Dear MRtrix experts,

I have general questions, I’m looking for advises regarding the following strategies. I’m not working with ODF so I’m wondering how the general strategies depicted in the forum can be applied on my data. I wish to disclaim that I’m a beginner in such processing.

Please find below some figures, I have 3 objectives :

- demonstrate that the some structures (for instance the singularity in blue with a triangular shape) has a different fiber orientation
- create a parcellation map based on fiber orientation
- extract relevant feature like the size and volume of this structure

### Strategies 1 (done except the parcellation):

- estimate tensor in subject spaces using dwi2tensor (using MRtrix)
- warp tensor in template spaces (using ANTs)
- average all tensors in template spaces to get a unique average tensor (using ANTs)
- extract eigenvector of the averaged tensor (using MRtrix)
- using FACT to compute the streamline (using MRtrix)
- display the streamlines and create a parcellation atlas in template space

### Strategies 2 (done except the parcellation):

- compute tractography in subject spaces using Tensor_Det or Tensor_Prob using DWI data (using MRtrix)
- warp all individual tractgrams in template spaces using ‘Registration: using transformations generated from other packages’ (using MRtrix and ANTs)
- add tractgrams using tckedit (using MRtrix)
- display the streamlines and create a parcellisation atlas in template space

Please find below some questions:

- Which strategy would you recommand ? Maybe none of them ? For strategies 1, my concern is that tckgen FACT differs a lot from Tensor_Det or Tensor_Prob.
- In strategy 2, I’m wondering what can I do to average my streamlines or extract relevant features. According to the following post : *.tck file add and average, there is no streamline averaging in MRtrix and tcksift or tcksift2 cannot be used in non-ODF data , could you confirm ?
- Is it relevant to use tckmap on non-ODF data. If relevant (I’m not sure), which metrics would you advise ? or could you indicate references/articles that used tckmap with non-ODF data ?
- Does MRtrix offer the possibility to create a parcellisation map based on eigen-vector or tractography. I’m really struggling with this step. I tried to combine tckgen with -direction 0,0,1 option followed by tckmap but it was not so easy to binarize the output of tckmap. Is there any command /method to create parcellisation map base on DTI.

Thanks in advance for your help.

Valéry

### Typical figure from strategy 1:

Data for each subject in template space:

Template images in template space