Slicer:Workshops:User Training 101

This is the introductory Slicer 2.6 training material.

Link to the NAC website

Introduction

You can begin to learn how to

• load and view data
• segment data and create 3D models
• use the DTI and fMRI modules

For a high level description of 3D Slicer, download this presentation

Software Installation

Before you can work through the tutorial materials you have to install the 3D slicer program and download the sample data sets and tutorials.

The Slicer software can be found in Slicer 2.6 Getting Started: Software & Sample Data .

Slicer 2 Materials

Contents	Presentation	Data
Slicer
Loading and Viewing Data	Slicer Training 1	Dataset Training 1
Manual Segmentation and Model Making	Slicer Training 2	Dataset Training 2
Level-Set Segmentation	Slicer Training 3	Dataset Training 3
Diffusion Tensor Imaging	Slicer Training 4	Dataset Training 4.1 Dataset Training 4.2
Functional Magnetic Resonance Imaging	Slicer Training 5	Dataset Training 5.1 Dataset Training 5.2
vtkFreeSurferReaders	Slicer Training 6	Dataset Training 6
Saving Data	Slicer Training 7	Dataset Training 7
Nrrd File Format	Slicer Training 8	Dataset Training 8
Dicom to Nrrd Conversion	Slicer Training 9	Dataset Training 9
EMBrainAtlasClassifier	Slicer Training 10	Dataset Training 10
Registration	Slicer Training 11	Dataset Training 11
fMRI Statistical Analysis	HST.583 Functional Magnetic Resonance Imaging	Tutorial documentation

Slicer Additional Resources

A rendering of the Limbic System from the SPL PNL brain atlas

• SPL PNL Brain Atlas
• IGT Tutorial Materials
• EMSegmenter for multi-channel data and white matter hyperintensities
• Data Fusion and Registration
• Using 3DSlicer in Astronomy
• How to use Slicer with BIRN
• CT based atlas of the abdomen. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.

Feedback and Bug reports

Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).

• Feedback about Slicer
• Bug reports

Acknowledgements

• Slicer is being developed by a community of contributors. For more information see the Slicer website.

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