Projects:RuleBasedSegmentation
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Objective: In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules. We have implemented our code in Slicer 2. We currently provide modules for the semi-automatic segmentation of the DLPFC and the Striatum.
DLPFC Progress: We have developed an algorithm for Semi-Automatic Segmentation of the DLPFC based on the rules of Core 3 collaborator, Dr. James Fallon. This algorithm was tested last year in Matlab with successful results. This year, we implemented the algorithm into a 3D SLICER module which works with the current Editor Tab. A screenshot of the module is shown below. The ITK Bayesian Segmentation Filter is currently being incorporated into the module.
DLPFC Key Investigators:
- Georgia Tech: Ramsey Al-Hakim, John Melonakos, Delphine Nain, Allen Tannenbaum.
- UCI: James Fallon
- Kitware: Luis Ibanez
- Isomics: Steve Pieper
DLPFC Representative Image and Descriptive Caption
Striatum Progress: We have developed an algorithm for delineation of the striatum into 5 physiological subregions (pre/post caudate, pre/post putamen, and nucleus accumbens) while requiring only minimal user input. We have implemented this algorithm from the geometric rules for delineating the striatum as defined by our Core 3 collaborator, Dr. James Levitt of the PNL, into a 3D SLICER module. The current run time for the algorithm is ~20 seconds after the initial user input. The user inputs a label map of the full striatum, the most superior/dorsal voxel of the putamen on each slice, and the anterior commisure voxel (see figure below). From these, the labelmap is delineated into the aforementioned subregions. The figure below shows a 3D model of the left and right striatum delineated into the five subregions.
Striatum Key Investigators:
- GTech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum.
- PNL: Sylvain Bouix, James Levitt, Marc Niethammer, Martha Shenton.
- Kitware: Luis Ibanez
- Isomics: Steve Pieper
Striatum Representative Image and Descriptive Caption
Progress:
- The Rule-Based Segmentation Module for DLPFC and Striatum Parcellation may be found in Slicer 2.
References:
- Ramsey Al-Hakim, James Fallon, Delphine Nain, John Melonakos, and Allen Tannenbaum. A dorsolateral prefrontal cortex semi-automatic segmenter. In SPIE Medical Imaging, 2006.
- J. Melonakos, K. Krishnan, and A. Tannenbaum. An ITK Filter for Bayesian Segmentation: itkBayesianClassifierImageFilter. Insight Journal, 2006.
- J. Melonakos, R. Al-Hakim, J. Fallon, and A. Tannenbaum. Knowledge-Based Segmentation of Brain MRI Scans Using the Insight Toolkit. Insight Journal, 2005.
Links:
