FEDI Command-Line Tools

FEDI provides a suite of command-line tools for processing and analyzing fetal and neonatal MRI data. Each module name follows a consistent naming convention, starting with fedi_, followed by the MRI modality (e.g., t1w, t2w, dmri, fmri) and a descriptive method name.

To list all available FEDI commands in your terminal, use:

fedi_<TAB>

To view help for a specific tool, use the --help option:

fedi_dmri_moco --help

The tools are categorized below for easier navigation.

Diffusion MRI

• fedi_dmri_moco: Corrects motion artifacts in diffusion MRI.

• fedi_dmri_reg: Performs image registration on dMRI data.

• fedi_dmri_qweights: Converts diffusion gradient scheme into Siemens-compatible format.

• fedi_dmri_rotate_bvecs: Rotates b-vectors to match ANTs transformations.

• fedi_dmri_outliers: Identifies and weights outliers (volume, slice, voxel) in dMRI data.

• fedi_dmri_snr: Computes the signal-to-noise ratio (SNR) of dMRI data.

• fedi_dmri_recon: Reconstructs the diffusion signal using 3D-SHORE.

• fedi_dmri_fod: estimates FODs for neonatal dMRI using a pretrained Spherical CNN model.

Miscellaneous

• fedi_apply_transform: Applies affine or nonlinear transformations to MRI data.

• fedi_testing: Generates test data and runs automated tests for all FEDI command-line tools.

Segmentation and Others

(Coming Soon.)