Input structure

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

BIDS parameter

We recommend to use dcm2bids ( or heuviconv ( 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.

If you need to filter some subjects/sessions/runs or some files you can create a bidsignore file using --bidsignore bids_ignore_path. (Check:

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 a BIDS structure and want to use -profile ABS you need to use the –fs option to point to your freesurfer folder output.

If you have any problems, contact us on NeuroStar (

Root parameter

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

├── S1
│   ├── dwi.nii.gz
│   ├── bval
│   ├── bvec
│   ├── t1.nii.gz
│   ├── rev_b0.nii.gz  (optional)
│   ├── aparc+aseg.nii.gz (optional)
│   └── wmparc.nii.gz  (optional)
└── S2
    ├── dwi.nii.gz
    ├── bval
    ├── bvec
    ├── t1.nii.gz
    ├── rev_b0.nii.gz  (optional)
    ├── aparc+aseg.nii.gz (optional)
    └── wmparc.nii.gz  (optional)

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.

  • t1.nii.gz is the T1 weighted image.

  • 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).

  • aparc+aseg.nii.gz (optional) is the freesurfer gm segmented image.

  • wmparc.nii.gz (optional) is the freesurfer wm segmented image.