Difference between revisions of "2012 Winter Project Week: Continuous 4D shapes"

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<gallery>
 
<gallery>
 
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
−
Image:HD_sub_cort_shapes.png|Snapshot of sub-cortical shape evolution.  Color denotes magnitude of velocity.
+
Image:10001_sub_corts_small.gif| Shape evolution of sub-cortical structures for subject 10001.  Color denotes magnitude of velocity.
 
</gallery>
 
</gallery>
  
Line 31: Line 31:
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
 +
 +
'''Segmentation'''
 +
 +
The 5 pairs of sub-cortical structures (caudate, hippocampus, globus, putamen, thalamus) segmentations were provided as binary images.  Triangular meshes were extracted using marching cubes, giving us 10 shapes at 3 time points.
 +
 +
'''Preprocessing'''
 +
 +
In order to prepare the shapes for longitudinal regression, the different time points must first be rigidly aligned.  We do not have point correspondences between our shapes, so we use a Gaussian mixture model based tool called gmmreg to rigidly align the shapes.
 +
 +
We initially align the entire shape complex, rather than individual shapes, in order to preserve the spatial relationship between the anatomical structures.  However, there was a small amount of translation and rotation remaining after this process that adversely impacts the growth estimation.  To further align the shapes, we also register each shape individually across time. 
 +
 +
'''Regression'''
 +
 +
Here, we estimate the continuous evolution of all 10 structures as a shape complex.  We look for a global deformation which best deforms the baseline shapes to match the target shapes over time.  We set the spatial extent at which the deformation varies to 10mm.
 +
 +
'''Remarks'''
 +
 +
HD group
 +
 +
* Caudate volume decreases for all 6 subjects.
 +
* Hippocampus volume decreases for 5 of 6 subjects.
 +
* Typical changes are on the range of 5% to 10%
 +
 +
Control group
 +
 +
* Caudate volume decreases for 3 of 7 subjects.
 +
* It is not uncommon to see a 10% decrease/increase in volume between time point in any given structure.
 +
 +
'''Conclusion'''
 +
 +
* We need to be very careful about the quality of the segmentations.  The changes we are interested in detecting could potentially be of the same order as segmentation error.
 +
* To improve the shape framework, we should estimate the baseline shape, which we currently assume is fixed.
 +
* We still need to look for other potentially significant measurements, aside from volume.
  
 
</div>
 
</div>
Line 40: Line 73:
  
 
'''10001'''
 
'''10001'''
 +
 +
[[Image:10001_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10001.  Color denotes magnitude of velocity. ]]
  
 
[[Image:10001_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10001. ]]
 
[[Image:10001_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10001. ]]
  
−
[[Image:10001_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10001. ]]
+
[[Image:10001_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10001. ]]
  
 
'''10002'''
 
'''10002'''
  
−
[[Image:10002_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10001. ]]
+
[[Image:10002_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10002.  Color denotes magnitude of velocity. ]]
 +
 
 +
[[Image:10002_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10002. ]]
  
−
[[Image:10002_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10001. ]]
+
[[Image:10002_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10002. ]]
  
 
'''10010'''
 
'''10010'''
 +
 +
[[Image:10010_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10010.  Color denotes magnitude of velocity. ]]
  
 
[[Image:10010_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10010. ]]
 
[[Image:10010_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10010. ]]
  
−
[[Image:10010_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10010. ]]
+
[[Image:10010_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10010. ]]
  
 
'''10018'''
 
'''10018'''
Line 61: Line 100:
 
[[Image:10018_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10018. ]]
 
[[Image:10018_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10018. ]]
  
−
[[Image:10018_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10018. ]]
+
[[Image:10018_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10018. ]]
  
 
'''10022'''
 
'''10022'''
Line 67: Line 106:
 
[[Image:10022_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10022. ]]
 
[[Image:10022_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10022. ]]
  
−
[[Image:10022_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10022. ]]
+
[[Image:10022_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10022. ]]
  
 
'''10027'''
 
'''10027'''
 +
 +
[[Image:10027_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10027.  Color denotes magnitude of velocity. ]]
  
 
[[Image:10027_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10027. ]]
 
[[Image:10027_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10027. ]]
  
−
[[Image:10027_right_left_volume_panel.png|thumb|600px|center| Evolution of left/right structures and total volume for subject 10027. ]]
+
[[Image:10027_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10027. ]]
  
 
<h3>Control Subjects</h3>
 
<h3>Control Subjects</h3>
  
 
'''10003'''
 
'''10003'''
 +
 +
[[Image:10003_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10003.  Color denotes magnitude of velocity. ]]
 +
 +
[[Image:10003_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10003. ]]
 +
 +
[[Image:10003_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10003. ]]
  
 
'''10004'''
 
'''10004'''
 +
 +
[[Image:10004_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10004.  Color denotes magnitude of velocity. ]]
 +
 +
[[Image:10004_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10004. ]]
 +
 +
[[Image:10004_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10004. ]]
  
 
'''10009'''
 
'''10009'''
 +
 +
[[Image:10009_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10009.  Color denotes magnitude of velocity. ]]
 +
 +
[[Image:10009_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10009. ]]
 +
 +
[[Image:10009_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10009. ]]
  
 
'''10014'''
 
'''10014'''
 +
 +
[[Image:10014_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10014. ]]
 +
 +
[[Image:10014_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10014. ]]
  
 
'''10016'''
 
'''10016'''
 +
 +
[[Image:10016_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10016. ]]
 +
 +
[[Image:10016_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10016. ]]
  
 
'''10017'''
 
'''10017'''
 +
 +
[[Image:10017_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10017. ]]
 +
 +
[[Image:10017_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10017. ]]
  
 
'''10059'''
 
'''10059'''
 +
 +
[[Image:10059_sub_corts_small.gif|thumb|800px|center| Shape evolution of sub-cortical structures for subject 10059.  Color denotes magnitude of velocity. ]]
 +
 +
[[Image:10059_sub_cort_volume_panel.png|thumb|600px|center| Evolution of volume of sub-cortical structures for subject 10059. ]]
 +
 +
[[Image:10059_right_left_volume_panel.png|thumb|800px|center| Evolution of left/right structures and total volume for subject 10059. ]]
  
 
<!-- [[Image:HD_all_sub_cort_volume.png|thumb|800px|center|'''Fig 1.''' Volume of sub-cortical segmentations for 6 HD subjects. ]] -->
 
<!-- [[Image:HD_all_sub_cort_volume.png|thumb|800px|center|'''Fig 1.''' Volume of sub-cortical segmentations for 6 HD subjects. ]] -->

Latest revision as of 16:19, 13 January 2012

Home < 2012 Winter Project Week: Continuous 4D shapes

  • Shape evolution of sub-cortical structures for subject 10001. Color denotes magnitude of velocity.

Key Investigators

James Fishbaugh, Hans Johnson, Guido Gerig

Objective

During the 2011 summer project week, we applied our shape regression framework to sub-cortical shapes from a single HD subject. For this project, we plan to begin processing multiple subjects. We would like to compare the trajectories of various measurements of interest, such as volume, across subjects at different stages of disease progression.

Approach, Plan

  • Estimate continuous trajectories for sub-cortical structures for multiple subjects
  • Investigate volume changes between subjects at different stages of disease progression
  • Explore shape evolution for other potentially significant measurements

Progress

Segmentation

The 5 pairs of sub-cortical structures (caudate, hippocampus, globus, putamen, thalamus) segmentations were provided as binary images. Triangular meshes were extracted using marching cubes, giving us 10 shapes at 3 time points.

Preprocessing

In order to prepare the shapes for longitudinal regression, the different time points must first be rigidly aligned. We do not have point correspondences between our shapes, so we use a Gaussian mixture model based tool called gmmreg to rigidly align the shapes.

We initially align the entire shape complex, rather than individual shapes, in order to preserve the spatial relationship between the anatomical structures. However, there was a small amount of translation and rotation remaining after this process that adversely impacts the growth estimation. To further align the shapes, we also register each shape individually across time.

Regression

Here, we estimate the continuous evolution of all 10 structures as a shape complex. We look for a global deformation which best deforms the baseline shapes to match the target shapes over time. We set the spatial extent at which the deformation varies to 10mm.

Remarks

HD group

  • Caudate volume decreases for all 6 subjects.
  • Hippocampus volume decreases for 5 of 6 subjects.
  • Typical changes are on the range of 5% to 10%

Control group

  • Caudate volume decreases for 3 of 7 subjects.
  • It is not uncommon to see a 10% decrease/increase in volume between time point in any given structure.

Conclusion

  • We need to be very careful about the quality of the segmentations. The changes we are interested in detecting could potentially be of the same order as segmentation error.
  • To improve the shape framework, we should estimate the baseline shape, which we currently assume is fixed.
  • We still need to look for other potentially significant measurements, aside from volume.

HD Subjects

10001

Shape evolution of sub-cortical structures for subject 10001. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10001.
Evolution of left/right structures and total volume for subject 10001.

10002

Shape evolution of sub-cortical structures for subject 10002. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10002.
Evolution of left/right structures and total volume for subject 10002.

10010

Shape evolution of sub-cortical structures for subject 10010. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10010.
Evolution of left/right structures and total volume for subject 10010.

10018

Evolution of volume of sub-cortical structures for subject 10018.
Evolution of left/right structures and total volume for subject 10018.

10022

Evolution of volume of sub-cortical structures for subject 10022.
Evolution of left/right structures and total volume for subject 10022.

10027

Shape evolution of sub-cortical structures for subject 10027. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10027.
Evolution of left/right structures and total volume for subject 10027.

Control Subjects

10003

Shape evolution of sub-cortical structures for subject 10003. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10003.
Evolution of left/right structures and total volume for subject 10003.

10004

Shape evolution of sub-cortical structures for subject 10004. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10004.
Evolution of left/right structures and total volume for subject 10004.

10009

Shape evolution of sub-cortical structures for subject 10009. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10009.
Evolution of left/right structures and total volume for subject 10009.

10014

Evolution of volume of sub-cortical structures for subject 10014.
Evolution of left/right structures and total volume for subject 10014.

10016

Evolution of volume of sub-cortical structures for subject 10016.
Evolution of left/right structures and total volume for subject 10016.

10017

Evolution of volume of sub-cortical structures for subject 10017.
Evolution of left/right structures and total volume for subject 10017.

10059

Shape evolution of sub-cortical structures for subject 10059. Color denotes magnitude of velocity.
Evolution of volume of sub-cortical structures for subject 10059.
Evolution of left/right structures and total volume for subject 10059.


References

  • Fishbaugh, J., Durrleman, S., Gerig, G. A Framework for Longitudinal Data Analysis via Shape Regression . SPIE Medical Imaging 2012: Image Processing. Vol. 8314. (To appear)
  • Fishbaugh, J., Durrleman, S., Gerig, G. Estimation of Smooth Growth Trajectories with Controlled Acceleration from Time Series Shape Data. Proc. of Medical Image Computing and Computer Assisted Intervention (MICCAI '11). September 2011.
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