TOADS-CRUISE

TOADS-CRUISE is the complete pipeline for brain extraction, structural segmentation, and cortical reconstruction of human brain cortex from a raw T1-weighted image. It consists of several different modules:

1) The shading artifact is corrected using N3 algorithm.
2) SPECTRE is used to extract the brain.
3) TOADS is used to generate the required images for Remove Dura algorithm.
4) Brain mask is refined using Remove Dura.
5) A second pass of TOADS generates the required input images for CRUISE algorithm.
6) CRUISE generates the inner, central, and outer surfaces.
7) Cortical thickness is computed by subtracting the inner surface levelset function from the outer surface levelset function.

Input:

Input Volume (N3 Correction panel)	The raw T1-weighted image to be processed.
Image modality (TOADS panel)	The pulse sequence of the T1-weighted image (MPRAGE or SPGR)

Input: parameters

The parameters for each of the component of TOADS-CRUISE are completely provided in the individual description page of each algorithm (N3, SPECTRE, Remove dura, TOADS, GVF and Nested TGDM).

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Example Usage

N3 output
SPECTRE output
Remove dura output
TOADS ouputs	Initial Level Set (WM mask) Filled WM membership Cortical GM membership
ACE outputs	Thinned ACE Skeleton ACE Enhanced GM membership
GVF output	Gradient Vector Field (x component)
Nested TGDM outputs (Levelset functions)	Inner Levelset Central Levelset Outer Levelset
Nested TGDM outputs (Cortical surfaces)	Inner Surface Central Surface Outer Surface