[Freesurfer] dt_recon issue

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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 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 dcallow@gmail.com 443-254-6298

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