Vervet MRI registration

Objective

Perform atlas-to-subject registration of vervet head MRI as part of external collaboration with VTech.

Methods

Original workflow utilized multi-step registration using FSL FLIRT, followed by diffeomorphic demons (reference to be added).

In this development, we consider the use of [BRAINSFit] package within 3D Slicer to achieve reproducible and reliable registration workflow using 3DSlicer and FOSS-only tools.

We use the following registration pipeline: Rigid (6-DOF) -> ScaleVersorRigid (9-DOF) -> Affine (12-DOF) -> BSpline. Probabilistic atlas is the moving image, registered to the space of the subject image.

Data

Input images: atlas image, generated following the details presented here, and 10 subject images.

Each vervet subject has a name! Meet our friends: Calvin, Gucci, Hugo, Issac, Louis, Marc, Oscar, Ralph, Tommy, and Valentino.

Results

For each of the 10 subjects, we show checkerboard slices in each direction (1) before registration, first row; (2) after rigid->scaleversor->affine registration, second row; and (3) after BSpline registration, third row.

Note the unsuccessful BSpline registration result for Issac.

The tarball with the transforms is available File:VervetRegistrationTransforms.tgz

Calvin

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Gucci

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Hugo

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Issac

Issac is a good example of BSpline registration failure.

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Ron noted, the reason might be that Issac had his mouth open, unlike most of the subjects registered successfully.

Louis

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Marc

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Oscar

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Ralph

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Tommy

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Valentino

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