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
ddcc2442@gmail.com
443-254-6298


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