I don't know, probably a better question for the FSL group
On 3/1/19 8:57 AM, Daniel Callow wrote:
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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@gmail.commailto:ddcc2442@gmail.com 443-254-6298
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