SimpleStereotactic

Simple Stereotactic is an unregistered 3D Slicer Extension to give sub-millimeter accuracy for use with the COMPASS™ Stereotactic Frame coordinate system.

The coordinates describe the parameters necessary to reproduce the targeting. Parameters are consistent with those for a Compass Stereotactic Frame. This project can be modified to accomodate other coordinate systems.

Installation:

See the installation file for complete installation instructions

Usage

This extension provides functionality to

Register images with a fiducial frame to the coordinate space of the head frame
Register an atlas of a given species to the Anterior Commissure and Posterior Commissure (AC/PC) of the provide subject
Plan and alter multiple trajectories for the placement of canulas to target points.

Detailed instructions using the Porcine_Sample_Data_with_Atlas.mrb are provided.

Example File

The example file provided, Porcine_Sample_Data_with_Atlas.mrb, is a medical record bundle (mrb) file with the following files zip-compressed within:

Sample_Pig_MPRAGE.nrrd: An MRI of a pig head with z-bar fiducials
Scan_Frame_Points.mrk.json: A sampling of points on the z-bar fiducial in the MRI.
porcine_atlas.nrrd: A numbered porcine atlas (see references).
porcine_atlas_color_table.ctbl: A 3D Slicer color table translating numbers to colors and labels for brain regions of the atlas.
Atlas_AC_PC.mrk.json: Fiducial points marking the Anterior Commissure (AC) and Posterior Commissure (PC) of the porcine atlas.

References

This software was used in the following paper:

A novel re-attachable stereotactic frame for MRI-guided neuronavigation and its validation in a large animal and human cadaver model

Christine A Edwards, Aaron E Rusheen, Yoonbae Oh, Seungleal B Paek, Joshua Jacobs, Kristen H Lee, Kendall D Dennis, Kevin E Bennet, Abbas Z Kouzani, Kendall H Lee

The source of the pig atlas is:

A three-dimensional digital segmented and deformable brain atlas of the domestic pig

Stéphan Saikali, Paul Meurice, Paul Sauleau, Pierre-Antoine Eliat, Pascale Bellaud, Gwenaelle Randuineau, Marc Vérin, Charles-Henri Malbert

In The Works

A experimental version of this Extension is in the works to navigate with a small animal frame. Such as with the Kopf Instruments Small Animal Stereotactic Instrument. To adequately complete this, the following are needed: