Dear all,
I would like to make amendments to the FSL dtifit call during trac-preproc.
In which way can I edit the call in trac-preproc?
# LS tensor estimation
set cmd = dtifit
set cmd = ($cmd -k $dwidir/dwi.nii.gz)
set cmd = ($cmd -m $brainmask)
set cmd = ($cmd -r $dwidir/bvecs)
set cmd = ($cmd -b $dwidir/bvals)
set cmd = ($cmd -o $dwidir/dtifit)
echo $cmd |& tee -a $LF |& tee -a $CF
if ($RunIt) then
$fs_time $cmd |& tee -a $LF
if ($status) goto error_exit
endif
The background is that I would like to save the tensor file for being able
to correct the tensor to be positive-definite (not possible within FSL).
Then I would have to map the scalar outputs of the tensor fit (originating
from the new corrected, positive-definite tensor) to the MNI template after
that (would it be sufficient then to re-run step 1.7 in trac-all)?
Thanks a lot
Barbara
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