Visualize Any Volume/Atlas in 3D Viewer

Drag & drop common volumetric files (.nii[.gz], .mgz) into 3D viewer

3D Viewer
Author
Affiliation

Zhengjia Wang

Dept. of Neurosurgery, University of Pennsylvania

Published

May 7, 2026

Instructions

Example 1: continuous volume

  • Drop the file volumes/Cingulum_Frontal_Parahippocampal_L.nii.gz folder (or any volume of your choice in .nii.gz, .mgz formats) as demonstrated in the animation above
  • The volume will show up in the viewer.
    • If the color is not continuous, you may change the color mode by expanding control panel > Custom Geometry Settings > Configure ROI Volumes > Cingulum_Frontal_Parahippocampal_L > Color Mode, choose “continuous”
    • To filter the volume, expand the control panel > Volume Settings > Voxel Type, choose the Cingulum_Frontal_Parahippocampal_L.nii.gz. You can change the color-map via Voxel Cmap, threshold the values via Voxel Min (lower bound) and Voxel Max (upper bound)
    • If this is an fMRI image, Volume Settings > Component Index allows you to set the time index
  • To clear the object, open Configure ROI Volumes > Clear Uploaded Volumes

Example 1: discrete volume (atlases/mask)

  • Drop the file volumes/aparc.a2009s+aseg.mgz folder as demonstrated in the animation above
  • The atlas will show up in the viewer.
    • If the color is not discrete, you may change the color mode by expanding control panel > Custom Geometry Settings > Configure ROI Volumes > aparc.a2009s_aseg > Color Mode, choose “discrete”
    • To filter the volume, expand the control panel > Volume Settings > Voxel Type, choose the aparc.a2009s+aseg.mgz. Then enter the Voxel Label the atlas key indices. For example, 17,53 are the left & right hippocampus
    • For FreeSurfer-generated atlases, you can find the color index labels here
    • You can turn the volume into surfaces by clicking on Volume Settings > Update ISO Surface
    • For discrete atlases/masks, set Volume Settings > Voxel Opacity to 0 to display the border of the masks rather than obscuring the underlay MRI (see screenshot below)
  • To clear the object, open Configure ROI Volumes > Clear Uploaded Volumes