Slicer:Workshops:User Training 101

Link to the NAC website

Introduction

This is a training compendium for neuroimage analysis using 3DSlicer.

This series of courses will teach you how to

• load and view data
• segment data and create 3D models
• perform Diffusion Tensor Imaging and fMRI analysis

For an overview of Slicer, dowload this slideshow

Software

The current version of Slicer that is fully supported is Slicer 2.6.

Please follow the Slicer 2.6 Getting Started instructions to install the version of the Slicer program appropriate to your platform.

Training Compendium

For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

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

'	Course	Dataset
	Data Loading and Visualization	Tutorial_with_dicom.zip
	Data Saving	Tutorial-with-dicom.zip
	Manual Segmentation	Tutorial_with_dicom.zip
	Level-Set Segmentation	Tutorial_with_dicom.zip
	Automatic Brain Segmentation	BrainAtlasClassifier.zip
	Registration	RegistrationSample.zip
	Diffusion Tensor Imaging Analysis	SlicerSampleDTI.zip Dwi-dicom.zip
	Nrrd File Format	Tensor_data.zip
	Nrrd to Dicom Conversion	Dwi-dicom.zip
	Functional Magnetic Resonace Imaging Analysis	FMRIData1_short.zip FMRIData2_long.zip
	FreeSurfer Reader	FreeSurferSubjects.zip

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.
• Airway inspector: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.

Feedback

• 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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