FSL-based segmentation pipeline

                                  EM segmentation pipeline
                                          Aug 10, 09

Atlas construction phase:

 Chose one subject form the dataset as the target image;

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

 Affine register all subjects to the target using flirt;

 Manually skull strip the target;

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

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

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

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

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

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

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

 Average the co-aligned images to generate the atlas;

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

 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;

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

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

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

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

 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

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