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nf-mouse

Inputs

Basic input directory

Section titled “Basic input directory”

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

  • Directoryinput_directory
    • Directorysub-01
      • sub-01_dwi.bval
      • sub-01_dwi.bvec
      • sub-01_dwi.nii.gz
      • sub-01_mask.nii.gz (optional)
    • Directorysub-02
      • sub-02_dwi.bval
      • sub-02_dwi.bvec
      • sub-02_dwi.nii.gz
      • sub-02_mask.nii.gz (optional)

nf-mouse allows to extract the brain with a nnUNet algorithm. If you don’t want to use this method, you also can provide a mask.

BIDS input directory (In development)

Section titled “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 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 will soon be BIDS compatible.