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/unfmontreal/Dcm2Bids) or heuviconv
(https://github.com/nipy/heudiconv) 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: https://github.com/bids-standard/bids-validator#bidsignore)
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 (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 --input
and requires the following file structure:
[root]
├── 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.