Transform .tck Files into MNI Space

Good evening MRTrix3 Experts,

I am running CSD probabilistic tractography on the S900 release of the Human Connectome Project dataset. I am trying to convert my .tck files to MNI space, and to do this I followed @eloydelas instructions from 2016, which can be reviewed at this link. My ultimate goal is to do the following:

  1. Transform .tck tractographies to MNI space
  2. Convert tractographies to voxel maps
  3. Average together tractographies for all subjects in a common space to create a spatial histogram/probabilistic map using a function like fslmaths in FSL.
  4. Calculate Dice Coefficients for the resultant map to assess overlap with ROIs from various atlases
  5. Below are examples of subject-space tractographies, and my failed MNI normalization of the same tract:

Subject-Space Tractography:

Failed MNI Normalisation:


My pipleline is delineated as follows:

  1. Create no-warp images in target space:**
warpinit \
    $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz \
     no-warp-[].nii
  1. Warp target images to subject space:
for s in ${subjects}
do
    for n in 0 1 2
    do   
                fnirt \
                      --ref=dtifit_output/DTI_FA.nii.gz \
                      --in=no-warp-${n}.nii \
                      --aff=standard2diff_${s}.mat \
                      --iout=warp-${n}_${s}.nii
     done
done
  1. Perform MNI normalisation on .tck images:
for s in ${subjects}                                                  
do
     tcktransform \
        ifod2_paths.tck \
        warp-[]_${s}.nii \
        ifod2_paths_mni.tck 
done

Please note that I also tried redoing this process perfoming the following intermediary step in FSL:

for s in ${subjects}                                                                                                  
do 
    for n in 0 1 2
    do
        fslorient \
            -copysform2qform \
            warp-${n}_${s}.nii
done

I would sincerely appreciate any advice this community may be able to offer!

Kind regards,
Linda

Hello MRTrix3 Experts,

I wanted to follow up with my last inquiry, to see if anyone might be able to help with these registration issues.

I look forward to seeing your replies!

Kind regards,
Linda