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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated!
Thanks, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298 *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild fsbuild@contbay.com wrote:
Hello Daniel.
It looks like you need a slash in front of Volumes for the path after —I /Volumes
- R.
On Feb 13, 2019, at 14:44, Daniel Davidson Callow dcallow@umd.edu wrote:
External Email - Use CautionHello,
I am trying to run dt_recon on my dti data using the following script.
dt_recon --debug --i Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon
with the following error
echo "ERROR: cannot find $InputVol" echo ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm goto error_exit ;
the DICOM files are named image000001.dcm through image000065.dcm
These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. Any advice on how I should structure this command would be greatly appreciated!
*Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
External Email - Use Caution
Thanks for pointing that out! Unfortunately after making the change
dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${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 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated!
Thanks,
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu mailto:dcallow@gmail.com 443-254-6298 *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> wrote:
Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I /Volumes - R.On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow@umd.edu <mailto:dcallow@umd.edu>> wrote: External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --i Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/1-65.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon with the following error echo "ERROR: cannot find $InputVol" echo ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm ERROR: cannot find Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm goto error_exit ; the DICOM files are named image000001.dcm through image000065.dcm These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. Any advice on how I should structure this command would be greatly appreciated! *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu <mailto:dcallow@gmail.com> 443-254-6298 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Is this what you mean by no variables??
dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
*Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
External Email - Use CautionThanks for pointing that out! Unfortunately after making the change
dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${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 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated!
Thanks,
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu mailto:dcallow@gmail.com 443-254-6298 *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> wrote:
Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I /Volumes - R.On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow@umd.edu <mailto:dcallow@umd.edu>> wrote: External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --iVolumes/DANIEL/tutorial_data/diffusion_recons/${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@gmail.com> 443-254-6298 _______________________________________________ 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
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 $LF
tee -a
echo
exit 1 ; exit 1
*Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow ddcc2442@gmail.com wrote:
Is this what you mean by no variables??
dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon
*Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
can you send the command line without the variables?
On 2/13/19 5:19 PM, Daniel Davidson Callow wrote:
External Email - Use CautionThanks for pointing that out! Unfortunately after making the change
dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${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 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 $LF
tee -a
echo
exit 1 ;
exit 1
Again the DICOM files are named image000001.dcm through image000065.dcm. These were 64 gradient images acquired on a SIEMENS scanner with 1 bo image. I assume there is an issue with how I am naming the input volumes for dt_recon. Any advice on how I should structure this command would be greatly appreciated!
Thanks,
*Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu mailto:dcallow@gmail.com 443-254-6298 *Daniel Callow* /PhD Student, Neuroscience and Cognitive Science/ Exercise for Brain Health Lab University of Maryland, College Park _ddcc2442@gmail.com mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 3:04 PM fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> wrote:
Hello Daniel. It looks like you need a slash in front of Volumes for the path after —I /Volumes - R.On Feb 13, 2019, at 14:44, Daniel Davidson Callow <dcallow@umd.edu <mailto:dcallow@umd.edu>> wrote: External Email - Use Caution Hello, I am trying to run dt_recon on my dti data using the following script. dt_recon --debug --iVolumes/DANIEL/tutorial_data/diffusion_recons/${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@gmail.com> 443-254-6298 _______________________________________________ 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
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
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 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 CautionThe 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
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 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 18:44:07 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 mailto:ddcc2442@gmail.com_ 443-254-6298
On Wed, Feb 13, 2019 at 6:31 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto: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> <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 $LF > > tee -a > > echo > > > exit 1 ; > > exit 1 > * > * > * > * > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 6:25 PM Daniel Callow <ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> > <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>> wrote: > > > Is this what you mean by no variables?? > > dt_recon --debug --i > /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/1-65.dcm > --s AES101.Ex --o /Volumes/DANIEL/tutorial_data/dtrecon > > *Daniel Callow* > /PhD Student, Neuroscience and Cognitive Science/ > Exercise for Brain Health Lab > University of Maryland, College Park > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>>_ > 443-254-6298 > > > On Wed, Feb 13, 2019 at 6:15 PM Greve, Douglas N.,Ph.D. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>> wrote: > > can you send the command line without the variables? > > > On 2/13/19 5:19 PM, Daniel Davidson Callow wrote: > > > > External Email - Use Caution > > > > Thanks for pointing that out! Unfortunately after making the > change > > > > dt_recon --debug --i > > > /Volumes/DANIEL/tutorial_data/diffusion_recons/${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> > <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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > <mailto: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>> > > <mailto: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>> > <mailto: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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > >> <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>> > > 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>> > 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
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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 _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
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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. < DGREVE@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 CautionIs 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>
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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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 > _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com> <mailto: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> <mailto: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> > <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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > <mailto: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>> > > <mailto: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>> > <mailto: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@umd.edu <mailto:dcallow@umd.edu>> > <mailto:dcallow@gmail.com <mailto:dcallow@gmail.com> <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>> > >> <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>> > > 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>> > 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-- *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
freesurfer@nmr.mgh.harvard.edu
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Daniel Callow -
Daniel Davidson Callow -
Greve, Douglas N.,Ph.D. -
Greve, Douglas N.,Ph.D.