Difference between revisions of "Slicer3.2:Training"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(137 intermediate revisions by 16 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
= Welcome to the Slicer3 101 Page (under construction)=
+
= Welcome to the 3D Slicer3.2 User Training 101=
 
+
*The information on this page applies to '''3D Slicer version 3.2'''.
 +
**If you are looking for materials about Slicer version 3.6, please visit the [https://www.slicer.org/wiki/Slicer3.6:Training#Software_tutorials Slicer3.6 training page]
 +
**If you are looking for materials about Slicer version 3.4, please visit the [https://www.slicer.org/wiki/Slicer3.4:Training#Software_tutorials Slicer3.4 training page]
 +
**If you are looking for materials about Slicer version 2, please visit the [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer2 101 page].
 
{| border="00" cellpadding="5" cellspacing="0"
 
{| border="00" cellpadding="5" cellspacing="0"
 
|-
 
|-
| rowspan="2"|  
+
| rowspan="2" align="left"|  
 
* Slicer 3 has been designed as
 
* Slicer 3 has been designed as
 
** an easy-to-use application for 3D image analysis and visualization,
 
** an easy-to-use application for 3D image analysis and visualization,
Line 12: Line 15:
 
*This page contains training materials and data sets for self-guided training in the use of Slicer3
 
*This page contains training materials and data sets for self-guided training in the use of Slicer3
  
*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
+
*'''For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
+
| style="background: #ebeced" colspan="2" align="center"| <b>[https://www.slicer.org/wiki/Slicer3:Slicer3Brand Slicer Logo]</b>
 
|-
 
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png |center|250px|Slicer logo]]  
+
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]  
| style="background: #ebeced"|
 
 
|}
 
|}
  
 
= Software Installation =
 
= Software Installation =
The [http://www.na-mic.org/Wiki/index.php/Slicer3:Downloads download instructions] will guide you through the installation of the Slicer3 software appropriate to your platform.  
+
The [http://www.slicer.org/pages/Downloads '''Slicer download page'''] contains links for downloading the different versions of Slicer 3.
 +
 
 
=Training Compendium=
 
=Training Compendium=
{| border="1" cellpadding="5"
+
{| border="1" cellpadding="5" width="1200px"
|- style="background:#b7ca79; color:black" align="left"  
+
|- style="background:#BBE9E2; color:black" align="left"  
| style="width:5%" | '''Level'''
+
| style="width:5%" | '''Category'''
 
| style="width:35%" | '''Tutorial'''
 
| style="width:35%" | '''Tutorial'''
 
| style="width:30%" | '''Sample Data'''  
 
| style="width:30%" | '''Sample Data'''  
 
| style="width:10%" | '''Image'''  
 
| style="width:10%" | '''Image'''  
 
|-
 
|-
| style="background:#f6e8b1; color:black" align="Center"| '''1'''
+
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.1"></span> '''1.1'''
| style="background:#b0cc99; color:#522200"| [[Media:Slicer3Training_LoadingAndVisualization.ppt| Data Loading and Visualization in Slicer3 ]]
+
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008_2.ppt| Data Loading and 3D Visualization in Slicer3 ]]
| style="background:#b0cc99; color:#522200"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
+
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz] <br> [http://www.na-mic.org/Wiki/index.php/media:SlicerSampleVisualization.zip SlicerSampleVisualization.zip‎ ]
| style="background:#f6e8b1; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
+
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|200px|LoadingandVisualization]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.2"></span> '''1.2'''
 +
| style="background:#D1FFF9; color:black"| [[Media:Manual Segmentation with 3DSlicer-mj.ppt‎| Manual segmentation with 3D Slicer]]
 +
| style="background:#D1FFF9; color:black"|
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:OrbitSegmentationt.png|200px]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.3"></span> '''1.3'''
 +
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>
 +
Background Materials:[[EMSegmenter| EMSegmenter History]]
 +
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>
 +
[[Media:AutomaticSegmentation.zip | ‎AutomaticSegmentation.zip  ]]
 +
 
 +
 
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|200px|EM Segmenter]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.4"></span> '''1.4'''
 +
| style="background:#D1FFF9; color:black"|[[Media:Na-MIC-Slicer-Registration.ppt|Affine and Deformable Registration in Slicer 3]]
 +
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz | SlicerSampleRegistration.tgz]]<br>
 +
[[Media:SlicerSampleRegistration.zip |SlicerSampleRegistration.zip]]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|200px|SlicerRegistration]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.5"></span> '''1.5'''
 +
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial7.pdf| Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3]]<br>
 +
Background Materials:[http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI DT-MRI module].
 +
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip| Slicer3DiffusionTutorialData.zip]] <br>
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|200px|Glyphs and tracts]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.6"></span> '''1.6'''
 +
| style="background:#D1FFF9; color:black"| [[Media:Slicer3Training ChangeTracker.ppt| Detecting subtle change in pathology]] <br>
 +
This tutorial consists of two MR scans of a patient with meningioma.
 +
| style="background:#D1FFF9; color:black"|[[Media:ChangeTracker-Tutorial-Data.zip|ChangeTracker-Tutorial-Data.zip ]]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:TumorGrowth-Tutorial-Image.png|200px|Meningioma Case]]
 +
|-
 +
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.7"></span> '''1.7'''
 +
| style="background:#D1FFF9; color:black"| [[media:Slicer3Training_WhiteMatterLesions_v2.3.pdf‎ |Detecting white matter lesions in lupus]] <br>
 +
This tutorial teaches how to use an automated, multi-level method to segment white matter brain lesions in lupus.
 +
| style="background:#D1FFF9; color:black"|Lupus Tutorial Data [[Media:LesionSegmentationTutorialData.tgz‎|(.tgz)]][[media:LesionSegmentationTutorialData.zip‎| (.zip)]]<br>
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:3dLupusLesionVolume.png|200px|Lesion Segmentation]]
 
|-
 
|-
| style="background:#f6e8b1; color:black" align="Center"| '''1'''
+
| style="background:#9BF2C5; color:black" align="Center"| <span id="1.8"></span> '''1.8'''
| style="background:#b0cc99; color:#522200"| [[Media:NAMIC-AHM07-EMTutorialV2.ppt|Basic EM Segmentation]]
+
| style="background:#D1FFF9; color:black"| [[Media:FreeSurferCourse_SoniaPujol.ppt‎|FreeSurfer Course]] <br>
| style="background:#b0cc99; color:#522200"| [[Media:EMSegTutorial-AHM2008.zip|EMSegTutorial-AHM2008.zip]]
+
This tutorial teaches how to visualize FreeSurfer segmentations and parcellation maps of the brain.
| style="background:#f6e8b1; color:black" align="Center"| [[Image:EMSegment.png|100px|EM Segmenter]]
+
| style="background:#D1FFF9; color:black"|[http://www.na-mic.org/Wiki/index.php/Image:FreeSurferData.tar.gz FreeSurfer Tutorial Data ] <br> [[media:FreeSurferTutorialData.zip|FreeSurferTutorialData.zip]]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:FreeSurferParcellation.PNG|200px|FreeSurfer segmentation]]
 
|-
 
|-
| style="background:#89725b; color:black" align="Center"| '''2'''
+
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.1"></span> '''2.1'''
| style="background:#b0cc99; color:#522200"| [[Media:EMSegTutorial-AHM2008.ppt|EM Advanced Course]]
+
| style="background:#D1FFF9; color:black"| [[media:ProgrammingIntoSlicer3_SoniaPujol.ppt‎ |Programming into Slicer3]]
'''Mini-tutorials:''' [[EMSegmenter Mini-Tutorials]]
+
This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.
| style="background:#b0cc99; color:#522200"| [[Media:EMSegTutorial-AHM2008.zip|EMSegTutorial-AHM2008.zip]]
+
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld_Plugin.zip| HelloWorld_Plugin.zip ]]
| style="background:#f6e8b1; color:black" align="Center"| [[Image:EMlowres.png|100px|EM Segmenter]]
+
 
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:ProgrammingCourse_Logo.PNG|200px|Programming]]
 
|-
 
|-
| style="background:#89725b; color:black" align="Center"| '''2'''
+
| style="background:#8EDEB5; color:black" align="Center"| <span id="2.2"></span> '''2.2'''
| style="background:#b0cc99; color:#522200"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Slicer3 Course for Developers]]
+
| style="background:#D1FFF9; color:black"|  [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
The Slicer3 course for developers teaches how to plug an external executable to Slicer3.
+
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the '''"Simple region growing"''' segmentation module.
This tutorial is intended for engineers and scientists who want to to integrate external programs with Slicer3.
+
<br>Background Materials: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning].
| style="background:#b0cc99; color:#522200"| [[Media:HelloWorld.zip|HelloWorld.zip]]
+
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#f6e8b1; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
+
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.1"></span> '''3.1'''
 +
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
 +
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
 +
| style="background:#D1FFF9; color:black"| 
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|200px|Slicer with robots]]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.2"></span> '''3.2'''
 +
| style="background:#D1FFF9; color:black"| [[Media:Brain Atlas Tutorial08.ppt| SPL-PNL Brain Atlas Tutorial]]
 +
This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial. <br>
 +
Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas].
 +
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL  Brain Atlas]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|200px|Brain Atlas]]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.3"></span> '''3.3'''
 +
| style="background:#D1FFF9; color:black"| [[Media:Abdominal_Atlas_Tutorial08.ppt| SPL Abdominal Atlas Tutorial]]
 +
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial.
 +
<br> Background Materials: [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas].
 +
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|200px|Abdominal Atlas]]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.4"></span> '''3.4'''
 +
| style="background:#D1FFF9; color:black"| [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XND Using XNAT Desktop and Slicer3 for remote data handling ]
 +
This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like [http://central.xnat.org '''XNAT Central'''] and retrieve catalog files that can be opened inside Slicer.
 +
| style="background:#D1FFF9; color:black"|
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:XNDmanage2.png|200px|XNAT Desktop Manager]]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.5"></span> '''3.5'''
 +
| style="background:#D1FFF9; color:black"| '''Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system'''
 +
These tutorials are intended for researchers who wish to utilize distributed computational resources.
 +
* [http://www.slicer.org/slicerWiki/images/1/1e/Gwe-basic-tutorial.ppt GWE Basic Tutorial]
 +
* [http://www.slicer.org/slicerWiki/images/a/a0/Gwe-basic-wcp-tutorial.ppt GWE Basic Tutorial Using Web Control Panel]
 +
* [http://www.slicer.org/slicerWiki/images/b/b4/Gwe-advanced-tutorial.ppt GWE Advanced Tutorial]
 +
* [http://www.slicer.org/slicerWiki/images/8/87/Gslicer-tutorial.ppt GSlicer3 Tutorial]
 +
| style="background:#D1FFF9; color:black"| [http://www.gridwizardenterprise.org/ '''Grid Wizard Enterprise''']
 +
 
 +
* GWE Information
 +
** [http://www.gridwizardenterprise.org/guides/install.html GWE Installation Guide]
 +
** [http://www.gridwizardenterprise.org/guides/config.html GWE Configuration Guide]
 +
** [http://www.gridwizardenterprise.org/guides/user.html End Users Guide]
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:GWE-overview.jpg|200px|GWE Overview]][http://www.youtube.com/watch?v=yXdRks5Wu5Q Featured Study Case (YouTube)]
 +
|-
 +
| style="background:#72b291; color:black" align="Center"| <span id="3.6"></span> '''3.6'''
 +
| style="background:#D1FFF9; color:black"| [http://www.youtube.com/watch?v=ebWqTHf5i5Y&hd=1 YouTube Video: Using "GWE's Record Set Explorer"]
 +
This tutorial is intended for researchers who wish to interactively review local or remote datasets; such as input values of parameter exploration experiements, their output results, result sets of XNAT queries or any other type of dataset.
 +
| style="background:#D1FFF9; color:black"|
 +
 
 +
* '''Sample data used in demo video:'''
 +
* [http://www.oasis-brains.org/pdf/oasis_cross-sectional.csv OASIS Brain DB Cross Sectional Remote DataSet]
 +
* [http://www.oasis-brains.org/pdf/oasis_longitudinal.csv OASIS Brain DB Longitudinal Remote DataSet]
 +
 
 +
* [http://www.gridwizardenterprise.org/rse '''RSE Project Site''']
 +
(there you can find: binaries, installation guides, source code, other useful documentation and project related information)
 +
 
 +
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Rse-gwe-exp.gif|200px|RSE browsing through the results of a parameter exploration experiment]]
 
|}
 
|}
 +
 +
* Category 1 = Basic functionality
 +
* Category 2 = Advanced functionality
 +
* Category 3 = Specialized application packages
 +
 +
=Additional Materials=
 +
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
 
<br /> Back to [[Training:Main|Training:Main]]
 
<br /> Back to [[Training:Main|Training:Main]]

Latest revision as of 17:27, 10 July 2017

Home < Slicer3.2:Training

Welcome to the 3D Slicer3.2 User Training 101

  • The information on this page applies to 3D Slicer version 3.2.
  • Slicer 3 has been designed as
    • an easy-to-use application for 3D image analysis and visualization,
    • an open-source environment for software development,
    • a technology delivery platform for community breakthroughs.
  • Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
  • This page contains training materials and data sets for self-guided training in the use of Slicer3
  • For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
Slicer Logo
Slicer logo

Software Installation

The Slicer download page contains links for downloading the different versions of Slicer 3.

Training Compendium

Category Tutorial Sample Data Image
1.1 Data Loading and 3D Visualization in Slicer3 SlicerSampleVisualization.tar.gz
SlicerSampleVisualization.zip‎
LoadingandVisualization
1.2 Manual segmentation with 3D Slicer OrbitSegmentationt.png
1.3 EM Segmentation Course

Background Materials: EMSegmenter History

AutomaticSegmentation.tar.gz

‎AutomaticSegmentation.zip


EM Segmenter
1.4 Affine and Deformable Registration in Slicer 3 SlicerSampleRegistration.tgz

SlicerSampleRegistration.zip

SlicerRegistration
1.5 Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3

Background Materials:DT-MRI module.

Slicer3DiffusionTutorialData.zip
Glyphs and tracts
1.6 Detecting subtle change in pathology

This tutorial consists of two MR scans of a patient with meningioma.

ChangeTracker-Tutorial-Data.zip Meningioma Case
1.7 Detecting white matter lesions in lupus

This tutorial teaches how to use an automated, multi-level method to segment white matter brain lesions in lupus.

Lupus Tutorial Data (.tgz) (.zip)
Lesion Segmentation
1.8 FreeSurfer Course

This tutorial teaches how to visualize FreeSurfer segmentations and parcellation maps of the brain.

FreeSurfer Tutorial Data
FreeSurferTutorialData.zip
FreeSurfer segmentation
2.1 Programming into Slicer3

This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree.

HelloWorld_Plugin.zip Programming
2.2 Image Guided Therapy Planning Tutorial

This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the "Simple region growing" segmentation module.
Background Materials: Neurosurgical Planning.

NeurosurgicalPlanningTutorialData.zip Neurosurgical Planning Overview
3.1 Slicer3 as a research tool for image guided therapy research (IGT)

This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.

Slicer with robots
3.2 SPL-PNL Brain Atlas Tutorial

This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial.
Background Materials: SPL-PNL Brain Atlas.

SPL-PNL Brain Atlas Brain Atlas
3.3 SPL Abdominal Atlas Tutorial

This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial.
Background Materials: SPL Abdominal Atlas.

SPL Abdominal Atlas Abdominal Atlas
3.4 Using XNAT Desktop and Slicer3 for remote data handling

This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like XNAT Central and retrieve catalog files that can be opened inside Slicer.

XNAT Desktop Manager
3.5 Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system

These tutorials are intended for researchers who wish to utilize distributed computational resources.

Grid Wizard Enterprise GWE OverviewFeatured Study Case (YouTube)
3.6 YouTube Video: Using "GWE's Record Set Explorer"

This tutorial is intended for researchers who wish to interactively review local or remote datasets; such as input values of parameter exploration experiements, their output results, result sets of XNAT queries or any other type of dataset.

(there you can find: binaries, installation guides, source code, other useful documentation and project related information)

RSE browsing through the results of a parameter exploration experiment
  • Category 1 = Basic functionality
  • Category 2 = Advanced functionality
  • Category 3 = Specialized application packages

Additional Materials

For a variety of data sets for downloading, check the following link.
Back to Training:Main