Slicer:Workshops:User Training 101

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

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 an overview, dowload this slideshow

Software Installation

Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to your platform, the tutorial guide for Slicer, the generic sample data set. This material is located 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

Data to Download

• Get the tutorial data with Dicom tutorial_with_dicom.zip

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

• Get this extra set of interoperative data mrt-images.zip
• Get this data for registration demonstrations: RegistrationSample.zip
• Get these data for DTI demonstrations: SlicerSampleDTI.zip dwi-dicom.zip
• Get these data for FreeSurfer demonstrations: FreeSurferSubjects.zip
• Get these data for EMAtlasBrainClassifier demonstrations: BrainAtlasClassifier.zip
• Get these data for EMSegmenter demonstrations: EMSegmentTutorial.zip
• Get these Tensor data for DTI Nrrd File Format demonstrations: TensorData.zip
• Get these Tensor data for DWI Nrrd File Format demonstrations: dwi-dicom.zip
• Get these data for fMRI demonstrations: fMRIData_short.zip, fMRIData_long.zip

Slicer Training

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

• Slicer Training 1: Loading and Viewing Data
• Slicer Training 2: Manual Segmentation and Model Making
• Slicer Training 3: Level-Set Segmentation
• Slicer Training 4: DT-MRI module
• Slicer Training 5: fMRI module
• Slicer Training 6: vtkFreeSurferReaders Module
• Slicer Training 7: Saving Data
• Slicer Training 8: Nrrd File Format
• Slicer Training 9: Dicom to Nrrd Conversion
• Slicer Advanced Training 10: EMBrainAtlasClassifier
• Slicer Advanced Training 11: Registration

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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