Processing steps¶
TractoFlow pipeline consist of 23 different steps : 14 steps for the diffusion weighted image (DWI) processing and 8 steps for the T1 weighted image processing.
Input¶
- Diffusion weighted image (DWI)
- b-values
- b-vectors
- T1 weighted image
- Reverse phase encoding B0 (Optional)
DWI processes¶
- Brain extraction (FSL)
- Denoising (Mrtrix3)
- Topup (FSL)
- Eddy (FSL)
- N4 bias correction (ANTs)
- Resample (Dipy)
- DTI metrics (Dipy)
- fODF metrics (Dipy)
T1 processes¶
- Brain extraction (ANTs)
- Denoising (Dipy)
- N4 bias correction (ANTs)
- Resample (Dipy)
- Registration (ANTs)
- Tissue segmentation (FSL)
Tractography¶
The particle filter tractography is performed. Two types of seeding are available: WM-GM interface or WM mask.