View source for Documentation/Labs/FiberTractMeasurementAndVisualization

= 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==
* tab delimited please
* 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.
* Put num fibers and num points at the beginning of the list again.
* If all models in a particular hierarchy have no points (have NAN values), the overall output value should be NAN.
* We need a test dataset with known output to make sure this is working. Lauren will make this dataset.
* 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. 
* A nightly test is needed. This should be improving the test of vtkDiffusionTensorMathematics in vtkTeem

==To be tested ==
* 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.

==Hierarchies==
*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.]
*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.

==Visualization==
*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.