Input structure

Two types of input are available in TractoFlow: BIDS and an in-house structure.

BIDS parameter

We recommend to use dcm2bids (https://github.com/cbedetti/Dcm2Bids) to create BIDS datasets.

TractoFlow supports BIDS as input data using --bids YOUR_BIDS_DATASET. TractoFlow does some verifications before launching the processing to valide the BIDS format.

In the case that some tags or informations are missing, TractoFlow will create a json file in results/Read_BIDS. Please complete missing informations and relaunch the pipeline replacing --bids YOUR_BIDS_DATASET with --bids_config results/Read_BIDS/tractoflow_bids_struct.json.

If you have any problems, contact us on NeuroStar (https://neurostars.org/tag/tractoflow).

Root parameter

It is possible not to follow the BIDS format. In that case, the input root parameter is called using --root and requires the following file structure:

[root]
├── S1
│   ├── dwi.nii.gz
│   ├── bval
│   ├── bvec
│   ├── rev_b0.nii.gz  (optional)
│   └── t1.nii.gz
└── S2
    ├── dwi.nii.gz
    ├── bval
    ├── bvec
    ├── rev_b0.nii.gz  (optional)
    └── t1.nii.gz

The root folder must contains subjects folders (e.g. S1, S2,…). Each subject folder contains the required images:

  • dwi.nii.gz are the diffusion weighted images.
  • bval is the b-value file in the FSL format.
  • bvec is the b-vector file in the FSL format.
  • rev_b0.nii.gz (optional) is the reversed phase encoded b0 image also called blip-up/blip-down. Used to correct distortion due to diffusion acquisition (Documentation).
  • t1.nii.gz is the T1 weighted image.