Re: [Freesurfer] dt_recon issue

2019-02-14 Thread Greve, Douglas N.,Ph.D. 
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 
> images01.dcm-images65.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/image02.dcm 
> unrecognized.
>
> --i 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image01.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image02.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image03.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image04.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image05.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image06.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image07.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image08.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image09.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image10.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image11.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image12.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image13.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image14.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image15.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image16.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image17.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image18.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image19.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image20.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image21.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image22.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image23.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image24.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image25.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image26.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image27.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image28.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image29.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image30.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image31.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image32.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image33.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image34.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image35.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image36.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image37.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image38.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image39.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image40.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image41.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image42.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image43.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image44.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image45.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image46.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image47.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image48.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image49.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image50.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image51.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image52.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image53.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image54.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image55.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image56.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image57.dcm 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101

Re: [Freesurfer] dt_recon issue

2019-02-14 Thread Greve, Douglas N.,Ph.D. 
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. 
> 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 
> >_
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> > 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 
> 
> >      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_re

Re: [Freesurfer] dt_recon issue

2019-02-14 Thread Daniel Callow 
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 _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> > 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 
> >  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 image01.dcm through
> > > image65.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 
> >

Re: [Freesurfer] dt_recon issue

2019-02-14 Thread Greve, Douglas N.,Ph.D. 
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  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 _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. 
> 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 
>  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 
> >_
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow
> mailto:ddcc2...@gma

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
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 *
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  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 _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  > > 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 _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> > 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 -

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
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  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 $LF
>
> tee -a
>
> echo
>
>
> exit 1 ;
>
> exit 1
> *
> *
> *
> *
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  > wrote:
>
>
> Is this what you mean by no variables??
>
> dt_recon --debug --i
> /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm
> --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> can you send the command line without the variables?
>
>
> On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
> >
> > External Email - Use Caution
> >
> > Thanks for pointing that out! Unfortunately after making the
> change
> >
> > dt_recon --debug --i
> >
> 
> /Volumes/DANIEL/tutorial_data/diffusion_recons/${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
> >
> > t

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
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 _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. 
> 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 
>  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 image01.dcm through
> > image65.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 
> >
> > 443-254-6298
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com 
> >_
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 3:04 PM fsbuild  
> > >> 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
> >>     mailto:dcal...@umd.edu>
> >> wrote:
> >>
> >>     External Email - Use Caution
> >>
>

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
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 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 *
443-254-6298


On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow  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 *
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
> 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  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 image01.dcm through
>> > image65.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

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Callow 
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 *
443-254-6298


On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. <
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  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 $LF
> >
> > tee -a
> >
> > echo
> >
> >
> > exit 1 ;
> >
> > exit 1
> >
> >
> > Again the DICOM files are named image01.dcm through
> > image65.dcm. These were 64 gradient images acquired on a SIEMENS
> > scanner with 1 bo image. I assume there is an issue with how I am
> > naming the input volumes for dt_recon. Any advice on how I should
> > structure this command would be greatly appreciated!
> >
> >
> > Thanks,
> >
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > dcal...@umd.edu 
> > 443-254-6298
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> >
> > On Wed, Feb 13, 2019 at 3:04 PM fsbuild  > > wrote:
> >
> > Hello Daniel.
> >
> > It looks like you need a slash in front of Volumes for the path
> > after —I
> > /Volumes
> >
> > - R.
> >
> >> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
> >> mailto:dcal...@umd.edu>> wrote:
> >>
> >> External Email - Use Caution
> >>
> >>
> >> Hello,
> >>
> >> I am trying to run dt_recon on my dti data using the following
> >> script.
> >>
> >> dt_recon --debug --i
> >>
>  Volumes/DANIEL/tutorial_data/diffusion_recons/${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 image01.dcm through image65.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

Re: [Freesurfer] dt_recon issue

2019-02-13 Thread Greve, Douglas N.,Ph.D. 
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  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 $LF
>
> tee -a
>
> echo
>
>
> exit 1 ;
>
> exit 1
>
>
> Again the DICOM files are named image01.dcm through 
> image65.dcm. These were 64 gradient images acquired on a SIEMENS 
> scanner with 1 bo image. I assume there is an issue with how I am 
> naming the input volumes for dt_recon. Any advice on how I should 
> structure this command would be greatly appreciated!
>
>
> Thanks,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> dcal...@umd.edu 
> 443-254-6298
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
>
> On Wed, Feb 13, 2019 at 3:04 PM fsbuild  > wrote:
>
> Hello Daniel.
>
> It looks like you need a slash in front of Volumes for the path
> after —I
> /Volumes
>
> - R.
>
>> On Feb 13, 2019, at 14:44, Daniel Davidson Callow
>> mailto:dcal...@umd.edu>> wrote:
>>
>> External Email - Use Caution
>>
>>
>> Hello,
>>
>> I am trying to run dt_recon on my dti data using the following
>> script.
>>
>> dt_recon --debug --i
>> Volumes/DANIEL/tutorial_data/diffusion_recons/${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 image01.dcm through image65.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 
>> 443-254-6298
>>
>> ___
>> 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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[Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Davidson Callow 
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 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 image01.dcm through image65.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 
443-254-6298
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Wed, Feb 13, 2019 at 3:04 PM fsbuild  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  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 image01.dcm through image65.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 
> 443-254-6298
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] dt_recon issue

2019-02-13 Thread fsbuild 
External Email - Use Caution

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  
wrote:External Email - Use 
CautionHello,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/dtreconwith the following 
errorecho "ERROR: cannot find $InputVol"echo ERROR: cannot find 
Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmERROR: cannot 
find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcmgoto 
error_exit ;the DICOM files are 
named image01.dcm through image65.dcmThese 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 
CallowPhD Student, Neuroscience and Cognitive ScienceExercise 
for Brain Health LabUniversity of Maryland, College 
Parkdcallow@umd.edu443-254-6298___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] dt_recon issue

2019-02-13 Thread Daniel Davidson Callow 
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 image01.dcm through image65.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 
443-254-6298
___
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