SPECTRE

A fully automated brain extraction algorithm that incorporates registration, tissue segmentation, and morphological techniques which are combined in a watershed principle, while paying special attention to the preservation of the boundary between the gray matter and the cerebrospinal fluid.

Input Types

You should be able to apply this algorithm to any 3D MRI image which has a skull.

Module Parameters

Main

Atlas List	A special file describing a SPECTRE Atlas, one should be supplied with this software. Check the base directory of your install for a directory called Atlas.
Initial Erosion distance	Erosion of the registration and segmentation based masks before applying fall-set or watershed based principle.
Image modality	Adjusts internal parameters based on the modality of the image. T1_SPGR SPGR T1Sequence parameters (Four FANTASM Classes) T1_ALT Alternative T1 Sequence parameters (Six FANTASM Classes) T1_MPRAGE  MPRAGE T1 Sequence parameters (Five FANTASM Classes) T2 T2 Sequence parameters (Four FANTASM Classes; Watershed Principle is inverted) FLAIR FLAIR Sequence parameters (Four FANTASM Classes; CSF is assumed to have the highest Centroid value)
Output in Original Image Space	Puts the image back in its original space.
Find Midsaggital Plane	Estimate the Midsaggital Plane.

Advanced

Run Smooth Brain Mask	Smooths the surface of the brain mask.
Resample data to Isotropic voxels	The output image will have isotropic voxels if enabled.
Initial probability threshold
Minimum probability threshold
MMC Dilation distance	Size of dilation when creating the topologically closed object using a morphological closing operation.
MMC Erosion distance	Size of erosion when creating the topologically closed object using a morphological closing operation.

FANTASM

This is the segmentation tool that SPECTRE uses to create its initial mask. See the FANTASM module documentation for more details.

MSP

Output Plane?	Whether to output a 3D binary volume representing the Midsaggital Plane (MSP).
Output Split-Halves?	Whether to output a segmentation showing both hemisphere as two labels.
Output Segmentation on Plane?	Whether to output a FANTASM segmentation along the MSP.

Optimized Automated Registration

This is the affine registration that SPECTRE uses to create its initial mask based on the input atlases. See the Optimized Automated Registration module documentation for more details.

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Example Usage

Input image.
Isotropic Image. One of the first steps within SPECTRE is to isotropically resample an image. It also brings the image into the same spatial orientation as the atlas images. In this case the left and right of the image are flipped to observe radiological convention.
FANTASM Output.
Probability Output. This is a probability mask based on registering the atlas masks to the input image.
The skull stripped output image.
The skull strip mask is also output as a binary mask.
The hemisphere mask if the MSP component is enabled..
Binary image representing the MSP.
The MSP in cross-section through a FANTASM three class segmentation of the brain mask. This is a 2D image used for debugging the MSP software.