Difference between revisions of "EMSegmenter-Tasks:CT-Hand-Bone"

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* Step 1: Create binarized atlas template and binarized CT scan
 
* Step 1: Create binarized atlas template and binarized CT scan
 
** Flip/Mirror the atlas (based on right hand scans) if left hand scan has to be segmented.
 
** Flip/Mirror the atlas (based on right hand scans) if left hand scan has to be segmented.
 
 
** The atlas template scan and the subject scan are processed in the same way.
 
** The atlas template scan and the subject scan are processed in the same way.
 
 
** Binary threshold image (based on Fiducials, TODO)
 
** Binary threshold image (based on Fiducials, TODO)
 
Extract the tissue and bones from the image. This could be done by specifying fiducials or by using fixed values(e.g. keep values between 150-3000 )
 
Extract the tissue and bones from the image. This could be done by specifying fiducials or by using fixed values(e.g. keep values between 150-3000 )
 
<!--Why not above a specific value?? -->
 
<!--Why not above a specific value?? -->
 
 
** Blur image
 
** Blur image
 
itk::DiscreteGaussianImageFilter is used to fill remaining holes. (parameter e.g. Variance=1.5, MaximumKernelWidth 5)
 
itk::DiscreteGaussianImageFilter is used to fill remaining holes. (parameter e.g. Variance=1.5, MaximumKernelWidth 5)
 
 
 
** Binary image
 
** Binary image
 
Use itk::BinaryThresholdImageFilter to remove artifacts. Set everything between 0 and 30 to 0, otherwise 255
 
Use itk::BinaryThresholdImageFilter to remove artifacts. Set everything between 0 and 30 to 0, otherwise 255
 
 
** extract largest component
 
** extract largest component
 
Use itk::BinaryThresholdImageFilter to extract label 255.
 
Use itk::BinaryThresholdImageFilter to extract label 255.
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* Step 2: Register the binarized atlas template to the binarized CT scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 
* Step 2: Register the binarized atlas template to the binarized CT scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 
** Step 2a: Use BRAINSFit to perform a affine registration.
 
** Step 2a: Use BRAINSFit to perform a affine registration.
 
 
** Register the atlas template linear to the subject scan and save the linear transformation. (BRAINSFit Rigid,Affine)
 
** Register the atlas template linear to the subject scan and save the linear transformation. (BRAINSFit Rigid,Affine)
 
 
** Step 2b: Use BRAINSDemonWarp to perform a non-linear registration.*
 
** Step 2b: Use BRAINSDemonWarp to perform a non-linear registration.*
 
* Register the atlas template non-linear to the subject scan. Use the linear transformation as initialization. (BRAINSDemonWarp)
 
* Register the atlas template non-linear to the subject scan. Use the linear transformation as initialization. (BRAINSDemonWarp)
 
 
 
** Step 2c: Use BRAINSResample together with the --deformationVolume option to resample the atlas files.
 
** Step 2c: Use BRAINSResample together with the --deformationVolume option to resample the atlas files.
 
* Step 3: Compute the intensity distributions for each structure <BR>
 
* Step 3: Compute the intensity distributions for each structure <BR>

Revision as of 13:57, 27 April 2011

Home < EMSegmenter-Tasks:CT-Hand-Bone

Return to EMSegmenter Task Overview Page

Description

Single channel automatic segmentation of CT hand scans into the finger bones. The task can be applied to right and and left hand scans. The pipeline consist of the following steps:

  • Step 1: Create binarized atlas template and binarized CT scan
    • Flip/Mirror the atlas (based on right hand scans) if left hand scan has to be segmented.
    • The atlas template scan and the subject scan are processed in the same way.
    • Binary threshold image (based on Fiducials, TODO)

Extract the tissue and bones from the image. This could be done by specifying fiducials or by using fixed values(e.g. keep values between 150-3000 )

    • Blur image

itk::DiscreteGaussianImageFilter is used to fill remaining holes. (parameter e.g. Variance=1.5, MaximumKernelWidth 5)

    • Binary image

Use itk::BinaryThresholdImageFilter to remove artifacts. Set everything between 0 and 30 to 0, otherwise 255

    • extract largest component

Use itk::BinaryThresholdImageFilter to extract label 255.

Use itk::ConnectedComponentImageFilter to label the objects in the binary image. Each distinct object is assigned a unique label.

Use itk::RelabelComponentImageFilter to sort the labels based on the size of the object: the largest object will have label #1, the second largest will have label #2, etc.

Use itk::BinaryThresholdImageFilter to extract label 1. This is the largest object in the data set.



  • Step 2: Register the binarized atlas template to the binarized CT scan via BRAINSFit (Johnson et al 2007)
    • Step 2a: Use BRAINSFit to perform a affine registration.
    • Register the atlas template linear to the subject scan and save the linear transformation. (BRAINSFit Rigid,Affine)
    • Step 2b: Use BRAINSDemonWarp to perform a non-linear registration.*
  • Register the atlas template non-linear to the subject scan. Use the linear transformation as initialization. (BRAINSDemonWarp)
    • Step 2c: Use BRAINSResample together with the --deformationVolume option to resample the atlas files.
  • Step 3: Compute the intensity distributions for each structure

Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.

  • Step 4: Automatically segment the CT scan into the structures of interest using EM Algorithm (Pohl et al 2007)

Anatomical Tree

The anatomical tree represents the structures to be segmented. Node labels displayed below contain a human readable structure name and in parentheses the internally used structure name.

  • Hand
    • Air
    • Tissue
    • Index finger / digitus secundus (II)
      • Proximal (II)
      • Medial (II)
      • Distal (II)
    • Middle finger / digitus medius (III)
      • Proximal (III)
      • Medial (III)
      • Distal (III)
    • Ring finger / digitus annularis (IV)
      • Proximal (IV)
      • Medial (IV)
      • Distal (IV)
    • Little finger / digitus minimus (V)
      • Proximal (V)
      • Medial (V)
      • Distal (V)

Atlas

Result

Collaborators

Vincent Magnotta (University of Iowa)

Acknowledgment

The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.

Citations