Slicer3:UIDesign:WorkingProblems:BCAnalysis:Dynamic

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Perfusion Analysis for Breast Cancer

Goal

Goal is to accommodate basic RECIST assessment for breast cancer (Response Evaluation Criteria In Solid Tumors). (RECIST is a set of published rules that define when cancer patients improve ("respond"), stay the same ("stable") or worsen ("progression") during treatments).

• Determine features that currently exist in Slicer
• Develop features that don't
• Provide a framework that knits features together in a comfortable workflow.

Perfusion Analysis Workflow

• Visualize the dataset dynamically
• Specify an ROI that includes tumor and apply to all timepoints Question: ROI or VOI? (either -- if slice, must be same slice)
• Plot contrast dilution curve
  • show time to peak in tumor
• Specify an ROI that includes blood pool and apply to all timepoints Question: again, ROI or VOI?
• Plot contrast dilution curve for this (on same graph)
  • show time to peak in blood pool
• show transit time (distance between peaks in each plot)
• save out timepoints ( Intensity(t) for each ROI -- include multiple tumors if desired)

First experiment

Below is a screenshot of first perfusion dataset. The dataset contains upward of 900 volumes. Loading the original DICOM images took a very long time; Junichi converted these images to nrrd format, but the loading still takes prohibitively long, and interacting is also very slow.

ideas:

• can we create a VOI and apply to each volume in the timeseries?
• Alternatively, for a first demo we can use a smaller dataset?

update:

From Jeff -- first dataset contains 15 timepoints, each 256x256x63 -- so we've found a bug in either:

• the timeseries loader in Slicer (probably in the thing that parses dicom header), or
• we have a malformed DICOM header.

This is causing Slicer to load 63x15 volumes containing a single 256x256 slice. I'll dig in to this today and see what's going on. Shouldn't be too hard to find. Junichi has given me a DCE dataset that loads properly for comparison.

The 4D Image analysis package is required for plotting -- need to expose this in Slicer3/Modules/CMakelists.txt file. Discussed with Junichi about possibility of having both 4DImage and 4DImageAnalysis modules exposed in the trunk for the demo; he sees no problem in this *without* the Scipy modeling part exposed. Too challenging now to build python/numpy/scipy by default.

CHANGES TO CODE to get FourDImage and FourDAnalysis to compile

• Exposed FourDImage and FourDAnalysis modules in Slicer3/Modules/CMakelists.txt
• Changed the code in vtkKWPlotGraph.cxx: replaced finite() function is replaced code that conforms to ISO C++/2003 so it would compile on win32
• Changed some code in vtkFourDAnalysisLogic.cxx because there is no equivalent to the isnormal() function. Instead, just used the same def for finite()... but this will not test for subnormal floats.
• Had to move pyconfig.h to Slicer3-lib/python-build/Include so FourDAnalysis module could compile (couldn't find this file, included by <Python.h> for some reason (maybe something wrong with my python install.
• Had to make some changes to FourDAnalysis/CMakeLists.txt to link with python libraries on win32.