Difference between revisions of "DBP3:Utah:AutoEndoSeg"

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= Current Activities =
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* 11/30/11 Greg and Josh met with Yi via Skype
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** Algorithm is still very sensitive to image cropping -- registration seems to fail unless cropping is exact
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** We can input an atlas image and get a correct result
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** Yi will investigate multiscale registration to see if that improves result
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** Yi will look for any bugs in code that might be affecting registration
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** Greg will send Yi current data for new atlas with larger crop region
 
= Notes on the Endocardial Segmentation Algorithm =
 
= Notes on the Endocardial Segmentation Algorithm =
 
Algorithm is a multi-atlas segmentation.
 
Algorithm is a multi-atlas segmentation.
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= Larger Atlas Images =
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= Larger Atlas Images 11/30/11=
 
* A second atlas was generated from cropped images that included a larger region of the initial MRI scans (namely, the appendage and a greater extent of the PVs was included in this second atlas).
 
* A second atlas was generated from cropped images that included a larger region of the initial MRI scans (namely, the appendage and a greater extent of the PVs was included in this second atlas).
 
* This atlas showed no marked improvement over the initial atlas
 
* This atlas showed no marked improvement over the initial atlas
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| [[File:CAMRA_N26_2_LGE.png|thumb|center]]
 
| [[File:CAMRA_N26_2_LGE.png|thumb|center]]
 
| [[File:CARMA_N26_2_Endo.png|thumb|center]]
 
| [[File:CARMA_N26_2_Endo.png|thumb|center]]
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|-
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| '''Atlas Image'''
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| [[File:CARMA_N19_Atlas_LGE.png|thumb|center]]
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| [[File:CARMA_N19_Atlas_Endo.png|thumb|center]]
 
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'''Note:''' The last segmentation (red) was derived from an image in the atlas; the other segmentations (green) were derived from similarly-cropped images, not in the atlas.

Latest revision as of 20:19, 30 November 2011

Home < DBP3:Utah:AutoEndoSeg

Current Activities

  • 11/30/11 Greg and Josh met with Yi via Skype
    • Algorithm is still very sensitive to image cropping -- registration seems to fail unless cropping is exact
    • We can input an atlas image and get a correct result
    • Yi will investigate multiscale registration to see if that improves result
    • Yi will look for any bugs in code that might be affecting registration
    • Greg will send Yi current data for new atlas with larger crop region

Notes on the Endocardial Segmentation Algorithm

Algorithm is a multi-atlas segmentation.

  1. Register (cropped) heart region of patient DEMRI to all of the n atlas DEMRI images and record n minimum metric values (mutual information)
  2. Transform all n atlas segmentations to patient DEMRI space
  3. Segmentation is a weighted average of the transformed atlas segmentation, where weights are determined by the mutual information values from step 1
  4. Pick a threshold as your segmentation

Notes on Yi's Slicer Module

  • The exposed parameter is the ratio of pixel samples for mutual information to the total number of pixels in the image.
  • We could also expose the threshold parameter in the final step
  • We can change or add atlas datasets by copying into the appropriate directory and editing the text file that lists them
  • Uses the ITK mutual information code. Does affine registration followed by b-spline
  • We will partner with Yi for module development at the Jan 2012 project week

Initial Experiences

  • Comparison of GA Tech and Utah-derived segmentations

(click to enlarge)

GA Tech Segmentation Utah Segmentation Thresholding Difference
CARMA GAT Endo.png
CARMA UT Endo.png
CARMA Diff Endo.png
Segmentation of an atlas image by GA Tech, using their endocardial auto-segmentation algorithm. Segmentation of the same image with the same algorithm by Utah. User-based variability in thresholding the probability mask output. (Green region - Utah; white region - GA Tech).

Larger Atlas Images 11/30/11

  • A second atlas was generated from cropped images that included a larger region of the initial MRI scans (namely, the appendage and a greater extent of the PVs was included in this second atlas).
  • This atlas showed no marked improvement over the initial atlas
  • Segmentations with the second atlas tended to not capture the entire blood pool, whereas, the first atlas tended to overestimate the blood pool.
  • Registration issues?
Mask and LGE Image Mask and Expert-defined Segmentation
Example 1
CARMA N24 LGE.png
CARMA N24 Endo.png
Example 2
CARMA N25 LGE.png
CARMA N25 Endo.png
Example 3
CAMRA N26 LGE.png
CARMA N26 Endo.png
Example 4
CAMRA N26 2 LGE.png
CARMA N26 2 Endo.png
Atlas Image
CARMA N19 Atlas LGE.png
CARMA N19 Atlas Endo.png
Cropped MRI image overlaid with the algorithm-defined blood pool. Expert manual segmentations (white) overlaid with the algorithm-defined blood pool (green).

Note: The last segmentation (red) was derived from an image in the atlas; the other segmentations (green) were derived from similarly-cropped images, not in the atlas.