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
  • CLARITY-Allen registration
    • Main outputs
    • GUI
    • Command-line
    • Visualize results
  • STA
    • Main Outputs
    • GUI
    • Command-line
  • CLARITY segmentation
    • Main outputs
    • GUI
    • Command-line
• Conversion
  • Tiff to Nifti
    • GUI
    • Command-line
• Registration
  • CLARITY-Allen registration
    • GUI
    • Command-line
  • MRI-Allen registration
    • GUI
    • Command-line
• Utilities
  • Intensity correction
    • Command-line
• HPC/SLURM clusters