From NITRC Wiki

Multi-Atlas Gyral Labeling

The purpose of this pipeline is to label the cortical surfaces reconstructed by CRUISE with gyral segmentations. The layout is separated into the following sections.

Gyral Labeling Layout

Labeling via Multiple Atlas Registration

This module registers N input atlases to a target volume, and then uses the mappings from the registration to transfer the labels from the atlases onto the target. STAPLE is run on all the mapped atlas labels to create a final labeled volume for the target.

Inputs:

• Atlases - The atlas volumes to be registered to the target volume.
• Atlas Labels - Labels on the atlases to be mapped to the target via the registration.
• Target - The target volume to be labeled.

Outputs:

• Labeled Results for Target - The labels results transfered to the target, using the segmentations provided by the atlases.
• Deformed Atlas Labels - (Optional Intermediate Result) The input atlas labels mapped to the target space.
• Registered Atlases - (Optional Intermediate Result) The input atlases mapped to the target space.
• Deformation Fields - (Optional Intermediate Result) The deformation fields used to map the atlases and labels to target space.
• Transformation Matrices - (Optional Intermediate Result) The transformation matrices used to perform the affine registrations prior to the non-linear registrations.

Volume Labels to Surface

This module transfers a set of volumetric labels to a target surface.

Inputs:

• Surface to Label - The cortical surface that the volumetric labels will be transfered to.
• Data Volume - The volumetric labels to be transfered

Outputs:

• Surface to Label - The labeled cortical surface result.

Cleanup Surface Labels

This module cleans up the labeled cortical surfaces by removing any major topological errors that might've been introduced during the volume to surface transfer.