Slicer:Workshops:User Training 101

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Contents

Introduction

This is a training compendium for using 3D Slicer version 2. If you are looking for information about Slicer version 3, please follow this Slicer3 101 page.

This work is jointly sponsored by NA-MIC, NAC and NCIGT.

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, download 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

Dicom to Nrrd 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

Feedback

Acknowledgements

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


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