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FALCON Usage Guide

Harness the power of FALCON with ease. Whether you're dealing with DICOM, Nifti, Analyze, or Metaimage file formats, FALCON seamlessly handles it all. This guide provides a walkthrough on how to use FALCON efficiently and effectively.

Supported File Formats

FALCON can process:

  • DICOM
  • Nifti
  • Analyze
  • Metaimage

You can work with either a single 4D image or multiple 3D images. Just point FALCON to the directory, and let it handle the magic.

Basic Syntax

To launch FALCON, follow this syntax:

falcon -m <path_to_4d_images> -r <registration_type> -i <iterations_per_level> -sf <starting_frame> -rf <reference_frame>

Examples

Pro Mode:

falcon -m /Documents/Sub001 -r deformable -i 100x50x25 -sf 0 -rf -1

This runs FALCON with deformable registration over a multi-scale, starting from the first frame, and using the last frame as the reference.

Lazy Mode:

For whole-body registration:

falcon -m /Documents/Sub001 -r deformable

For brain-only studies (faster processing):

falcon -m /Documents/Sub001 -r rigid

Lazy mode keeps things simple. Many parameters are either inferred or set based on common standards, removing the guesswork.

Important Points

⚠️ If the inferred start frame doesn't align with your needs, manually set it. FALCON has a conservative internal threshold, but adjustments are sometimes necessary. For more insights, refer to the associated manuscript.

Help & Further Options

For detailed command line options or if you need assistance:

falcon --help

Remember, when specifying iterations in the -i option, use the format valueXvalueXvalue. For instance, -i 50x50x50 signifies 50 iterations at each level.