2009 prostate segmentation challende MICCAI - Revision history

Noby: Replaced content with 'http://wiki.na-mic.org/Wiki/index.php/2009_prostate_segmentation_challenge_MICCAI'

2009-05-15T13:18:42Z

Replaced content with 'http://wiki.na-mic.org/Wiki/index.php/2009_prostate_segmentation_challenge_MICCAI'

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2009-05-12T10:55:07Z

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Noby: Created page with '=Goal= To discuss the state-of-art segmentation of Prostate MRI in the context of MRI-guided prostate therapy, through comparison of the segmentation methods using sample data. =...'

2009-05-12T10:41:33Z

Created page with '=Goal= To discuss the state-of-art segmentation of Prostate MRI in the context of MRI-guided prostate therapy, through comparison of the segmentation methods using sample data. =...'

New page

=Goal=
To discuss the state-of-art segmentation of Prostate MRI in the context of MRI-guided prostate therapy, through comparison of the segmentation methods using sample data.
=Organizer=
*Nobuhiko Hata (co-lead organizer, BWH, Boston, MA)
*Gabor Fichtinger (co-lead organizer, Queens Univ, Kingston, ON)
*Sota Oguro (Data managing, BWH, Boston, MA)
*Haytham Elhawary (Slicer module for validation, BWH, Boston, MA)

=Rule=
#Download 3D Slicer for viewing and manipulating the dataset we provide.
#(Optional) Download the tutorial and its associated images regarding prostate image processing from Slicer's website.
#Download the Prostate MRI and the manual segmentation (as training data) from the website of National Center for Image Guided Therapy (PI: Jolesz and Tempany).
#Download the Prostate MRI of the challenge subject.
#Submit segmentation results with the paper describing the method developed and applied. The segmentation result should be [http://teem.sourceforge.net/nrrd/index.html NRRD format ] and loadable to Slicer. The segmentation result should aligned to original MRI when loaded to Slicer.
#segmentation result should maintain the same grayscale value assinged to the training dataset. Namely,
#the organizer will score the segmentation result by comparing it with manual segmentation of the expert using the announced comparison scheme.
#Repeat step above at the workshop.

=Dates=
#Training data available: May, 2009

#Submission of results: June 29, 2009

#Submission of papers (with results): July 20, 2009

#Workshop: September 2009

=Download=
#[http://www.slicer.org/pages/Special:SlicerDownloads 3D Slicer]
#[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning Prostate MRI tutorial for 3D Slicer]
#[[2009ProstateChallengeTrainingData |Training MRI data and segmentation(N=10)]]
#[[2009ProstateChallengeData |Subject data (for paper submission)]]
#Subject data (for contest on-site)

=Evaluation scheme=
*95% Hausdorff distance (HD)

The HD between two point datasets formed by the edges of the segmented prostate sub-anatomy from the MRI and manual segmentation. We will measured the accuracy of alignment between these two segmentations, by extracting the edges from the subsections. The HD is the maximum distance of a set to the nearest point in the other set. More formal description of the HD can be found at:

Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.

*Dice Similarity Coefficient (DSC)

The DSC, which has been used in evaluation of segmentation, gives a measure of the volumetric overlap between the segmented livers from the registered images. The DSC indicates twice the number of voxels which are shared by or are common to both registered datasets. The denominator is the total number of voxels in both datasets. The DSC can range from zero to one, where zero is no alignment between registered livers and one is perfect alignment. An example of DSC used in prostate segmetation can be found at

A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

← Older revision		Revision as of 13:18, 15 May 2009
Line 1:		Line 1:
−	~~=Goal=~~	+	http://wiki.na-mic.org/Wiki/index.php/2009_prostate_segmentation_challenge_MICCAI
−	~~To discuss the state-of-art segmentation of Prostate MRI in the context of MRI-guided prostate therapy, through comparison of the segmentation methods using sample data.~~
−	~~=Organizer=~~
−	*Nobuhiko Hata (co-lead organizer, BWH, Boston, MA, Email hata at-mark bwh.harvard.edu)
−	*Gabor Fichtinger (co-lead organizer, Queens Univ, Kingston, ON)
−	*Sota Oguro (Data managing, BWH, Boston, MA)
−	*Haytham Elhawary (Slicer module for validation, BWH, Boston, MA)
−	*Theo van Walsum (Organizer of the umbrella MICCAI workshop "3D segmentation in Clinic").
−
−	~~=Rule=~~
−	~~#Download 3D Slicer for viewing and manipulating the dataset we provide.~~
−	~~#(Optional) Download the tutorial and its associated images regarding prostate image processing from Slicer's website.~~
−	~~#Download the Prostate MRI and the manual segmentation (as training data) from the website of National Center for Image Guided Therapy (PI: Jolesz and Tempany).~~
−	~~#Download the Prostate MRIs and segmentation results by the experts.~~
−	#Submit segmentation results with the paper describing the method developed and applied. The segmentation result should be [http://teem.sourceforge.net/nrrd/index.html NRRD format ] and loadable to Slicer. The segmentation result should aligned to original MRI when loaded to Slicer.
−	~~#segmentation result should maintain the same grayscale value assigned to each anatomy in the training dataset. See the description of the training dataset,~~
−	~~#the organizer will score the segmentation result by comparing it with manual segmentation of the expert using the announced comparison scheme.~~
−	~~#Repeat step above at the workshop.~~
−
−	~~=Dates=~~
−	~~#Training data available: May, 2009~~
−
−	~~#Submission of results: June 29, 2009~~
−
−	~~#Submission of papers (with results): July 20, 2009~~
−
−	~~#Workshop: September 2009~~
−
−	~~=Download=~~
−	~~#[http://www.slicer.org/pages/Special:SlicerDownloads 3D Slicer]~~
−	#[http://wiki.na-mic.org/Wiki/index.php/~~IGT:ToolKit/Prostate-Planning Prostate MRI tutorial for 3D Slicer]~~
−	~~#[[2009ProstateChallengeTrainingData \|Training MRI data and segmentation]]~~
−	~~#[[2009ProstateChallengeData \|Subject data (for paper submission)]]~~
−	~~#Subject data (for contest on-site)~~
−
−	~~=Evaluation scheme=~~
−	*95% Hausdorff distance (HD)
−
−
−	The HD between two point datasets formed by the edges of the segmented prostate sub-anatomy from the MRI and manual segmentation. We will measured the accuracy of alignment between these two segmentations, by extracting the edges from the subsections. The HD is the maximum distance of a set to the nearest point in the other set. More formal description of the HD can be found at:
−
−	Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
−
−	*Dice Similarity Coefficient (DSC)
−
−	The DSC, which has been used in evaluation of segmentation, gives a measure of the volumetric overlap between the segmented livers from the registered images. The DSC indicates twice the number of voxels which are shared by or are common to both registered datasets. The denominator is the total number of voxels in both datasets. The DSC can range from zero to one, where zero is no alignment between registered livers and one is perfect alignment. An example of DSC used in prostate segmetation can be found at
−
−	A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

@@ Line 30: / Line 30: @@
 #[http://www.slicer.org/pages/Special:SlicerDownloads 3D Slicer]
 #[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning Prostate MRI tutorial for 3D Slicer]
-#[[2009ProstateChallengeTrainingData |Training MRI data and segmentation(N=6)]]
+#[[2009ProstateChallengeTrainingData |Training MRI data and segmentation]]
 #[[2009ProstateChallengeData |Subject data (for paper submission)]]
 #Subject data (for contest on-site)

@@ Line 2: / Line 2: @@
 To discuss the state-of-art segmentation of Prostate MRI in the context of MRI-guided prostate therapy, through comparison of the segmentation methods using sample data.
 =Organizer=
-*Nobuhiko Hata (co-lead organizer, BWH, Boston, MA)
+*Nobuhiko Hata (co-lead organizer, BWH, Boston, MA, Email hata at-mark bwh.harvard.edu)
 *Gabor Fichtinger (co-lead organizer, Queens Univ, Kingston, ON)
 *Sota Oguro (Data managing, BWH, Boston, MA)

@@ Line 12: / Line 12: @@
 #(Optional) Download the tutorial and its associated images regarding prostate image processing from Slicer's website.
 #Download the Prostate MRI and the manual segmentation (as training data) from the website of National Center for Image Guided Therapy (PI: Jolesz and Tempany).
-#Download the Prostate MRI of the challenge subject.
+#Download the Prostate MRIs and segmentation results by the experts.
 #Submit segmentation results with the paper describing the method developed and applied. The segmentation result should be [http://teem.sourceforge.net/nrrd/index.html NRRD format ] and loadable to Slicer. The segmentation result should aligned to original MRI when loaded to Slicer.
-#segmentation result should maintain the same grayscale value assinged to the training dataset. See the description of the training dataset,
+#segmentation result should maintain the same grayscale value assigned to each anatomy in the training dataset. See the description of the training dataset,
 #the organizer will score the segmentation result by comparing it with manual segmentation of the expert using the announced comparison scheme.
 #Repeat step above at the workshop.

@@ Line 6: / Line 6: @@
 *Sota Oguro (Data managing, BWH, Boston, MA)
 *Haytham Elhawary (Slicer module for validation, BWH, Boston, MA)
 =Rule=