This project is in active development and does not have any regulatory approval
This repository contains a collection of modules for 3D Slicer on the topic of deep brain stimulation and other applications—see the modules section below for a general overview.
The Lead-OR module provides an interface for setting micro electrodes configuration in space. See the Lead-OR page for installation instructions and how to load a sample dataset. See the Lead-OR section in the Lead-DBS manual for the integration with electrophysiology recordings.
WarpDrive allows for manual interaction with the deformation fields that result from non linear registration. The idea is to be able to fix for miss-alignments between source and target images (and models). See the WarpDrive page for more information.
This module outputs transforms that represent stereotactic planning trajectories from the planning settings. A routine to import plannings from Brainlab and ROSA is implemented. Output transforms are taken as an input to the Lead-OR module.
The import atlas module implements a routine to import Lead-DBS atlases. A Lead-DBS installation is needed so the path to the atlas can be provided. Atlases are imported into a model hierarchy in Slicer. Atlases can also be loaded by drag-and-dropping the atlas_index.mat files.
This module implements a routine to load AC,PC and MS coordinates from the ACPC_autodetect.mat file generated from Lead-DBS. The ACPC transform is also computed on load.
This module takes a curve as an input and creates a fiberbundle, with fibers spanning varying radius along the curve.
This CLI module implements similar logic as platimatch's landmark_warp, but with variable radial basis functions. It used by WarpDrive to calculate transformations.
This CLI module creates a grid transform from a composite one. The logic is as the one in Slicer's transforms module, but implemented in a CLI. This is useful to run it in the background and get progress indication, as used in WarpDrive.
Such a scene can be represented when using Lead-DBS and modules of this extension. See the Lead-OR page to load a sample dataset in Slicer.
- Oxenford, S., Ríos, A. S., Hollunder, B., Neudorfer, C., Boutet, A., Elias, G. J. B., Germann, J., Loh, A., Deeb, W., Salvato, B., Almeida, L., Foote, K. D., Amaral, R., Rosenberg, P. B., Tang-Wai, D. F., Wolk, D. A., Burke, A. D., Sabbagh, M. N., Salloway, S., … Horn, A. (2024). WarpDrive: Improving spatial normalization using manual refinements. Medical Image Analysis, 91, 103041. https://doi.org/10.1016/j.media.2023.103041
- Oxenford, S., Roediger, J., Neudorfer, C., Milosevic, L., Güttler, C., Spindler, P., Vajkoczy, P., Neumann, W.-J., Kühn, A., & Horn, A. (2022). Lead-OR: A multimodal platform for deep brain stimulation surgery. ELife, 11, e72929. https://doi.org/10.7554/eLife.72929