Difference between revisions of "BRAINSMush"

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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.
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Back to [[NA-MIC Brains Collaboration]]
  
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<math>M=aT_1+bT_2</math>
 
  
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'''Summary:'''
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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.
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'''M=a*T1+b*T2'''
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The basic assumption for this algorithm is that the T1 and T2 images have been co-registered and have a minimal bias field.
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'''Algorithm'''
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#Use initial guess to brain using a conservative box placed about the center of the image
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#Minimize the above equation for a and b constants
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#Threshold the image
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#Erode the thresholded mask
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#Keep largest connected region
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#Dilate mask
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#Use resulting mask and repeat steps 2-6 using resulting mask
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'''Progress:'''
 
'''Progress:'''
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* 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
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*Standalone application now has been tested on several datasets.
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#Support for editing in multiple planes simultaneously
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*Source code has been posted on NITRC
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#Ability to telegraph traces into other planes
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*Integrated with BRAINS Software
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#Ability to export traces as binary images for integration into Slicer3
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#Ability to export traces as BRAINS2 mask objects
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'''To Do:'''
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#Traces will be saved in VTK XML format
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*Abstract submitted to SPIE
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'''Key Investigators:'''
 
'''Key Investigators:'''
  
 
* University of Iowa: Steven Dunn, Ronald Pierson, Greg Harris, Hans Johnson, Vincent Magnotta
 
* University of Iowa: Steven Dunn, Ronald Pierson, Greg Harris, Hans Johnson, Vincent Magnotta
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'''Figures:'''
 
'''Figures:'''
  
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<gallery Caption="BRAINSTracer" widths="300px" heights="300px" perrow="2">
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<gallery Caption="BRAINSMush" widths="300px" heights="300px" perrow="3">
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Image:BRAINSTracer1.png|BRAINS Tracer showing vtkContourWidget and telegraphing of ROIs
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Image:Mush-Brain-T1.png|T1 Weighted Image
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Image:BRAINSTracer2.png|BRAINS Tracer with the splash screen
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Image:Mush-Brain-T2.png|T2 Weighted Image
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Image:Mush-Brain-Image.png|Resulting Mush Image
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Image:Coronal-Mush-Mask.png|Resulting Mask, Coronal view, from the Mush brain algorithm
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Image:Axial-Mush-Mask.png|Resulting Mask, Axial view, from the Mush brain algorithm
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Image:Sagittal-Mush-Mask.png|Resulting Mask, Sagittal view, from the Mush brain algorithm
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Image:Mush-Brain-Box.png|Initial brain box used in the first stage of the algorithm
 
</gallery>
 
</gallery>
  
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*[http://www.psychiatry.uiowa.edu University of Iowa Department of Psychiatry]
 
*[http://www.psychiatry.uiowa.edu University of Iowa Department of Psychiatry]
 
*[http://mri.radiology.uiowa.edu University of Iowa MRI Center]
 
*[http://mri.radiology.uiowa.edu University of Iowa MRI Center]
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*[http://www.themindinstitute.org The MIND Institute]
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'''Usage:'''
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'''Papers:'''
 
'''Papers:'''

Latest revision as of 15:54, 10 December 2008

Home < BRAINSMush

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.


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.


Algorithm

  1. Use initial guess to brain using a conservative box placed about the center of the image
  2. Minimize the above equation for a and b constants
  3. Threshold the image
  4. Erode the thresholded mask
  5. Keep largest connected region
  6. Dilate mask
  7. Use resulting mask and repeat steps 2-6 using resulting mask


Progress:

  • Standalone application now has been tested on several datasets.
  • Source code has been posted on NITRC
  • Integrated with BRAINS Software

To Do:

  • Abstract submitted to SPIE


Key Investigators:

  • University of Iowa: Steven Dunn, Ronald Pierson, Greg Harris, Hans Johnson, Vincent Magnotta


Figures:

  • BRAINSMush

  • T1 Weighted Image

  • T2 Weighted Image

  • Resulting Mush Image

  • Resulting Mask, Coronal view, from the Mush brain algorithm

  • Resulting Mask, Axial view, from the Mush brain algorithm

  • Resulting Mask, Sagittal view, from the Mush brain algorithm

  • Initial brain box used in the first stage of the algorithm


Links:


Usage:


Papers:

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