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 HD-BET
Bias Correction	N4 bias field correction
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