How to display voxel intensities

Thank you, it was very helpful to see what kind of data you work with. Voxels of this tract volume are actually continuous, so it should be loaded with default settings (as scalar volume). You can then adjust its color mapping and display it as a foreground volume:

Adjust color mapping in Volumes module:

Show tract as foreground volume:

Show tract using volume rendering:

To avoid the need for these 15-20 clicks to set up visualization, you could add a simple Python scripted module, which would load a tract image and set up all the visualization by a single click. You can learn about how to create such module from Slicer programming tutorials. We are here to help if you need any help with it. If this is a common task then we can add it to the FreeSurfer importer module.

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