Inputs

Basic input directory

nf-mouse_flow only needs diffusion MRI images. The input structure should look like this:

• Directoryinput_directory

  • Directorysub-01

    • sub-01_dwi.nii.gz
    • sub-01_dwi.bval
    • sub-01_dwi.bvec
  • Directorysub-02

    • sub-02_dwi.nii.gz
    • sub-02_dwi.bval
    • sub-02_dwi.bvec

BIDS input directory (In development)

The BIDS (Brain Imaging Data Structure) input directory is a standardized way to organize and describe neuroimaging and behavioral data. The nf-mouse_flow pipeline expects the input data to be organized in the BIDS format. Good resources to convert your raw DICOMs files in a BIDS structure include dcm2bids and/or heudiconv. It is recommended that users validate their BIDS layout using the official bids-validator tool docker image or the web-based version.

nf-mouse_flow will soon be BIDS compatible.