HDBrainExtraction

3D Slicer extension for skull stripping in brain MRI images using HD-BET brain extraction tool.

As per request of the HD-BET team, if you are using HD-BET, please cite the following publication:

Isensee F, Schell M, Tursunova I, Brugnara G, Bonekamp D, Neuberger U, Wick A, Schlemmer HP, Heiland S, Wick W, Bendszus M, Maier-Hein KH, Kickingereder P. Automated brain extraction of multi-sequence MRI using artificial neural networks. Hum Brain Mapp. 2019; 1–13. https://doi.org/10.1002/hbm.24750

Tutorial

• Install latest Slicer Preview Release of 3D Slicer
• Install HDBrainExtraction extension
• Start 3D Slicer
• Go to Sample Data module and load MRBrainTumor1 data set
• Go to HD Brain Extraction Tool module
• Select Input volume -> MRBrainTumor1
• Select Skull-stripped volume -> Create new volume
• Select Brain segmentation -> Create new segmentation
• Click Apply
  • If you are prompted to install any additional packages then accept that and wait for a couple of minutes. IMPORTANT: You may need up to 20GB free disk space to intall all required Python packages. If installation fails due to running out of disk space then it may leave Python packages in the Slicer installation in an inconsistent state and fixing it may only be possible by removing the entire Slicer install folder and reinstall the application.
  • If a GPU is available then results are computed within about 20 seconds. If computation is done on CPU then it may take 5-10 minutes!
• To display the skull-stripped volume in 3D: go to Data module and drag-and-drop the skull-stripped volume into the 3D view.
• To display the brain mask in 3D: go to Data module and drag-and-drop the segmented into the 3D view.

User interface

• Inputs
  • Input volume: input brain MRI
• Outputs
  • Skull-stripped volume: if a volume node is selected here then it will contain the skull-strippted volume (i.e., a volume where region outside the brain is blanked out)
  • Brain segmentation: if a segmentation node is selected here then it will contain a brain segment, which specifies the brain region
• Advanced:
  • Device:
    • auto: first GPU is used if CUDA is installed; otherwise CPU is used
    • cpu: use the CPU for computation, it is slower and may produce slightly lower quality result
    • gpu N: use the N-th GPU

Note: HD-BET downloads the model file (about 65MB) in the user's home directory in hd-bet_params folder. The folder can be removed if HD-BET is no longer used (the tool downloads the model again if needed).

Contact

Please post any questions to the Slicer Forum.

Developers of this extension are not associated with the developers of the HD-BET brain extraction tool, just provide the convenient 3D Slicer based user interface.