Problems with Tractography to mask image


I am trying to convert fiber bundles to label maps. However, when I use the ‘Tractography to mask image’ module, my slicer app crashes. I have tried this on multiple slicer versions with no luck (4.8.1, nightly build). For the label map I’m using the one generated from the baseline image.

Alternatively, I also tried loading the fiber bundles as models and use the ‘model to label map’ module. However, on doing this, the entire label gets filled with the assigned label value(see image below)

Is there something I need to do differently?



  • the Tractography to Mask Image issue will be fixed in tomorrow’s SlicerPreview build:
  • I think the issue with ModelToLabelMap is that it is designed for closed surfaces, so it runs a fill operation which isn’t well-defined for streamlines.

You should be able to convert model to labelmap robustly by using segmentations infrastructure:

  • go to Segment editor module, select a master volume that will define geometry of the labelmap
  • go to Segmentations module
  • import from model
  • export to labelmap

To clarify tractography-specific usage, it’s good to use the dedicated module. It upsamples the polylines (fibers) to more accurately find the voxels intersected by the points along the fibers. Though I’m interested to know if the Segment Editor does something similar with polylines as well?

Segmentations can only deal with surface meshes (not lines), so it requires the input to have tubes instead of just centerlines. Currently, you can define labelmap resolution by selecting a reference volume and optionally specifying an oversampling factor.