BRAINSMush - Revision history

Vmagnotta at 15:54, 10 December 2008

2008-12-10T15:54:57Z

Vmagnotta at 15:48, 10 December 2008

2008-12-10T15:48:04Z

Vmagnotta at 15:44, 10 December 2008

2008-12-10T15:44:26Z

Vmagnotta at 15:43, 10 December 2008

2008-12-10T15:43:51Z

Vmagnotta at 15:05, 10 December 2008

2008-12-10T15:05:23Z

Vmagnotta at 15:04, 10 December 2008

2008-12-10T15:04:13Z

Vmagnotta at 14:55, 10 December 2008

2008-12-10T14:55:08Z

Vmagnotta at 14:54, 10 December 2008

2008-12-10T14:54:57Z

Vmagnotta at 14:53, 10 December 2008

2008-12-10T14:53:40Z

Vmagnotta: New page: To develop a new interface to BRAINS that builds upon NA-MIC tools. The interface should support all major platforms including Windows, Mac, Linux, and other Unix flavors. '''Progress:''...

2008-12-10T14:46:30Z

New page: To develop a new interface to BRAINS that builds upon NA-MIC tools. The interface should support all major platforms including Windows, Mac, Linux, and other Unix flavors. '''Progress:''...

New page

To develop a new interface to BRAINS that builds upon NA-MIC tools. The interface should support all major platforms including Windows, Mac, Linux, and other Unix flavors.

'''Progress:'''
* A new tracing (editing) tool is being developed to serve as a testing ground for the new GUI. The tracing tool uses the vtkContourWidget and is built on KWWidgets. The Slicer3 look and feel has been integrated. This tracing tool is nearing a beta release and will include the following features
#Support for editing in multiple planes simultaneously
#Ability to telegraph traces into other planes
#Ability to export traces as binary images for integration into Slicer3
#Ability to export traces as BRAINS2 mask objects
#Traces will be saved in VTK XML format

'''Key Investigators:'''

* University of Iowa: Vincent Magnotta, Hans Johnson, Nancy Andreasen, Kent Williams
* The MIND Institute: Jeremy Bockholt

'''Figures:'''

<gallery Caption="BRAINSTracer" widths="300px" heights="300px" perrow="2">
Image:BRAINSTracer1.png|BRAINS Tracer showing vtkContourWidget and telegraphing of ROIs
Image:BRAINSTracer2.png|BRAINS Tracer with the splash screen
</gallery>

'''Links:'''
*[http://www.psychiatry.uiowa.edu University of Iowa Department of Psychiatry]
*[http://mri.radiology.uiowa.edu University of Iowa MRI Center]
*[http://www.themindinstitute.org The MIND Institute]

'''Papers:'''

← Older revision		Revision as of 15:54, 10 December 2008
Line 1:		Line 1:
		+	Back to [[NA-MIC Brains Collaboration]]
		+
		+
		+	'''Summary:'''
	BRAINS Maximize Uniformity Summation Heuristic (MUSH). This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.		BRAINS Maximize Uniformity Summation Heuristic (MUSH). This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.

@@ Line 1: / Line 1: @@
-This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.
+BRAINS Maximize Uniformity Summation Heuristic (MUSH). This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.
@@ Line 22: / Line 22: @@
 *Source code has been posted on NITRC
 *Integrated with BRAINS Software

@@ Line 34: / Line 34: @@
 Image:Mush-Brain-T1.png|T1 Weighted Image
 Image:Mush-Brain-T2.png|T2 Weighted Image
-Image:Mush-Brain-Image|Resulting Mush Image
+Image:Mush-Brain-Image.png|Resulting Mush Image
 Image:Coronal-Mush-Mask.png|Resulting Mask, Coronal view, from the Mush brain algorithm
 Image:Axial-Mush-Mask.png|Resulting Mask, Axial view, from the Mush brain algorithm

@@ Line 31: / Line 31: @@
 '''Figures:'''
-<gallery Caption="BRAINSMush" widths="300px" heights="300px" perrow="2">
+<gallery Caption="BRAINSMush" widths="300px" heights="300px" perrow="3">
-Image:BRAINSTracer1.png|BRAINS Tracer showing vtkContourWidget and telegraphing of ROIs
+Image:Mush-Brain-T1.png|T1 Weighted Image
-Image:BRAINSTracer2.png|BRAINS Tracer with the splash screen
+Image:Mush-Brain-T2.png|T2 Weighted Image
 </gallery>

@@ Line 1: / Line 1: @@
 This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.
 '''M=a*T1+b*T2'''
+The basic assumption for this algorithm is that the T1 and T2 images have been co-registered and have a minimal bias field.
 '''Progress:'''
-* A new tracing (editing) tool is being developed to serve as a testing ground for the new GUI. The tracing tool uses the vtkContourWidget and is built on KWWidgets. The Slicer3 look and feel has been integrated. This tracing tool is nearing a beta release and will include the following features
+*Standalone application now has been tested on several datasets.
-#Support for editing in multiple planes simultaneously
+*Source code has been posted on NITRC
-#Ability to telegraph traces into other planes
+*Integrated with BRAINS Software
-#Ability to export traces as binary images for integration into Slicer3
 '''Key Investigators:'''

@@ Line 6: / Line 6: @@
 The basic assumption for this algorithm is that the T1 and T2 images have been co-registered and have a minimal bias field.
 '''Algorithm'''
@@ Line 26: / Line 27: @@
 * University of Iowa: Steven Dunn, Ronald Pierson, Greg Harris, Hans Johnson, Vincent Magnotta
 '''Figures:'''
-<gallery Caption="BRAINSTracer" widths="300px" heights="300px" perrow="2">
+<gallery Caption="BRAINSMush" widths="300px" heights="300px" perrow="2">
 Image:BRAINSTracer1.png|BRAINS Tracer showing vtkContourWidget and telegraphing of ROIs
 Image:BRAINSTracer2.png|BRAINS Tracer with the splash screen
@@ Line 38: / Line 40: @@
 *[http://www.psychiatry.uiowa.edu University of Iowa Department of Psychiatry]
 *[http://mri.radiology.uiowa.edu University of Iowa MRI Center]
-*[http://www.themindinstitute.org The MIND Institute]
 '''Papers:'''

← Older revision		Revision as of 14:55, 10 December 2008
Line 1:		Line 1:
	This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.		This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.

−	'''M=aT1+bT2''	+	'''M=aT1+bT2'''

← Older revision		Revision as of 14:54, 10 December 2008
Line 1:		Line 1:
−	This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized to ~~minimze~~ the variance in the resulting images across voxels within the brain.	+	This is a tool to generate brain a volume mask from an input T1 and T2-weighted images. The resulting volume mask omits dura, skull, eyes, etc., but includes surface CSF. This application has recently been modified allowing the algorithm to run using only the T1 and T2-weighted images. In this application the following equation is optimized for the values '''a''' and '''b''' to minimize the variance in the resulting images across voxels within the brain.
		+
		+	'''M=aT1+bT2''

−	~~<math>M=aT_1+bT_2</math>~~