Hi Barbara - You can just insert the command that does your correction right after that dtifit command line. As long as your command produces the same set of outputs with the same naming convention (dtifit_FA.nii.gz, dtifit_V1.nii.gz, ...), all subsequent steps will work the same.

Hope this helps, a.y

On Thu, 11 Sep 2014, Barbara Kreilkamp wrote:

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