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.