NITRC: Hammer And WML Modules for 3D Slicer: hammer

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hammer_faq > Complete registration pipeline of HAMMER

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Complete registration pipeline of HAMMER

Pre-processing steps:
1. AC (anterior commissure)-PC (posterior commisure) alignment.
2. Remove extra-cranial tissue.
3. Segment brain tissue into white matter, gray matter and cerebrospinal fluid.
4. Set the label values for white matter, gray matter and cerebrospinal fluid to 250, 150, 10, respectively.

Running HAMMER:
1. Do the linear registration to remove the global difference.
2. Run HAMMER to estimate the local deformations.

AC-PC alignment step

You may use the AC-PC alignment module in 3D Slicer to correct the anterior and posterior commissures. The tutorial and document can be found at (http://www.slicer.org/slicerWiki/index.p...).

Skull stripping step

You may use the skull stripping module in 3D Slicer to remove the extra-cranial tissues of brain. The tutorial and document can be found at (http://www.slicer.org/slicerWiki/index.p...).

Tissue segmentation step

There are a lot of modules in 3D Slicer for image segmentation. Here we suggest to use the EM segmentation module in 3D Slicer. The document and tutorial can be found at (http://www.slicer.org/slicerWiki/index.p...) and (http://www.slicer.org/slicerWiki/index.p...).

Linear registration step

There are a lot of linear registration methods available in 3D Slicer. We suggest to use the affine registration module in 3D slicer. The document and tutorial can be found at (http://www.slicer.org/slicerWiki/index.p...).

Run HAMMER

The step-by-step tutorial can be found in the download panel of this page. We show all snapshots of using HAMMER in 3D Slicer from skull stripping module to HAMMER registration module.

RE: Run HAMMER

3D slicer encourages to reuse the existing modules as much as possible. Therefore our HAMMER registration module performs the deformable registration which only estimate the local deformations.