Documentation/Labs/FiberTractMeasurementAndVisualization

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Motivation

  • Enable studies using fiber tract hierarchies to measure from many white matter structures
  • Improve/Fix diffusion tractography visualization

Features

  • Measure diffusion data quantities from all scalar arrays and tensor arrays on fiber tracts
  • Export into text file that is excel-readable
  • Test and fix fiber tract visualization
  • Test and fix diffusion tensor scalar measurements

Design and implementation

To do lists for features and bugs

Fiber Tract Measurements

  • 2. some values are nan and some are #NAN. The nan values seem to come from the scalar measures that look incorrect in visualization, and the other values are present for those tracts. There is a bug in vtkDiffusionTensorScalarMeasurements.cxx.
  • 4. If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
  • 5. We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
  • 6. Output Text File must exist already or the module won't run. Work around: we created the text file first outside of slicer. Would be great if the module created its own new output text file.
  • 7. A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

To be tested

  • 1. tab delimited please: Added Tab/Comma/Space option to the module. Use --separator Tab/Comma/Space on the command line
  • 3. Put num fibers and num points at the beginning of the list again.
  • 8. fixed: Large numbers are reported in scientific notation with rounding. 1.51e+06 = 1514700, but the actual number of points was 1514703. Please don't round the integers because we want the number of points measured to be consistent.
  • 9. BUG: Only the first hierarchy added to the scene can be measured from.
  • 12. Bug: select multiple clusters with Ctrl and move into a child of the top-level hierarchy. Then, toggle visibility using the eye next to this hierarchy child node. Two bugs happen. Clusters will “jump out” of the hierarchy. Also, the visibility of the multiple clusters is not updated. [Note: at Project week this was found to be a general bug with hierarchies that MRML does not get updated with multiple nodes, only one node is actually moved.] Status: multi-nodes selection is currently disabled. A slicer bug filed for support of multiple node re-parenting: http://www.na-mic.org/Bug/view.php?id=3936
  • 10. When you move nodes within the hierarchy and then save it, the mrml file is not checked to be saved. This means slicer is not always aware that the mrml file has been modified. Bug fixed: http://www.na-mic.org/Bug/view.php?id=3966

Hierarchies

Visualization

  • 11. There are bugs with scalar measures that are due either to a) incorrect computation (likely with the nan issue in the measurements) and/or b) scalar range not updating.

Finished

  • QNAN output in cluster is ok but propagated to hierarchy is not
  • Please call Num_Polylines Num_Fibers instead so users can understand.
  • what is the category of the module> should be under diffusion tractography
  • Don’t skip clusters even if they have no points/lines. Put NAN at the cluster level for the measures, 0 for the points/lines, and then don’t propagate to the hierarchy level (skip it then)