2009 Winter Project Week ChangeTracker - Revision history

Fedorov: /* Key Investigators */

2009-01-09T17:12:28Z

Key Investigators

Fedorov: /* Key Investigators */

2009-01-09T17:12:00Z

Key Investigators

Fedorov: /* Volume rendering of label data */

2009-01-09T14:22:34Z

Volume rendering of label data

Fedorov at 14:16, 9 January 2009

2009-01-09T14:16:04Z

Fedorov at 21:39, 8 January 2009

2009-01-08T21:39:14Z

Fedorov at 21:32, 8 January 2009

2009-01-08T21:32:13Z

Fedorov: /* Key Investigators */

2009-01-08T21:27:11Z

Key Investigators

Fedorov: /* Volume rendering of label data */

2009-01-08T21:11:51Z

Volume rendering of label data

Fedorov: /* Volume rendering of label data */

2009-01-08T20:52:06Z

Volume rendering of label data

Fedorov: /* Volume rendering of label data */

2009-01-08T20:50:29Z

Volume rendering of label data

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 * Luis Ibanez, Kitware
 * Curtis Lisle, Knowledgevis
 <div style="margin: 20px;">

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 * ''Tumor segmentation'':discussed with Luis and Karthik capabilities of LesionSizingToolkit: potentially very useful for improved accuracy of meningioma segmentation. Currently in the process of evaluating the performance of the feature detection on meningioma data
 * ''Volume rendering'': worked with Karthik, Will, Curt and Steve on fine-tuning label data volume rendering (see below for details). Evaluated different approaches for visualizing tumor and growth results.
-* ''CompareView'' for results visualization: worked with Jim to implement changes to configure the layout with CompareView, but still debugging setting images for slice views
+* ''CompareView'' for results visualization: worked with Jim to implement changes to configure the layout with CompareView. Found a workaround to the problem we found in CompareView initialization (thanks, Steve!)
 * ''Module error handling'': discussed with Jim changes to the module error handling in Slicer (see below for the proposed modifications)
 * ''Time-series analysis'' functionality in Slicer: 5-year development roadmap within NAC project. Following discussions with Wendy and Steve, currently there are no specifications or finalized plans. Advantages: improved memory efficiency and data access. Short term solution -- augmenting ChangeTracker with the additional wizard step to specify the number of timepoints.

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 ===Volume rendering of label data===
 We investigated the behavior of volume rendering on the sample data from tumor growth analysis. We identified that it is crucial to use nearest neighbor interpolation for label volume rendering. It appears that the behavior of the opacity mapping function is rather unexplained (see the screenshots):
 * although the input label map contains only three intensity values (background 0, shrinking 12 and growth 14), the cut-off location of the opacity mapping for the shrinking label affects rendering
 * the results of volume rendering are drastically different from the surface recovered with marching cubes (see the screenshots)
 Programmatic initialization of the opacity transfer function for two-label data:
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 ''Current solutions/workarounds we consider: use surface rendering from Marching cubes instead of volume rendering.''
 ===Module error handling in Slicer===

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 <h1>Progress</h1>
 * ''Tumor segmentation'':discussed with Luis and Karthik capabilities of LesionSizingToolkit: potentially very useful for improved accuracy of meningioma segmentation. Currently in the process of evaluating the performance of the feature detection on meningioma data
-* ''Time-series analysis'' functionality in Slicer: 5-year development roadmap within NAC project. Following discussions with Wendy and Steve, currently there are no specifications or finalized plans. Advantages: improved memory efficiency and data access. Short term solution -- augmenting ChangeTracker with the capability to select the number of timepoints.
+* ''Volume rendering'': worked with Karthik, Will, Curt and Steve on fine-tuning label data volume rendering (see below for details). Evaluated different approaches for visualizing tumor and growth results.
 * ''CompareView'' for results visualization: worked with Jim to implement changes to configure the layout with CompareView, but still debugging setting images for slice views
 * ''Module error handling'': discussed with Jim changes to the module error handling in Slicer (see below for the proposed modifications)
-* ''Longitudinal lesion analysis in Lupus'': put together a [http://wiki.na-mic.org/Wiki/index.php/ChangeTracker:Lupus_DBP requirement document] with the desired features in ChangeTracker (or ChangeTracker derivative)
+* ''Time-series analysis'' functionality in Slicer: 5-year development roadmap within NAC project. Following discussions with Wendy and Steve, currently there are no specifications or finalized plans. Advantages: improved memory efficiency and data access. Short term solution -- augmenting ChangeTracker with the additional wizard step to specify the number of timepoints.
 </div>

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 * ''Volume rendering'': worked with Karthik, Will, Curt and Steve on fine-tuning label data volume rendering. See below for details.
 * ''CompareView'' for results visualization: worked with Jim to implement changes to configure the layout with CompareView, but still debugging setting images for slice views
-* ''Module error handling'': discussed with Jim changes to the module error handling in Slicer (see below)
+* ''Module error handling'': discussed with Jim changes to the module error handling in Slicer (see below for the proposed modifications)
 * ''Longitudinal lesion analysis in Lupus'': put together a [http://wiki.na-mic.org/Wiki/index.php/ChangeTracker:Lupus_DBP requirement document] with the desired features in ChangeTracker (or ChangeTracker derivative)
 </div>
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 ''Current solutions/workarounds we consider: use surface rendering from Marching cubes instead of volume rendering.''
 ===References===
 * E.Konukoglu, W.M.Wells, S.Novellas, N.Ayache, R.Kikinis, P.M.Black, K.M.Pohl. Monitoring Slowly Evolving Tumors. Proc. of 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008, pp.812-815 [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 link]

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 * ''CompareView'' for results visualization: worked with Jim to implement changes to configure the layout with CompareView, but still debugging setting images for slice views
 * ''Module error handling'': discussed with Jim changes to the module error handling in Slicer (see below)
 </div>
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 </div>
 ===Relevant projects of interest===

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 |[[Image:transfer_function2.jpg|thumb|300px|Transfer function showing interpolation artifacts (note the difference in opacity mapping; nearest interpolation is used in both cases)]]
 |}
 The datasets for testing are available [http://wiki.na-mic.org/Wiki/index.php/Image:Rendering_data.zip here], and the transfer function can be seen on the screenshots.

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 |}
-The datasets for testing are available [http://wiki.slicer.org/slicerWiki/index.php/Image:rendering_data.zip here], and the transfer function can be seen on the screenshots.
+The datasets for testing are available [http://wiki.slicer.org/slicerWiki/index.php/Image:labeldata.zip here], and the transfer function can be seen on the screenshots.
 ''Current solutions/workarounds we consider: use surface rendering from Marching cubes instead of volume rendering.''