Slicer:Workshops:User Training 101 SPujol

Link to the NAC website

Introduction

This is a training compendium for neuroimage analysis using Slicer2.6. This series of course 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, dowload this slideshow

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 (lot).

• Training 1: Loading and Viewing Data
• Training 2: Manual Segmentation and Model Making
• Training 3: Level-Set Segmentation
• Training 4: Diffusion Tensor Imaging Analysis
• Training 5: Functional Magnetic Resonance Imaging Analysis
• Training 6: FreeSurferReader
• Training 7: Volume, Model and Scene Saving
• Training 8: Nrrd File Format
• Training 9: Dicom to Nrrd Conversion
• Advanced Training 10: Automatic Segmentation of Brain Structures
• Advanced Training 11: Registration

Training Material

Software Tool

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

Training Datasets

• Get these data for Training 1,2,3: tutorial_with_dicom.zip
• Get these data for Training 4: SlicerSampleDTI.zip dwi-dicom.zip
• Get these data for Training 5: fMRIData_short.zip, fMRIData_long.zip
• Get these data for Training 6: FreeSurferSubjects.zip
• Get these data for Training 7: tutorial_with_dicom.zip
• Get these data for Training 8: TensorData.zip
• Get these data for Training 9: dwi-dicom.zip
• Get these data for Training 10: BrainAtlasClassifier.zip
• Get these data for Training 11: RegistrationSample.zip
• Get these extra set of interoperative data mrt-images.zip
• Get these data for EMSegmenter demonstrations: EMSegmentTutorial.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.

Feedback and Bug reports

• 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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