2012 Winter Project Week: Continuous 4D shapes - Revision history

Jfishbaugh at 16:19, 13 January 2012

2012-01-13T16:19:56Z

Jfishbaugh at 15:54, 13 January 2012

2012-01-13T15:54:02Z

Jfishbaugh at 15:53, 13 January 2012

2012-01-13T15:53:27Z

Jfishbaugh at 15:51, 13 January 2012

2012-01-13T15:51:40Z

Jfishbaugh at 15:51, 13 January 2012

2012-01-13T15:51:10Z

Jfishbaugh at 15:47, 13 January 2012

2012-01-13T15:47:53Z

Jfishbaugh at 15:45, 13 January 2012

2012-01-13T15:45:51Z

Jfishbaugh at 15:32, 13 January 2012

2012-01-13T15:32:40Z

Jfishbaugh at 15:31, 13 January 2012

2012-01-13T15:31:12Z

Jfishbaugh at 15:21, 13 January 2012

2012-01-13T15:21:44Z

@@ Line 63: / Line 63: @@
 * 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.
 </div>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
 Image:10001_sub_corts_small.gif| Shape evolution of sub-cortical structures for subject 10001.  Color denotes magnitude of velocity.
 </gallery>

@@ Line 3: / Line 3: @@
 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.
 </gallery>

@@ Line 47: / Line 47: @@
 '''Remarks'''
 HD group
@@ Line 64: / Line 61: @@
 '''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.
 </div>

← Older revision		Revision as of 15:51, 13 January 2012
Line 47:		Line 47:

	'''Remarks'''		'''Remarks'''
		+
		+	* 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.

	HD group		HD group

@@ Line 34: / Line 34: @@
 '''Segmentation'''
-The 5 pairs of sub-cortical structures (caudate, hippocampus, globus, putamen, thalamus) were provided as binary segmentations.  Triangular meshes were extracted using marching cubes, giving us 10 shapes at 3 time points.
+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'''
@@ Line 52: / Line 52: @@
 * Caudate volume decreases for all 6 subjects.
 * Hippocampus volume decreases for 5 of 6 subjects.
 Control group
-* Caudate volume decreases for 3 of 7 subjects
+* Caudate volume decreases for 3 of 7 subjects.

← Older revision		Revision as of 15:32, 13 January 2012
Line 47:		Line 47:

	'''Remarks'''		'''Remarks'''
		+
		+	* Caudate volume decreases for all 6 HD subjects.
		+	* Hippocampus volume decreases for 5 out of 6 HD subjects.
		+

	</div>		</div>

← Older revision		Revision as of 15:21, 13 January 2012
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	<h3>Progress</h3>		<h3>Progress</h3>
		+
		+	'''Segmentation'''
		+
		+	The 6 pairs of sub-cortical structures (amygdala, caudate, hippocampus, globus pallidus, putamen, lateral ventricle) were segmented using a deformable atlas based pipeline used at the University of Utah. The quality of the ventricles was very poor, so they were further improved by an active contour based segmentation tool, itkSNAP. After this stage, we have 12 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 12 structures as a shape complex. Three snapshots in time are shown in Fig. 1. We also investigate the evolution of shape volume, summarized in Fig 2. It is important to note that we only model the evolution of shape, and volume is simply measured continuously after regression.
		+
		+	'''Remarks'''
		+

	</div>		</div>