Modules & Workflows


The pipeline is combined of different “Modules” depending on their functionality Functions for each module are grouped together:

  • connect -> Connectivity
  • conv -> Conversion (Input/Output)
  • reg -> Registration
  • seg -> Segmentation
  • lbls -> Labels
  • utilfn -> Utilities
  • sta -> Structure Tensor Analysis
  • stats -> Statistics


The workflow (flow) module combines multiple functions for ease of use to preform a desired task. For example, for a standard reg/seg analysis a user would run:

# First perform registration of whole-brain clarity data to ARA
miracl flow reg_clar -h

# then perform segmentation & feature extraction of full resolution clarity data  
miracl flow seg -h


# perform structure tensor analysis
miracl flow sta -h