web/fsbrain_volume.md

In dfsp-spirit/nitools: Managing and Visualizing Brain Surface Data

fsbrain volume visualization

These are brain volume visualizations created using the fsbrain R package.

Lightbox views

A lightbox showing every 5th frame of a T1W volume, sagittal plane. A bounding box has been computed, so that empty space around the brain has been clipped automatically:

The same can be done for the axial and coronal planes.

You can also add activation data, p-values, colors from a segmenation like aseg or aparc+aseg, or whatever, as an overlay from a second volume file. Of course there is no need to plot all slices or every nth slice, you can select arbitrary combinations of slice indices to plot.

The function to achieve this is volvis.lightbox, or the more convenient replacement volvis.lb in newer fsbrain versions (>=0.5.0).

Voxel-based 3D renderings

It is now possible to view volumes (the whole brain, segmentations, voxel-based activation values, or brain structures) in 3D in a voxel view. Here are two examples:

• whole brain, aparc+aseg segmentation (24 MB animated GIF)
• brain ventricles, extracted from aseg segmentation (10 MB animated GIF)

Sorry for the glossy look and bad lighting in the images, this is fixed in the code already. Examples for how to generate this can be found in the unit tests directory.

Animations

You can also render the volume slices into an animation. The result looks like this:

The same can be done for the axial and coronal planes. Examples for how to generate this can be found in the unit tests directory.

Please cite the fsbrain package when using these animations/videos.

dfsp-spirit/nitools documentation built on Jan. 26, 2024, 8:24 p.m.