External Email - Use Caution
Hi Doug,
I was looking at the dt_recon code and was wondering if it would be
possible to incorporate a field map into the eddy_correct portion? I tried
to test it on one subject and tried to add --field=$pathtofieldmap to the
eddy_correct command however I got the following error.
cd /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./ectmp
eddy_correct /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi.nii
/Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec.nii 0
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp0000
Unrecognised interpolation method:
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES101.Ex./dwi-ec_tmp0001
Unrecognised interpolation method:
--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed
I probably did this in a silly way. I wonder if and how I could add a field
map I created to the eddy_correct command in dt_recon.
Below is what I tried to change....
set fec = $OutDir/dwi-ec.nii
if($DoEddyCorrect) then
echo "#@#-------------------------------" | tee -a $LF
echo "Eddy/Motion Correct" | tee -a $LF
date | tee -a $LF
set ectmp = $OutDir/ectmp
mkdir -p $ectmp
pushd $ectmp > /dev/null
set cmd = (eddy_correct $f $fec $ECRefTP
*--field=/Volumes/DANIEL/AES101/AES101.Ex/FieldMap2dti_smoothed*)
#set cmd = ($cmd; mri_convert ${fec:r} $fec)
#set cmd = ($cmd; rm -f ${fec:r})
#set cmd = (cp $f $fec)
echo "cd `pwd`" | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
if(! -e $fec) then
echo "ERROR: when running eddy_correct" | tee -a $LF
exit 1;
endif
popd > /dev/null
rm -r $ectmp
echo "" | tee -a $LF
echo "" | tee -a $LF
else
echo "#@#-------------------------------" | tee -a $LF
echo "Skipping Eddy/Motion Correct" | tee -a $LF
set fec = $f
endif
Thanks for any help you can provide,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>*
443-254-6298
