Tutorials

The tutorial structure generally matches the module/function structure of MIRACL. Refer to the Legend section for syntax information.

Choose the tutorial for the function you are interested in from its respective module in the sidebar/TOC or go to our Getting started section for a tutorial on MIRACL's general usage.

Note that not all functions have tutorials yet…we are working on it!!!

Table of contents:

• Legend
• Getting started
  • Command-line
  • GUI
• Workflows
  • ACE **new feature**
    • Main Inputs
    • CLI
    • Main outputs
    • Example of running ACE on single subject (segmenation + registration + voxelization + warping) (link to sample data):
    • Example of running ACE flow on multiple subjects:
    • Example of running only ACE segmentation module on one single subject (link to sample data):
    • Example of running only ACE cluster wise analysis on voxelized and warped segmentation maps (link to sample data):
    • Jupyter notebook
  • CLARITY-Allen registration
    • Main outputs
    • GUI
    • Command-line
    • Visualize results
  • STA
    • Main Outputs
    • GUI
    • Command-line
    • Jupyter notebook
  • CLARITY segmentation
    • Main outputs
    • GUI
    • Command-line
• Conversion
  • Tiff to Nifti
    • GUI
    • Command-line
• Registration
  • CLARITY-Allen registration
    • GUI
    • Command-line
    • Jupyter notebook
  • MRI-Allen registration
    • GUI
    • Command-line
  • itk-SNAP re-orient image
• Stats
  • ACE CLuster only **new**
    • Main Inputs
    • CLI
    • Example usage (link to sample data):
    • Jupyter notebook
• Segmentation
  • ACE Segmentation Function
    • CLI
• Utilities
  • Intensity correction
    • Command-line
• HPC/SLURM clusters