2010 Winter Project Week Congealing Testing Debugging - Revision history

Lauren: /* Key Investigators */

2010-01-08T18:56:00Z

Key Investigators

Lauren: /* Key Investigators */

2010-01-08T17:26:52Z

Key Investigators

Lauren: /* Key Investigators */

2010-01-08T17:26:10Z

Key Investigators

Lauren at 17:25, 8 January 2010

2010-01-08T17:25:39Z

Lauren: /* Key Investigators */

2010-01-08T17:21:09Z

Key Investigators

Lauren: /* Key Investigators */

2010-01-08T17:19:56Z

Key Investigators

Lauren at 17:17, 8 January 2010

2010-01-08T17:17:17Z

Lauren at 17:15, 8 January 2010

2010-01-08T17:15:47Z

Lauren at 17:13, 8 January 2010

2010-01-08T17:13:41Z

Lauren: Created page with 'NOTOC Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) f…'

2010-01-08T17:09:41Z

Created page with '__NOTOC__ <gallery> Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) f…'

New page

__NOTOC__
<gallery>
Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors.
Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
Image: namic.png|The output deformation filed by HAMMER
Image: hammer.png|HAMMER in Slicer3
</gallery>

==Key Investigators==
* BWH: Lauren O'Donnell
* Kitware: Luis Ibanez

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Test and debug congealing registration implementation in ITK (in NAMIC Sandbox).
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
Initial issue: congealing does not work with recent ITK. The goal is to figure out where the problem is. Run existing tests from sandbox and test on 26-subject FA dataset. Debug.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We found the following flag is needed to run congealing: ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=OFF. We tested the code with existing tests from Serdar and also on a 26-subject FA dataset. We debugged initial crashing problems and patched a bug assuming all input images had the same size. To use this code in its current version however it may be advisable to pad all imput images to the same dimensions.

</div>
</div>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%; color: red;">

==References==

@@ Line 36: / Line 36: @@
 We found that the multiresolution B splines may have a bug as results were "smeared". Luis suggests the optimizer may not be using the correct size scale. However the initial size 8 grid seems to work well. See above image results.
-Some congealing tests initially crashed with recent ITK. We are running against the backwards compatible ITK now to see if Serdar's original tests pass.
+Some congealing tests initially crashed with recent ITK. We are running against the backwards compatible ITK now to see if Serdar's original tests pass.  (So far 36/96 have passed including ones that failed with recent ITK.)
 </div>
 </div>

@@ Line 36: / Line 36: @@
 We found that the multiresolution B splines may have a bug as results were "smeared". Luis suggests the optimizer may not be using the correct size scale. However the initial size 8 grid seems to work well. See above image results.
-Some congealing tests initially crashed with recent ITK. We are running against the backwards compatible ITK now.
+Some congealing tests initially crashed with recent ITK. We are running against the backwards compatible ITK now to see if Serdar's original tests pass.
 </div>
 </div>

@@ Line 21: / Line 21: @@
 <h3>Approach, Plan</h3>
-Initial issue: congealing does not work with recent ITK.  The goal is to figure out where the problem is. The plan is to run existing tests from sandbox and test on 26-subject FA dataset.  Debug.
+Initial issue: congealing does not work with recent ITK.  The goal is to figure out where the problem is. The plan is to run existing tests from sandbox and also test on 26-subject FA dataset, and debug.
 </div>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:z15-aff.png|Affine registration result on subject 15.
-Image:z15-b8.png|Affine registration result on subject 15.
+Image:z15-b8.png|B-spline 8 registration result on subject 15.
-Image: z15-b16.png|Affine registration result on subject 15.
+Image: z15-b16.png|B-spline 16 registration result on subject 15.
-Image: z15-b32.png|Affine registration result on subject 15.
+Image: z15-b32.png|B-spline 32 registration result on subject 15.
 </gallery>

@@ Line 21: / Line 21: @@
 <h3>Approach, Plan</h3>
-Initial issue: congealing does not work with recent ITK.  The goal is to figure out where the problem is. Run existing tests from sandbox and test on 26-subject FA dataset.  Debug.
+Initial issue: congealing does not work with recent ITK.  The goal is to figure out where the problem is. The plan is to run existing tests from sandbox and test on 26-subject FA dataset.  Debug.
 </div>
@@ Line 30: / Line 30: @@
 We got congealing to run without errors or crashes.  However more work would be needed for it to be compatible with recent changes/improvements in ITK.
-We found the following flag is needed to run congealing: ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=OFF.
+We found the following backwards-compatible flag is needed to run congealing: ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=OFF.
 We tested the code with existing tests from Serdar and also on a 26-subject FA dataset.  We debugged initial crashing problems and patched a bug assuming all input images had the same size.  To use this code in its current version however it may be advisable to pad all imput images to the same dimensions.
@@ Line 36: / Line 36: @@
 We found that the multiresolution B splines may have a bug as results were "smeared". Luis suggests the optimizer may not be using the correct size scale. However the initial size 8 grid seems to work well. See above image results.
 </div>
 </div>

@@ Line 28: / Line 28: @@
 <h3>Progress</h3>
-We found the following flag is needed to run congealing: ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY:BOOL=OFF.  We tested the code with existing tests from Serdar and also on a 26-subject FA dataset.  We debugged initial crashing problems and patched a bug assuming all input images had the same size.  To use this code in its current version however it may be advisable to pad all imput images to the same dimensions.
+We got congealing to run without errors or crashes.  However more work would be needed for it to be compatible with recent changes/improvements in ITK.
 </div>
@@ Line 35: / Line 41: @@
 <div style="margin: 20px;">
 <div style="width: 27%; float: left; padding-right: 3%; color: red;">
 ==References==

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:z15-aff.tif|Affine registration result on subject 15.
+Image:z15-aff.png|Affine registration result on subject 15.
 Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) for the selected point on the fixed image (left, cross). Point indicated by a cross on the middle and right column is the point on the moving image that is the most similar to the picked point on the fixed image.
 Image: namic.png|The output deformation filed by HAMMER

2010 Winter Project Week Congealing Testing Debugging - Revision history

Lauren: /* Key Investigators */

Lauren: /* Key Investigators */

Lauren: /* Key Investigators */

Lauren at 17:25, 8 January 2010

Lauren: /* Key Investigators */

Lauren: /* Key Investigators */

Lauren at 17:17, 8 January 2010

Lauren at 17:15, 8 January 2010

Lauren at 17:13, 8 January 2010

Lauren: Created page with '__NOTOC__ Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) f…'

Lauren: Created page with 'NOTOC Image:HammerAttribute.jpg|Components of Hammer Attribute Vectors. Image:HammerSimilarity.png|Similarity map (middle column) computed on moving image (right) f…'