Color and opacity rendered volumes


I am trying to render a 3D MRI scan and 3D segmentation of the Fornix. These are both stored as nifti files, so I am able to open them and use the ‘Volume Rendering’ module to display them in the 3D view.

I want to achieve the following, but I have absolutely no idea how to do it so I would greatly appreciate any advice:

  1. Reduce the opacity of the rendered MRI scan volume. The purpose of showing this volume is just to give the audience a subtle clue as to the orientation and position of the brain; i want it to be much less visible than it currently is by default.
  2. Change the colour of the Fornix segmentation volume. All the voxels have the value ‘1’ in the nifti file, so by default this is just rendered as a white volume. I want it to be some other colour like green or red so it stands out more (at the moment it blends in too much with the actual MRI scan).

Thank you so much for your help, I have been stuck on this for a little bit now.

To provide a broad external anatomical context, we often segment the skin and the brain surface and display them as semi-transparent surfaces. They are both easy to segment:

  • skin can be segmented by simple thresholding, followed by smoothing and wrapping as described in this segmentation recipe
  • segmentation of the brain surface (skull stripping) is provided by many modules, for example I would recommend the simple SwissSkullStripper extension or the higher-quality, more robust, but more computationally demanding HDBrainExtraction extension

When you load the nifti file, make sure you choose Segmentation in the Description column in the Add data window. You can then easily adjust color, opacity, etc. in both slice and 3D views, using Segmentations module.

Thank you, this is very informative.

I tried to load the nifti file as a Segmentation instead of a Volume, and now when I apply a linear transformation to Posterior/Anterior flip it, it renders as black for some reason.

Before flipping:

After flipping:

This is the linear transform matrix I am applying:

Determinant of this transformation matrix is -1, which means that it turns the object inside out. That’s why it appears black. Do you actually need to apply such transform, or just played around with the values?