13 17:13 image000062.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276476 Feb 13 17:13 image000063.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276490 Feb 13 17:13 image000064.dcm
> >
> > -rwxrwxrwx1 administratorstaff1276478 Feb 13 17:13 image000065.dcm
> >
> > -rwxrwxrwx1 administratorstaff5458789 Feb 13 17:13 orig.mgz
> >
> > Thank you!
> > *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 Thu, Feb 14, 2019 at 3:39 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:
> >
> > I never saw an email with the result of the ls -l command
> >
> > On 2/14/19 3:36 PM, Daniel Callow wrote:
> > >
> > > 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 <mailto:dgr...@mgh.harvard.edu>
> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>
> > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu
> <mailto: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>
> <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 <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 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>>
> > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>>>
> > > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>> <mailto: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>
> > > <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...@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>>
> > <mailto: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>>
> > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>
> <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>>>
> > > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>
> <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>>
> > <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>>>
> > > <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 <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>
> <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 <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>>>
> > > > <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 <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>
> > <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 <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>>>
> > > <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 <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>
> <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 <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...@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>>
> > <mailto: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>>
> > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>
> <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>>>
> > > <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>
> <mailto:dcal...@gmail.com <mailto:dcal...@gmail.com>>
> > <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>>>
> > > > <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
> <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>
> > <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
> <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
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> > <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
> <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>>
> > > <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
> <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>>
> > > <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>>
> > <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
> > >
> > > --
> > > *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
> >
> >
> >
> > The information in this e-mail is intended only for the
> person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in
> error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
>
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