Modules & Workflows¶

Modules¶

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

Workflows¶

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

Or

# perform structure tensor analysis
miracl flow sta -h