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