Projects:RuleBasedSegmentation - Revision history

Ygao at 01:08, 16 November 2013

2013-11-16T01:08:12Z

Melonakos at 15:11, 4 December 2007

2007-12-04T15:11:01Z

Melonakos at 00:22, 28 November 2007

2007-11-28T00:22:29Z

Melonakos at 00:04, 5 October 2007

2007-10-05T00:04:36Z

Melonakos at 14:00, 2 October 2007

2007-10-02T14:00:10Z

Melonakos at 21:41, 21 September 2007

2007-09-21T21:41:22Z

Melonakos at 14:04, 4 September 2007

2007-09-04T14:04:46Z

Melonakos at 14:04, 4 September 2007

2007-09-04T14:04:27Z

Melonakos at 14:04, 4 September 2007

2007-09-04T14:04:20Z

Melonakos at 14:02, 4 September 2007

2007-09-04T14:02:22Z

@@ Line 1: / Line 1: @@
-  Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
+  Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:Stony Brook|Stony Brook University Algorithms]]
 __NOTOC__
 = Rule Based Segmentation =

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
+__NOTOC__
 = Rule Based Segmentation =
@@ Line 7: / Line 7: @@
 = Description =
-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.
+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. This is important, since we use Bayesian classifiers in order to enhance the Fallon method. The motivation of the DLPFC semi-automatic segmenter was to minimize segmentation time of the DLPFC by incorporating the rules of Dr. Fallon into an algorithm, while still giving the user control of the segmentation process.  The time to segment the DLPFC was reduced from over 30 minutes to approximately 5 minutes. The algorithm is based on the average proportional distances of the posterior boundary from the temporal lobe tip and the anterior boundary from the frontal pole. Each hemisphere must be done separately. The average shape is a parallelogram from the movement of the middle frontal gyrus dorsally as moving posteriorly through coronal slices  Dr. James Fallon has visited Georgia Tech in December 2005 to train our local researchers about his heuristic rules. He will be visiting again on May 17-18, 2007 for further testing and algorithmic development as well as clinical applications.
 ''Striatum Progress''

@@ Line 10: / Line 10: @@
 This is important, since we use Bayesian classifiers in order to enhance the Fallon method.
 The motivation of the DLPFC semi-automatic segmentor was to minimize segmentation time of the DLPFC by incorporating the rules of Dr. Fallon into an algorithm, while still giving the user control of the segmentation process.  The time to segment the DLPFC was reduced from over 30 minutes to approximately 5 minutes. The algoirthm is based on the average proportional distances of the posterior boundary from the temporal lobe tip and the anterior boundary from the frontal pole. Each hemisphere must be done separately. The average shape is a parallelogram from the movement of the middle frontal gyrus dorsally as moving posteriorly through coronal slices  Dr. James Fallon has visited Georgia Tech in December 2005 to train our local reseachers about his heuristic rules. He will be visting again on May 17-18, 2007 for further testing and algorithmic development as well as clinical applications.
 ''Striatum Progress''
@@ Line 33: / Line 18: @@
 [[Image:Striatum1.png|[[Image:Striatum1.png|Image:Striatum1.png]]]] [[Image:Striatum2.png|[[Image:Striatum2.png|Image:Striatum2.png]]]]
 = Key Investigators =
-* Georgia Tech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum.
+* Georgia Tech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum, John Melonakos
 * PNL: Sylvain Bouix, James Levitt, Marc Niethammer, Martha Shenton.
 * Kitware: Luis Ibanez
 * Isomics: Steve Pieper
 = Publications =
-= Links =
+[http://www.na-mic.org/Special:Publications?text=Projects%3ADLPFC&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked| NA-MIC Publications Database]

@@ Line 17: / Line 17: @@
 ''DLPFC Publications''
-http://www.na-mic.org/Special:Publications?text=Projects%3ADLPFC&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked
+[http://www.na-mic.org/Special:Publications?text=Projects%3ADLPFC&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked| NA-MIC Publication Database]
 ''DLPFC Key Investigators''

@@ Line 15: / Line 15: @@
 [[Image:Dlpfc-slicer.png|[[Image:Dlpfc-slicer.png|DLPFC Slicer Module]]]]
-''DLPFC References''
+''DLPFC Publications''
-* Ramsey Al-Hakim, James Fallon, Delphine Nain, John Melonakos, and Allen Tannenbaum. A dorsolateral prefrontal cortex semi-automatic segmenter. In SPIE Medical Imaging, 2006.
+http://www.na-mic.org/Special:Publications?text=Projects%3ADLPFC&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&sponsors=checked&searchbytag=checked
 ''DLPFC Key Investigators''
@@ Line 47: / Line 45: @@
 * Isomics: Steve Pieper
 = Links =

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]], [[Algorithm:GATech|Georgia Tech Algorithms]]
-'''Objectives'''
+= Rule Based Segmentation =
 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'''
+= Description =
 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.
@@ Line 23: / Line 21: @@
 * J. Melonakos, R. Al-Hakim, J. Fallon, and A. Tannenbaum. Knowledge-Based Segmentation of Brain MRI Scans Using the Insight Toolkit. Insight Journal, 2005.
-'''DLPFC Key Investigators'''
+''DLPFC Key Investigators''
 * Georgia Tech: Ramsey Al-Hakim, John Melonakos, Delphine Nain, Allen Tannenbaum.
@@ Line 30: / Line 28: @@
 * Isomics: Steve Pieper
-'''Striatum Progress'''
+''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 Representative Image and Descriptive Caption''
@@ Line 49: / Line 40: @@
 * The Rule-Based Segmentation Module for DLPFC and Striatum Parcellation may be found in Slicer 2.
-'''Links'''
+= Key Investigators =
 * [[Algorithm:GATech|Georgia Tech Algorithms]]
 * [[NA-MIC_Collaborations|NA-MIC Collaborations]]

@@ Line 13: / Line 13: @@
 The motivation of the DLPFC semi-automatic segmentor was to minimize segmentation time of the DLPFC by incorporating the rules of Dr. Fallon into an algorithm, while still giving the user control of the segmentation process.  The time to segment the DLPFC was reduced from over 30 minutes to approximately 5 minutes. The algoirthm is based on the average proportional distances of the posterior boundary from the temporal lobe tip and the anterior boundary from the frontal pole. Each hemisphere must be done separately. The average shape is a parallelogram from the movement of the middle frontal gyrus dorsally as moving posteriorly through coronal slices  Dr. James Fallon has visited Georgia Tech in December 2005 to train our local reseachers about his heuristic rules. He will be visting again on May 17-18, 2007 for further testing and algorithmic development as well as clinical applications.
-'''DLPFC Representative Image and Descriptive Caption'''
+''DLPFC Representative Image and Descriptive Caption''
 [[Image:Dlpfc-slicer.png|[[Image:Dlpfc-slicer.png|DLPFC Slicer Module]]]]