Projects:UtahAtlasSegmentation - Revision history

Marianna: /* Publications */

2010-05-14T13:25:45Z

Publications

Marianna: /* Publications */

2010-05-14T13:25:35Z

Publications

Melonakos at 15:51, 13 May 2010

2010-05-13T15:51:14Z

Prastawa at 19:01, 11 May 2010

2010-05-11T19:01:30Z

Hjmjohnson: /* Key Investigators */

2010-05-11T16:40:09Z

Key Investigators

Hjmjohnson: /* ABC Bias Correction Module */

2010-05-11T16:39:27Z

ABC Bias Correction Module

Hjmjohnson: /* External use and modifications of ABC */

2010-05-11T16:37:57Z

External use and modifications of ABC

Gerig: /* Atlas Based Brain Segmentation (ABC) */

2010-05-11T16:18:50Z

Atlas Based Brain Segmentation (ABC)

Gerig: /* Atlas Based Brain Segmentation */

2010-05-11T16:18:20Z

Atlas Based Brain Segmentation

Gerig: /* Key Investigators */

2010-05-11T16:17:54Z

Key Investigators

← Older revision		Revision as of 13:25, 14 May 2010
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	= Publications =		= Publications =
−
−	~~''In Print''~~
	* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AUtahAtlasSegmentation NA-MIC Publications Database on Atlas Based Classification (ABC) for Healthy Brain MRI]		* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AUtahAtlasSegmentation NA-MIC Publications Database on Atlas Based Classification (ABC) for Healthy Brain MRI]

@@ Line 48: / Line 48: @@
 ''In Print''
-* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AUtahAtlasSegmentation&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&searchbytag=checked&sponsors=checked| NA-MIC Publications Database on Atlas Based Classification (ABC) for Healthy Brain MRI]
+* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AUtahAtlasSegmentation  NA-MIC Publications Database on Atlas Based Classification (ABC) for Healthy Brain MRI]
 = Key Investigators =

@@ Line 45: / Line 45: @@
 In order to meet existing strong demands for a stand-alone MRI bias correction method with FLASH images, part of the ABC code has been made available as a separate module and distributed via NITRC (http://www.nitrc.org/projects/probbiascor) by the MIND Institute group lead by Mark Skully and Jeremy Bockholt.
-= Publications related to this software development =
+= Publications =
-* Marcel Prastawa, John H. Gilmore, Weili Lin, and Guido Gerig. Automatic Segmentation of MR Images of the Developing Newborn Brain. Medical Image Analysis (MedIA). Vol 9, Issue 5, October 2005, Pages 457-466.
+''In Print''
-* Marcel Prastawa, Elizabeth Bullitt, Sean Ho, and Guido Gerig. A Brain Tumor Segmentation Framework Based on Outlier Detection . Medical Image Analysis (MedIA). Vol 8, Issue 3, September 2004, Pages 275-283.
+* [http://www.na-mic.org/publications/pages/display/?search=Projects%3AUtahAtlasSegmentation&submit=Search&words=all&title=checked&keywords=checked&authors=checked&abstract=checked&searchbytag=checked&sponsors=checked| NA-MIC Publications Database on Atlas Based Classification (ABC) for Healthy Brain MRI]
 = Key Investigators =

@@ Line 2: / Line 2: @@
 __NOTOC__
-= Atlas Based Brain Segmentation =
+= Atlas Based Classification (ABC) for Healthy Brain MRI =
-Automatic segmentation can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool that provides an automatic segmentation pipeline in a modular framework.
+Automatic segmentation of brain MR images can be performed reliably using priors from brain atlases and an image generative model. We have developed a tool called ABC that provides an automatic segmentation pipeline in a modular framework.
-The processing pipeline is composed tasks such as filtering the input images, registering the multimodal input images and the brain atlas to a common space, followed by iterative steps which interleave segmentation, inhomogeneity correction, and atlas warping.
+The processing pipeline is composed of tasks such as filtering the input images, registering the multimodal input images and the brain atlas to a common space, followed by iterative steps which interleave segmentation, inhomogeneity correction, and atlas warping.
 Our tool generates bias corrected images, fuzzy classification maps, and discrete segmentation labels. The tool has been used to automatically segment thousands of adult and toddler images from the University of North Carolina (UNC), and is also being used as a skull stripping mechanism for DTI processing at UNC and Utah. An example of the output of the tool is shown below.
@@ Line 16: / Line 16: @@
-The tool has been integrated into Slicer as an extension, and it can also be executed as a stand-alone application. Both versions are available for download through NITRC: http://www.nitrc.org/projects/abc .
+The ABC tool has been integrated into Slicer as an extension, and it can also be executed as a stand-alone application. Both versions are available for download through NITRC: http://www.nitrc.org/projects/abc .
 {|
 |-
@@ Line 23: / Line 23: @@
 |}
-== External use and modifications of ABC ==
+== External Use and Modifications of ABC ==
-A predicessor of ABC has been distributed to a large number of other research groups associated with ongoing image analysis projects at UNC Chapel Hill and the University of Utah, and to research groups linked to these investigators. High profile projects include the Silvio Conte Center (http://www.psychiatry.unc.edu/conte/, PI John H. Gilmore, UNC) with processing of over 1000 infant MRI, and the Autism Centers of Excellence Project IBIS (http://www.ibis-network.org/, PI Joseph Piven, UNC) where over 650 infant brain MRI will be processed with this tool. To segment infant brains with age range 6months to 2 years as part of this longitudinal study, new age-specific atlases have been developed to be used as spatial priors for ABC.
+An earlier version of ABC has been distributed to a large number of other research groups associated with ongoing image analysis projects at the University of North Carolina - Chapel Hill and the University of Utah, and to research groups linked to these investigators. High profile projects include the Silvio Conte Center (http://www.psychiatry.unc.edu/conte/, PI John H. Gilmore, UNC) involving the processing of over 1000 infant MRI, and the Autism Centers of Excellence Project IBIS (http://www.ibis-network.org/, PI Joseph Piven, UNC) where over 650 infant brain MRI will be processed with this tool. In order to segment infant brains with age range of 6 months to 2 years as part of this longitudinal study, new age-specific atlases have been developed to be used as spatial priors for ABC.
-The ABC method has also been modified and extensively used by the University of Iowa, Hans Johnson as part of a large, multi-center Huntington Disease study. Experience with a couple of hundred datasets at IOWA demonstrated the excellent robustness and reliability of the methodology.
+The ABC method has also been modified and extensively used by the Hans Johnson from University of Iowa, as part of a large, multi-center Huntington Disease study. Experience with a couple of hundred datasets at Iowa demonstrated the excellent robustness and reliability of the methodology.
 {|
@@ Line 36: / Line 36: @@
 |}
-The probability maps for the atlas were created from a set of 729 3T multi-modal image data sets (IOWA, Hans Johnson).  Improvements made were to include a measure of Venus Blood as a part of the model, and to add explicit tissue regions outside the head for tissue types that are not part of the brain. This atlas definitions are available from
+The probability maps for the atlas were created from a set of 729 3T multi-modal image data sets (Iowa, Hans Johnson).  Improvements made were to include a measure of Venus Blood as a part of the model, and to add explicit tissue regions outside the head for tissue types that are not part of the brain. This atlas definitions are available from
 svn co https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC/Atlas_20100510
-Under guidance of Hans Johnson, a branch of the ABC NITRC code has been modified to meet the needs of the IOWA group. This includes integration of a new Bspline-based registration from BRAINSFit, integration of BRAINSROIAuto, and to make it work with data with arbitrary orientation, and modifications of the interface (svn to https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC).
+Under guidance of Hans Johnson, a branch of the ABC NITRC code has been modified to meet the needs of the Iowa group. This includes integration of a new Bspline-based registration from BRAINSFit, integration of BRAINSROIAuto, and to make it work with data with arbitrary orientation, and modifications of the interface (svn to https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC).
 == ABC Bias Correction Module ==
-To meet still strong demands for a stand-alone MRI bias correction method with FLASH images, part of the ABC code has been made available as a separate module and distributed via NITRC (http://www.nitrc.org/projects/probbiascor) by the MIND Institute group lead by Mark Skully and Jeremy Bockholt.
+In order to meet existing strong demands for a stand-alone MRI bias correction method with FLASH images, part of the ABC code has been made available as a separate module and distributed via NITRC (http://www.nitrc.org/projects/probbiascor) by the MIND Institute group lead by Mark Skully and Jeremy Bockholt.
 = Publications related to this software development =

@@ Line 57: / Line 57: @@
 *Utah Algorithms: Marcel Prastawa, Guido Gerig
 *UNC Algorithms: Martin Styner
-*External research collaboration: Hans Johnson, MIND Institute, Iowa
+*External research collaboration: Hans Johnson, The University of Iowa

@@ Line 27: / Line 27: @@
 A predicessor of ABC has been distributed to a large number of other research groups associated with ongoing image analysis projects at UNC Chapel Hill and the University of Utah, and to research groups linked to these investigators. High profile projects include the Silvio Conte Center (http://www.psychiatry.unc.edu/conte/, PI John H. Gilmore, UNC) with processing of over 1000 infant MRI, and the Autism Centers of Excellence Project IBIS (http://www.ibis-network.org/, PI Joseph Piven, UNC) where over 650 infant brain MRI will be processed with this tool. To segment infant brains with age range 6months to 2 years as part of this longitudinal study, new age-specific atlases have been developed to be used as spatial priors for ABC.
-The ABC method has also been modified and extensively used by the University of Iowa, MIND Institute, Hans Johnson as part of a large, multi-center Huntington Disease study. Experience with a couple of hundred datasets at IOWA demonstrated the excellent robustness and reliability of the methodology.
+The ABC method has also been modified and extensively used by the University of Iowa, Hans Johnson as part of a large, multi-center Huntington Disease study. Experience with a couple of hundred datasets at IOWA demonstrated the excellent robustness and reliability of the methodology.
 {|
 |-
 | [[Image:ABC-MIND1.png|thumb|center|250px|Output of the segmentation plugin, showing the bias corrected image and the probabilities for white and gray matter.]]
-| [[Image:ABC-MIND2.png|thumb|center|250px|ABC tool applied to TBI MRI data.]]
+| [[Image:ABC-MIND2.png|thumb|center|250px|BRAINSABC expanded prior class images.]]
-| [[Image:ABC-MIND3.png|thumb|center|250px|ABC tool applied to TBI MRI data.]]
+| [[Image:ABC-MIND3.png|thumb|center|250px|BRAINSABC expanded prior class images.]]
 |}
-The probability maps for the atlas were created from a set of 729 3T multi-modal image data sets (MIND Institute, IOWA, Hans Johnson).  Improvements made were to include a measure of Venus Blood as a part of the model, and to add explicit tissue regions outside the head for tissue types that are not part of the brain. This atlas definitions are available from
+The probability maps for the atlas were created from a set of 729 3T multi-modal image data sets (IOWA, Hans Johnson).  Improvements made were to include a measure of Venus Blood as a part of the model, and to add explicit tissue regions outside the head for tissue types that are not part of the brain. This atlas definitions are available from
 svn co https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC/Atlas_20100510
-Under guidance of Hans Johnson, a branch of the ABC NITRC code has been modified to meet the needs of the IOWA group. This includes integration of a new Bspline-based registration from BRAINSFit, integration of BRAINSROIAuto to make it work with data with arbitrary orientation, and modifications of the interface (svn to https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC).
+Under guidance of Hans Johnson, a branch of the ABC NITRC code has been modified to meet the needs of the IOWA group. This includes integration of a new Bspline-based registration from BRAINSFit, integration of BRAINSROIAuto, and to make it work with data with arbitrary orientation, and modifications of the interface (svn to https://www.nitrc.org/svn/brains/BRAINS/trunk/BRAINSTools/BRAINSABC).
 == ABC Bias Correction Module ==

← Older revision		Revision as of 16:17, 11 May 2010
Line 57:		Line 57:
	*Utah Algorithms: Marcel Prastawa, Guido Gerig		*Utah Algorithms: Marcel Prastawa, Guido Gerig
	*UNC Algorithms: Martin Styner		*UNC Algorithms: Martin Styner
		+	*External research collaboration: Hans Johnson, MIND Institute, Iowa