Dear MRtrix community, I have read some papers on the TDI (tract density index), such as 10.1001/jamaneurol.2023.3284 and “Redirecting”. I found that this is a very interesting indicator. However, when I tried to reproduce it, I didn’t know how to obtain the standardized map of TDI. As described in this literature( doi: 10.1038/s41467-019-09344-1),
"ExploreDTI toolbox for Matlab has been used to extract estimates of axonal water fraction28. Next, we discarded the volumes with a b-value of 1000 s mm−2 and whole-brain deterministic tractography was subsequently performed in the native DWI space using StarTrack software . A damped Richardson-Lucy algorithm was applied for spherical deconvolutions72. A fixed fibre response corresponding to a shape factor of α = 1.5 × 10–3 mm2 s−1 was adopted, coupled with the geometric damping parameter of 8. Two hundred algorithm iterations were run. The absolute threshold was defined as three times the spherical fibre orientation distribution (FOD) of a grey matter isotropic voxel and the relative threshold as 8% of the maximum amplitude of the FOD73. A modified Euler algorithm74 was used to perform the whole-brain streamline tractography, with an angle threshold of 35°, a step size of 0.5 mm and a minimum streamline length of 15 mm. We co-registered the structural connectome data to the standard MNI 2 mm space using the following steps: first, whole-brain streamline tractography was converted into streamline density volumes where the intensities corresponded to the number of streamlines crossing each voxel. Second, a study-specific template of streamline density volumes was generated using the Greedy symmetric diffeomorphic normalisation (GreedySyN) pipeline distributed with ANTs. This provided an average template of the streamline density volumes for all subjects. The template was then co-registered with a standard 2 mm MNI152 template using flirt tool implemented in FSL. This step produced a streamline density template in the MNI152 space. Third, individual streamline density volumes were registered to the streamline density template in the MNI152 space template and the same transformation was applied to the individual whole-brain streamline tractography using the trackmath tool distributed with the software package Tract Querier75, and to the axonal water fraction maps, using ANTs GreedySyn. This step produced a whole-brain streamline tractography and axonal water fraction maps in the standard MNI152 space.”
It seems that I need to reprocess the data of hundreds of subjects in the HCP. I wonder if matrix3 can perform such an operation? Does this require powerful computing power and a large amount of RAM support? Are there any other ways to obtain the standard TDI map?
I have only a minimal amount of experience with MATRIX. If my question seems naive, please forgive me, and I sincerely appreciate your patient attention in advance.