FSL-based segmentation pipeline

                                  EM segmentation pipeline
                                          Aug 10, 09

Atlas construction phase:

 Chose one subject form the dataset as the target image;

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 Using the Slicer3 module to perform histogram matching from all other subjects to the target;

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 Affine register all subjects to the target using flirt;

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 Manually skull strip the target;

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 Apply the brain mask to all subjects to obtain brain matter;

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 Perform bias correction on the brain matters using the binary within ITK Insight Applications.

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 Affine register the brain matters of all subjects to that of the target using flirt, and save the

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 transform as .mat;
 Subsequently, using Diffeomorphic Demons registration to register all subjects to the target

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 and save the deformation field as .mha;
 Inverse the skull mask to obtain skull matter for all subjects;

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 Apply the above obtained affine transformations and Demons deformations to deform their

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 corresponding skull matter;
 Combine the brain matter and skull matter for each subject to obtain co-aligned brain images;

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 Average the co-aligned images to generate the atlas;

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 Apply KMS segmentation on all subjects, followed by manually correction of the segmenta-

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 tions;
 Collect all the segmentation results to generate tissue maps and the ECC masks.

• EM segmentation phase:

 Using the image of each subject as the target and the atlas as the source;

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 For each subject, affine register its whole head image to the whole head atlas;

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 Use the aligned brain mask from atlas to skull strip the subject image;

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 Affine register the brain matter in the atlas to the masked brain matter of the subject, and save

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 the transform as .mat;
 Subsequently, using Diffeomorphic Demons registration to register the brain matter in the

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 atlas to that of the subject, and save the deformations as .mha;
 Apply the above obtained affine transformation and demons deformation to the tissue maps

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 and ECC mask;
 Perform EM segmentation using the Slicer2/Slicer3 module.