Difference between revisions of "Slicer:Workshops:User Training 101"

From NAMIC Wiki
Jump to: navigation, search
Line 22: Line 22:
  
 
{| border="1"
 
{| border="1"
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| '''Contents'''
 
| '''Contents'''
 
| '''Presentation'''
 
| '''Presentation'''
 
| '''Data'''
 
| '''Data'''
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| '''Slicer'''
 
| '''Slicer'''
 
|
 
|
 
|
 
|
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Loading and Viewing Data
 
| Loading and Viewing Data
 
|
 
|
Line 36: Line 36:
 
|
 
|
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 1]]
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 1]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Manual Segmentation and Model Making
 
| Manual Segmentation and Model Making
 
|
 
|
Line 42: Line 42:
 
|
 
|
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 2]]
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 2]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Level-Set Segmentation
 
| Level-Set Segmentation
 
|
 
|
Line 48: Line 48:
 
|
 
|
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 3]]
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 3]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Diffusion Tensor Imaging
 
| Diffusion Tensor Imaging
 
|
 
|
Line 54: Line 54:
 
|
 
|
 
[[Media:SlicerSampleDTI.zip| Dataset Training 4.1]] [[Media:Dwi-dicom.zip|Dataset Training 4.2]]
 
[[Media:SlicerSampleDTI.zip| Dataset Training 4.1]] [[Media:Dwi-dicom.zip|Dataset Training 4.2]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Functional Magnetic Resonance Imaging
 
| Functional Magnetic Resonance Imaging
 
|
 
|
Line 60: Line 60:
 
|
 
|
 
[[Media:FMRIData1_short.zip|Dataset Training 5.1]] [[Media:FMRIData2_long.zip|Dataset Training 5.2]]
 
[[Media:FMRIData1_short.zip|Dataset Training 5.1]] [[Media:FMRIData2_long.zip|Dataset Training 5.2]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| vtkFreeSurferReaders
 
| vtkFreeSurferReaders
 
|
 
|
Line 66: Line 66:
 
|
 
|
 
[[Media:FreeSurferSubjects.zip|Dataset Training 6 ]]
 
[[Media:FreeSurferSubjects.zip|Dataset Training 6 ]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Saving Data
 
| Saving Data
 
|
 
|
Line 72: Line 72:
 
|
 
|
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 7]]
 
[[Media:Tutorial-with-dicom.zip|Dataset Training 7]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Nrrd File Format
 
| Nrrd File Format
 
|
 
|
Line 78: Line 78:
 
|
 
|
 
[[Media:Tensor_data.zip|Dataset Training 8]]
 
[[Media:Tensor_data.zip|Dataset Training 8]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Dicom to Nrrd Conversion
 
| Dicom to Nrrd Conversion
 
|
 
|
Line 84: Line 84:
 
|
 
|
 
[[Media:Dwi-dicom.zip|Dataset Training 9]]
 
[[Media:Dwi-dicom.zip|Dataset Training 9]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| EMBrainAtlasClassifier
 
| EMBrainAtlasClassifier
 
|
 
|
Line 90: Line 90:
 
|
 
|
 
[[Media:BrainAtlasClassifier.zip|Dataset Training 10 ]]
 
[[Media:BrainAtlasClassifier.zip|Dataset Training 10 ]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| Registration
 
| Registration
 
|
 
|
Line 96: Line 96:
 
|
 
|
 
[[Media:RegistrationSample.zip|Dataset Training 11 ]]
 
[[Media:RegistrationSample.zip|Dataset Training 11 ]]
|- bgcolor="#ddffff"
+
|- bgcolor="#c2c2c2"
 
| fMRI Statistical Analysis
 
| fMRI Statistical Analysis
|
+
|[http://ocw.mit.edu/OcwWeb/Health-Sciences-and-Technology/HST-583Fall-2004/CourseHome/ HST.583 Functional Magnetic Resonance Imaging]
[http://ocw.mit.edu/OcwWeb/Health-Sciences-and-Technology/HST-583Fall-2004/CourseHome/ HST.583 Functional Magnetic Resonance Imaging]
+
|[http://mgh-edu.nbirn.net/tutorial.html Tutorial documentation]
|
 
[http://mgh-edu.nbirn.net/tutorial.html Tutorial documentation]
 
|
 
<br />
 
 
|}
 
|}
  

Revision as of 14:15, 31 May 2007

Home < Slicer:Workshops:User Training 101

This is the introductory Slicer 2.6 training material.

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


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).


Acknowledgements

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


Back to Training:Main