Input structure

Two types of input are available in MouseFlow: BIDS [Not yet released] 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.

MouseFlow supports BIDS as input data using --bids YOUR_BIDS_DATASET. MouseFlow 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, MouseFlow 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/mouseflow_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/mouseflow).

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
│   ├── S1_dwi.nii.gz
│   ├── S1.bval
│   └── S1.bvec
└── S2
    ├── S2_dwi.nii.gz
    ├── S2.bval
    └── S2.bvec

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.