IGT:ToolKit/Neurosurgical-Planning

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Neurosurgical Planning for Image Guided Therapy using Slicer3

Overview

This tutorial reviews Slicer3's Image Guided Therapy capabilities using the example of preoperative planning for neurosurgery. It covers how to perform multiple tasks in Slicer3, including:

• Image registration
• Segmentation and model making
• Diffusion Tensor Imaging and tractography
• Using an atlas

Tutorial Materials

• Tutorial slides for the neurosurgical planning tutorial: pdf (recommended) or ppt
• Neurosurgical planning tutorial dataset - contains:
  • Patient dataset
  • SPL-PNL brain atlas
  • MRML scene registering the patient with the atlas
  • MRML scene registering the patient's anatomical MRI with the patient's DTI
  • MRML scene registering of precomputed tensor data for the patient's DTI

To Complete the Entire Tutorial

• Tutorial slides for the entire neurosurgical planning tutorial: pdf (recommended) or ppt
• Entire tutorial dataset - contains
  • Anatomical MRI dataset
  • Language fMRI dataset
  • SPL-PNL brain atlas
  • DTI dataset
  • MRML scene registering the patient with the atlas
  • MRML scene registering the patient's anatomical MRI with teh patient's DTI
  • The patient's precomputed tensor data
  • MRML scenes (and associated files) showing the results of each tutorial step

To complete a Section of the Tutorial

Part 1 - Affine Registration

• anatomical MRI dataset
• language fMRI dataset
• Tutorial slides for part 1 of the neurosurgical planning tutorial

Part 2 - Segmentation and Model Making

• anatomical MRI dataset
• MRML scene of Part 1 results
• Tutorial slides for part 2 of the neurosurgical planning tutorial

Part 3 - Incorporating an Atlas

• anatomical MRI dataset
• SPL-PNL brain atlas
• MRML scene of Part 2 results
• Additional files for part 3
• Tutorial slides for part 3 of the neurosurgical planning tutorial

Part 4 - Diffusion Tensor

• anatomical MRI dataset
• DTI dataset
• MRML scene of Part 3 results
• Additional files for part 4
• Tutorial slides for part 4 of the neurosurgical planning tutorial

Part 5 - Annotating the Preoperative Plan

• anatomical MRI dataset
• language fMRI dataset
• SPL-PNL brain atlas
• DTI dataset
• MRML scene of Part 4 results
• Additional files for part 5
• Tutorial slides for part 5 of the neurosurgical planning tutorial

Bonus Materials

This is a subset of the data above, which demonstrates some of the capabilities of the tractography package in Slicer 3.3. Snapshots 1-4 demonstrate a progression of the analysis of the interrelation of the morphology and DTI.

1. general view
2. location of the precentral gyrus based the surface of the white matter
3. peritumoral seeding of tractography: The general appearance is that of a "ball of spaghettis" with two tentacles,
4. exploration of the "tentacles": fiducial based seeding in the cerebral peduncle and in the vicinity of Brocca's area reveal potential corticospinal tract and acuate fasciculus

MRML scene and data in a zip file

Software Installation Instructions

Go to the Slicer3 Install site.

People

• Danielle Pace
• Nobuhiko Hata