2013 Summer Project Week:TractAtlasCluster - Revision history

Lauren: /* Key Investigators */

2013-06-21T14:12:25Z

Key Investigators

Lauren: /* Key Investigators */

2013-06-20T20:33:12Z

Key Investigators

Lauren at 09:51, 17 June 2013

2013-06-17T09:51:12Z

Lauren at 09:50, 17 June 2013

2013-06-17T09:50:22Z

Lauren: /* Delivery Mechanism */

2013-06-17T09:47:52Z

Delivery Mechanism

Lauren: /* Key Investigators */

2013-06-17T09:46:33Z

Key Investigators

Lauren: /* Key Investigators */

2013-06-12T18:02:43Z

Key Investigators

Lauren: /* References */

2013-06-12T18:02:09Z

References

Lauren at 18:01, 12 June 2013

2013-06-12T18:01:35Z

Lauren at 18:00, 12 June 2013

2013-06-12T18:00:54Z

@@ Line 8: / Line 8: @@
 ==Key Investigators==
 * BWH: Lauren O'Donnell
-* Slicer gurus
+* Slicer gurus: thanks Steve Pieper
-* Open source/python/vtk gurus.
+* Open source/python/vtk gurus: thanks Bill Lorensen
 <div style="margin: 20px;">
@@ Line 32: / Line 32: @@
 <h3>Progress</h3>
-Provided source code to collaborators in Toronto, and code was installed and tested successfully at their lab. New test scripts were written. Code was initially updated to work with vtk6. For possible ease of distribution, code was tested against a new install of Canopy (new Enthought python) distribution (that includes scipy) with their provided vtk package. However that vtk package lacked some vtkCellArray wrappings needed by our code (that are present when compiling and wrapping vtk from source). A bug report was filed with Enthought regarding the wrappings, and a discussion with Bill Lorensen indicates it may be due to an older version of vtk distributed with Canopy. Other progress: Discussions with Steve Pieper about likely/planned python packages in slicer.
+Provided source code to collaborators in Toronto, and code was installed and tested successfully at their lab. New test scripts were written. Code was updated and initially tested to work with vtk6. For possible ease of distribution, code was tested against a new install of Canopy (new Enthought python) distribution (that includes scipy) with their provided vtk package. However that vtk package lacked some vtkCellArray wrappings needed by our code (that are present when compiling and wrapping vtk from source). A bug report was filed with Enthought regarding the wrappings, and a discussion with Bill Lorensen indicated it is due to an older version of vtk distributed with Canopy. Enthought has now told us they will update their vtk package to a more recent vtk5. Other progress: Discussions with Steve Pieper about likely/planned python packages in slicer.
 </div>

@@ Line 32: / Line 32: @@
 <h3>Progress</h3>
+Provided source code to collaborators in Toronto, and code was installed and tested successfully at their lab. New test scripts were written. Code was initially updated to work with vtk6. For possible ease of distribution, code was tested against a new install of Canopy (new Enthought python) distribution (that includes scipy) with their provided vtk package. However that vtk package lacked some vtkCellArray wrappings needed by our code (that are present when compiling and wrapping vtk from source). A bug report was filed with Enthought regarding the wrappings, and a discussion with Bill Lorensen indicates it may be due to an older version of vtk distributed with Canopy. Other progress: Discussions with Steve Pieper about likely/planned python packages in slicer.
 </div>

@@ Line 3: / Line 3: @@
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
 Image:Clusters.png|Tract clusters in a healthy control brain.
-Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
+Image:Clusters_points.png|Clusters across subjects, relative to landmarks from fMRI.
 </gallery>

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
-Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
+Image:Clusters.png|Tract clusters in a healthy control brain.
 Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
 </gallery>

@@ Line 46: / Line 46: @@
 ##Extension -- commandline
 ##Extension -- loadable
-#Other (Please specify)
+#Other (Please specify) YES: eventual plan is an extension but depends on packages not yet in Slicer python.
 ==References==

@@ Line 25: / Line 25: @@
 Our python package includes code implementing tract clustering, atlas labeling, registration, and fMRI-DTI modeling as part of the atlas. References are below.
-Our plan for the project week is to focus on Slicer compatibility and user accessibility of the code.
+Our plan for the project week is to focus on Slicer compatibility and user accessibility/cleanup/documentation of the code.
 </div>

@@ Line 48: / Line 48: @@
 ==References==
 * Unbiased Groupwise Registration of White Matter Tractography
 LJ O’Donnell, WM Wells III, AJ Golby, CF Westin

← Older revision		Revision as of 18:01, 12 June 2013
Line 14:		Line 14:

	<h3>Objective</h3>		<h3>Objective</h3>
−	The goal is to work on Slicer integration and user packaging ~~for~~ Python tract atlasing and clustering code.	+	The goal is to work on Slicer integration and user packaging to enable open-source release of Python tract atlasing and clustering code.