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