Scripts

This section provides documentation for the individual command-line scripts included in MicaFlow.

Each script can be run independently using the micaflow [command] syntax and has its own set of parameters.

Quick Reference

Script	Description
Apply Sdc	Apply precomputed distortion correction
Apply Warp	Apply transformations to images
Bet	Brain extraction using SynthSeg
Bias Correction	N4 bias field correction
scripts/bids	Automated BIDS directory scanning and processing
Calculate Jaccard	Calculate similarity between segmentations
Compute Fa Md	Compute DTI metrics (FA, MD)
Coregister	Image coregistration using ANTs
Denoise	Denoise diffusion-weighted images
Motion Correction	Motion correction for DWI
Sdc	Susceptibility distortion correction
Synthseg	Deep learning segmentation with SynthSeg
Texture Generation	Generate texture features
Normalize	Normalize intensity values