Difference between revisions of "FSL-based segmentation pipeline"
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| − | + | ==Abstract== | |
| − | + | This page describes the FSL-based EM segmentation. Page created by Aug, 09. | |
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| − | + | === Segmentation pipeline === | |
| + | # 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 segmentations; | ||
| + | ## 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. | ||
| − | + | === Segmentation Results === | |
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Revision as of 21:17, 21 August 2009
Home < FSL-based segmentation pipelineAbstract
This page describes the FSL-based EM segmentation. Page created by Aug, 09.
Segmentation pipeline
- 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 segmentations;
- 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.
