{{documentation/versioncheck}}
{| cellpadding="20" border="0"
|+This page contains pointers to the different versions of the Slicer4, Slicer3, and Slicer2 training portfolios. Each portfolio includes a series of tutorials and pre-computed datasets.
 
'''[[Documentation/Nightly/Training|Slicer 5]] ::[[Documentation/4.10/Training|Slicer 4.10]] ::[[Documentation/4.8/Training|Slicer 4.8]] ::[[Documentation/4.6/Training|Slicer 4.6]] ::[[Documentation/4.5/Training|Slicer 4.5]] ::[[Documentation/4.4/Training|Slicer 4.4]] ::[[Documentation/4.3/Training|Slicer 4.3]] :: [[Documentation/4.2/Training|Slicer 4.2]] :: [[Slicer_3.6:Training|Slicer 3.6]] :: [[Slicer3.4:Training|Slicer 3.4]] :: [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Slicer 3.2] :: [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Slicer 2]'''
|-
|[[image:SlicerTraining.png|link=https://www.slicer.org/wiki/Documentation/4.8/Training]]<nowiki>|}</nowiki>
|}

Documentation/4.10/Training

2022-11-22T18:40:58Z

JChris.FillionR: Consolidated content of 4.10 and Nightly pages. This was done by saving the page source in text files and using visual diff and merge tool like "meld". Differences were resolved introspecting the wiki edit history.

<noinclude>{{documentation/versioncheck}}
</noinclude>
=Introduction: Slicer {{documentation/version}} Tutorials=

*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
*For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to '''[https://scholar.harvard.edu/soniapujol/home Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.]'''

*Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer5.0. The concepts are still useful but some interface elements and features may be different in updated versions.

__TOC__

=Quick Start Guide=

==Downloading and Installing Slicer==
{| width="100%"
|
*The [https://spujol.github.io/3DSlicerQuickStartGuide/ Quick Start Guide] shows how to install and start 3D Slicer
*Author: Sonia Pujol, Ph.D.
*Based on 3D Slicer 5.0 / 4.11
| align="right" |
[[image:QuickStart_image.png|250px|SlicerWelcome tutorial]]
|}

=General Introduction=

==Slicer Welcome Tutorial==
{| width="100%"
|
*The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0 Slicer Welcome tutorial] is an introduction to Slicer.
*Author: Sonia Pujol, Ph.D.
*Audience: First-time users who want a general introduction to the software
*Modules: Welcome to Slicer, Sample Data
*Based on 3D Slicer 4.8
*Compatible with Slicer 4.10.1
| align="right" |
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{| width="100%"
|
*The [https://www.dropbox.com/s/v3lyivwgdoro7yn/Slicer4.10minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial] is a brief introduction to the advanced 3D visualization capabilities of Slicer.
*Author: Sonia Pujol, Ph.D.
*Audience: First-time users who want to discover Slicer in 4 minutes
*Modules: Welcome to Slicer, Models
*Based on Slicer version 4.8
*Compatible with Slicer 4.10.1
*The [[Media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
| align="right" |
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
|}

=3D Visualization=
==Data Loading and 3D Visualization==
{| width="100%"
|
*Slicer 5.0
**The [https://spujol.github.io/SlicerVisualizationTutorial/ Slicer 5.0 Basics of data loading and visualization tutorial] shows how to load and visualize DICOM images and 3D models in 3D Slicer. [https://docs.google.com/presentation/d/12Lbq-QBCxP2p9FkF3_YM5Ng7pItfspMG0FP_20wQglA/edit?usp=sharing French version]
**Author: Sonia Pujol, Ph.D.
**Modules: DICOM, Volume Rendering, Models
**Audience: End-users
**Based on: 3D Slicer version 5.0/4.11
**The [https://www.dropbox.com/s/03emcqnlec4t2s5/3DVisualizationDataset.zip?dl=1 Data Loading and Visualization dataset] contains a thoraco-abdominal CT scan, an MRI brain dataset and 3D models of brain structures.

*Slicer 4.10
**The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx pptx]) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
**Author: Csaba Pinter
**Modules: Welcome to Slicer, Data, Volume Rendering, Models.
**Audience: End-users
**Based on Slicer 4.9
**Compatible with Slicer 4.10.1
**The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contains an MR scan and a series of 3D models of the brain.

| align="right" |
[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|200px|]]
[[Image:Slicer4DataLoading_tutorial.png|right|200px|]]
|}

==DICOM==
{| width="100%"
|
*The [https://spujol.github.io/SlicerDICOMTutorial/ DICOM and Slicer] tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0.
*Author: Sonia Pujol, Ph.D.
*Modules: DICOM, Volumes
*Based on: 3D Slicer version 5.0/4.11
*The [https://spujol.github.io/SlicerDICOMTutorial/ 3D Slicer DICOM Tutorial Data] contains a torso-CT and a breast MRI.
| align="right" |
[[Image:SlicerAndDICOM.png|right|250px|]]
|}

{| width="100%"
|
*The [https://www.dropbox.com/s/8pm5mty2c0zwmyk/3DVisualizationDICOM_Slicer4.10_SoniaPujol.pdf?dl=0 3D Visualization of DICOM images] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
*Modules: DICOM, Volumes, Volume Rendering, Models.
*Based on: 3D Slicer version 4.8
*Compatible with 3D Slicer version 4.10
*The [[Media:3DVisualization DICOM images part1.zip| 3DVisualizationDICOM_part1]] and [[Media:3DVisualization DICOM images part2.zip| 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
| align="right" |
[[Image:Slicer4RSNA_2.png|right|250px|]]
|}

==Open Anatomy Browser==
{| width="100%"
|
[[Image:OABrowser.png|right|250px|]]

*The [https://www.dropbox.com/s/f2641iu27hif8p4/OpenAnatomyTutorial_SoniaPujol-MikeHalle.pdf?dl=0 Open Anatomy Browser] tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases.
*Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D.
*Audience: End-users

|}

=Tutorials for software developers=

==PerkLab's Slicer bootcamp training materials==
{| width="100%"
|
*The [http://perk.cs.queensu.ca/ Laboratory for Percutaneous Surgery at Queen's University] has made available training material of its internal yearly bootcamp, covering topics, such as 3D Slicer overview, basic visualization, segmentation, registration, scripting and module development, surgical navigation, DICOM, reproducible medical image computing research methodology, version control, and research project management.
**[https://github.com/PerkLab/PerkLabBootcamp/blob/master/Doc/day3_2_SlicerProgramming.pptx?raw=true Scripting and module development tutorial]
**[https://github.com/PerkLab/PerkLabBootcamp/tree/master/Doc All other tutorials]
*Author: Andras Lasso, Csaba Pinter, Tamas Ungi, Csaba Pinter, Matthew Holden, Kyle Sunderland
*Audience: Developers, Users
*Based on: 3D Slicer version 4.10
| align="right" |
[[Image:PerkLabSlicerProgrammingTutorial.png|right|250px|]]
|}

==Slicer Programming Tutorial==
{| width="100%"
|
*The [https://spujol.github.io/SlicerProgrammingTutorial/ Slicer Programming tutorial] guides through the integration of a python module in Slicer. It provides an introduction to the Python Console and the Qt Widget toolkit in 3D Slicer.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*Based on: 3D Slicer version 5.0/4.11
| align="right" |
[[Image:SlicerProgrammingTutorial.png|right|250px|]]
|}

==Slicer script repository==

For additional Python scripts examples, please visit the [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository].

==Developing and contributing extensions for 3D Slicer==
{| width="100%"
|
*The [http://goo.gl/IP4cdg Developing and contributing extensions for 3D Slicer tutorial] is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
*Authors: Andrey Fedorov, Jean-Christophe Fillion-Robin, Steve Pieper
*Audience: Developers
*Based on: 3D Slicer version 4.4
| align="right" |
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
|}

=Segmentation=
{| width="100%"
|
*Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
**'''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia.
**'''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
**Audience: Users and developers interested in segmentation and 3D printing
**Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
**Based on: 3D Slicer version 4.7
| align="right" |[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
|---
|
*'''[https://www.youtube.com/watch?v=BJoIexIvtGo Video tutorial: Whole heart segmentation from cardiac CT]''' shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes.
**Author: Andras Lasso, PhD
**Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
**[http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd Sample data set]
**Based on: 3D Slicer version 4.8
| align="right" |[[Image:WholeHeartSegYoutube.png|280px]]
|---
|
*'''[https://www.youtube.com/watch?v=0at15gjk-Ns Video tutorial: Femur and pelvis segmentation from CT]''' shows how to use the Segment Editor module for segmenting pelvis and femur from CT volumes.
**Author: Andras Lasso, PhD
**Audience: Users who need to segment bones in CT images for visualization, quantification, or simulation.
**Sample data set: https://wiki.cancerimagingarchive.net/display/Public/TCGA-PRAD (Subject TCGA-VP-A878)
**Based on: 3D Slicer version 4.8
| align="right" |[[Image:FemurSegmentationYoutube.png|280px]]
|---
|
*'''[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]''' provide step-by-step description of useful segmentation techniques.
** Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping.
| align="right" |[[Image:SegmentationRecipes.png|280px]]
|---
|
*'''[https://spujol.github.io/SkullStrippingTutorial/ The Skull Stripping tutorial]''' shows how to perform skull-stripping in CT and MR data.
**Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD
**Audience: Users interested in brain segmentation
**Based on: 3D Slicer version 4.11
| align="right" |[[Image:SkullStripping.png|280px]]
|}

=Image Phenotyping=
{| width="100%"
|
*Based on: 3D Slicer version 4.10
*The [https://spujol.github.io/ImagePhenotypingTutorial/ Image Phenotyping tutorial] is an introduction to brain tumor segmentation and image phenotyping using the Slicer Radiomics extension.
*Authors: Sonia Pujol, Ph.D.
*Audience: Clinical researchers
*Dataset: [https://www.dropbox.com/s/hdlduw6oqnf2n72/Meningioma.nrrd?dl=0 Meningioma dataset]
| align="right" |[[File:ImagePhenotyping.png|250px]]

|}

=Registration=

==Slicer4 Image Registration==

{| width="100%"
|
*The [https://www.dropbox.com/s/chrugp2j2as5gop/ImageRegistration_Slicer4.8_SoniaPujol.pdf?dl=0 Registration tutorial] shows how to perform intra- and inter-subject registration within Slicer.
*Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
*Audience: Users and developers interested in image registration
*Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
| align="right" |[[File:registration_Slicer4.png|250px]]
|}

*Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10

{| width="100%"
|
*The [https://spujol.github.io/3DSlicerTutorial-Registration Brain Tumor Registration] is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up.
*Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D.
*Audience: Users and developers interested in image registration
*Dataset: [[Special:FilePath/RegLib C37 Data.zip| Registration Library Case #37]]
| align="right" |[[File:RigidRegistration.jpg|250px]]
|}

*Based on: 3D Slicer version 4.10

==Slicer Registration Case Library==
{| width="100%"
|
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides real-life example cases of using the Slicer registration tools. They include pre-computed dataset and step-by-step instructions for users to follow.

:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

=Slicer Extensions=
==Slicer4 Diffusion Tensor Imaging Tutorial==
{| width="100%"
|
*The [https://spujol.github.io/SlicerDiffusionMRITutorial Diffusion MRI Tutorial] is an introduction to the basics of loading diffusion weighted images in Slicer, estimating tensors and generating fiber tracts.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.8; Compatible with Slicer version 4.10.2
*The [https://www.dropbox.com/s/gba2zsn276x43up/SlicerDiffusionMRITutorialData.zip?dl=1 Slicer Diffusion MRI Tutorial dataset] contains an MR Diffusion Weighted Imaging scan of the brain.
*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
| align="right" |
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{| width="100%"
|
*The [https://spujol.github.io/NeurosurgicalPlanningTutorial/ Neurosurgical Planning tutorial] course guides end-users through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: Clinicians and Clinical Researchers
*Modules: Segment Editor, Tractography
*Based on 3D Slicer version 4.10
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] contains a Diffusion Weighted Imaging scan of a brain tumor patient.
| align="right" |
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 Quantitative Imaging tutorial==
{| width="100%"
|
*The [[Media:QuantitativeImaging Slicer4.5.pdf| Slicer4 Quantitative Imaging tutorial]] guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
*Authors: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
*Based on: 3D Slicer version 4.5
*The [[Media:QuantitativeImaging.zip| Quantitative Imaging dataset]] contains a series of MR and PET/CT data.
| align="right" |
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}

==Slicer4 IGT==
{| width="100%"
|
*[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
*Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
*Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
*Modules: SlicerIGT Extension
*Based on: Slicer4.3.1-2014.09.14
*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
| align="right" |
[[Image:SlicetIGT.png|right|150px|]]
|}

==Slicer4 Radiation Therapy Tutorial==

{| width="100%"
|
*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
*Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
*Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
*Based on Slicer 4.7
| align="right" |
[[Image:SlicerRTUseCaseImage.png|right|150px|]]
|}

==Slicer Pathology==
{| width="100%"
|
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*Dataset: Available directly with the Slicer Pathology Slicer extension.
| align="right" |
[[File:SlicerPathologyScreenShot8.png | 200px]].
|}

==SPHARM-PDM==
{| width="100%"
|
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
| align="right" |
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
|}

==Fiber Bundle Volume Measurement==
{| width="100%"
|
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
*Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
| align="right" |
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
|}

==Slicer4 Lung CT Analyzer==
{| width="100%"
|
*The [https://github.com/rbumm/SlicerLungCTAnalyzer LungCTAnalyzer tutorial] and the [https://www.youtube.com/watch?v=fpLxm7uAvZQ LungCTAnalyzer video-based demo] show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients.
*Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
*Audience: End-users
*Modules: LungCTSegmenter, LungCTAnalyzer
*Based on: 3D Slicer version 5.0 (4.11)
| align="right" |
[[Image:LungCTAnalyzer.png|right|250px|]]

|}

=3D Slicer version 4.7 Tutorial Contest=

For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]

===Segmentation for 3D printing===
{| width="100%"
|
*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing.
*Author: Csaba Pinter (Queen's University, Canada)
*[https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
| align="right" |
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
|}

===Slicer Pathology===
{| width="100%"
|
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*Dataset: Available directly with the Slicer Pathology Slicer extension.
| align="right" |
[[File:SlicerPathologyScreenShot8.png | 200px]].
|}

===Simple Python Tool for Quality Control of DWI data===
{| width="100%"
|
*The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
*Author: Laurent Chauvin (ETS Montreal)
*Dataset: Not available.
| align="right" |
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
|}

===SPHARM-PDM===
{| width="100%"
|
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
| align="right" |
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
|}

===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
{| width="100%"
|
*The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
*Dataset: Not available.
| align="right" |
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
|}

===Fiber Bundle Volume Measurement===
{| width="100%"
|
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
*Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
| align="right" |
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
|}

=YouTube videos=
{| border="1" cellpadding="5" width="1200px"
| style="width:33%" |[[Image:Verterbra.png|right|250px|]] [https://www.youtube.com/watch?v=Uht6Fwtr9hE How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia]
| style="width:33%" |[[Image:Femurmodel.png|right|250px|]] [https://www.youtube.com/watch?v=0at15gjk-Ns Creating a femur model from CT volume using 3D Slicer - Author: PerkLab]
| style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat]
|}
{| border="1" cellpadding="5" width="1200px" |
| style="width:25%" |[[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter]
| style="width:25%" |[[Image:LocalThresholdEffect.png|right|250px|]] [https://www.youtube.com/watch?time_continue=26&v=cevlMLyhfK8&feature=emb_logo Local Threshold Effect - Author: Kyle Sunderland]
| style="width:25%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso]
| style="width:25%" |[[Image:MONAILabel.png|right|250px|]] [https://www.youtube.com/watch?v=PmD8umlcpF4 MONAI Label(Slicer 4.11)- Author: Andres Diaz-Pinto]
|}

Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].

=Teams Contributions=
{| width="100%"
|
*This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
*Authors: Steve Pieper Ph.D.
*Audience: First time users and developers interested in Slicer 4.1 new features.
*Length: 0h20m
| align="right" |[[Image:Webinar-Slicer-4.1.png|250px]]
|}
 
----
 
{| width="100%"
|
*This ''Intro to Slicer 4.0 [http://vimeo.com/37671358 webinar]'' provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages.
*Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
*Length: 1h20m
| align="right" |[[Image:Webinar.png|250px]]
|}
 
----
 
==International resources==
International resources in Chinese and in German are made available by the Slicer community.

==Resources in Chinese==
{| width="100%"
|
A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. The tutorials below are examples of Slicer tutorials in Chinese.

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗]

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派]

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案]

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五]

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法]

*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索]
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247483658&idx=1&sn=ad08fe01c61d6999a36f2960b34287ec&chksm=eacc0b38ddbb822e60206afcf0bb67562432bb275463b20ad6ac7d243ccc1429afaa8f2177ea#rd 3D printing 如何用3D Slicer实现模型3D打印束旭俊]

The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]

 

| align="right" |
[[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
|}

==Resources in German==

*[https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles)

==Murat Maga's blog posts about using 3D Slicer for biology==

*[https://blogs.uw.edu/maga/2017/04/11/getting-started-with-3d-slicer-as-a-biologist/ Slicer for Biologists]
*[https://blogs.uw.edu/maga/2017/04/11/a-worked-example-getting-and-visualizing-data-from-digimorph/ Loading data from DigiMorph]
*[https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM]
*[https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom]

==Using the (legacy) Editor==

===Fast GrowCut===

{| width="100%"
|
*The [[Media:FastGrowCutTutorial.pdf|Fast GrowCut tutorial]] shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
*Authors: Hillary Lia
*Audience: Users interested in segmentation
| align="right" |[[File:FastGrowCutLogo.png|200px]]
|}

{| width="100%"
*'''[https://www.youtube.com/channel/UC8vxI0-dEWrw0_tBF-v8xGA/videos Video-based segmentation tutorials from CHU de Rouen (France)]
** Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips.
| align="right" |[[Image:ChuRouen.png|180px]]
|}

===Use case: Slicer in paleontology===

This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:

*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
*[http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-v.html Open Source Paleontologist: 3D Slicer: The Tutorial Part V]
*[http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]

Documentation/Nightly/Training

2022-11-22T18:37:31Z

2022-03-21T22:48:03Z

JChris.FillionR: /* Slicer 5.0: Removed Charts and DoubleArrays module */

<noinclude>__TOC__</noinclude>
==Slicer backward incompatible changes==

===Slicer 5.0: API changes since 4.10===

*Removed protected method <tt>vtkMRMLModelDisplayableManager::FindPickedDisplayNodeFromMesh</tt>

==== Supporting only Python 3.6 and above ====
Slicer python code has been updated to support Python 3.6 and above syntax using [https://github.com/asottile/pyupgrade pyupgrade] to automatically update the syntax.

Install pyupgrade: <code>PythonSlicer -m pip install pyupgrade</code>

* Running:
** On 1 file: <code>PythonSlicer -m pyupgrade --py36-plus MyPythonFile.py</code>
** On multiple files: Here is my pyupgrade-script.py written to automate running pyupgrade across all python files in the Slicer repo. It was run by <code>PythonSlicer pyupgrade-script.py</code>
<syntaxhighlight lang="python">
# pyupgrade-script.py
import os
import subprocess

search_directory = "C:/Users/MyUserName/Documents/GitHub/Slicer"
for root, _, files in os.walk(search_directory):
for file_item in files:
file_path = os.path.join(root, file_item)
if os.path.isfile(file_path) and file_path.endswith(".py"):
subprocess.call(["PythonSlicer", "-m", "pyupgrade", "--py36-plus", file_path])
</syntaxhighlight>

====Python 2 to Python 3====

Slicer core has been updated to only support Python 3.

C++ classes and python scripts have been updated to use idioms and constructs only available in Python 3.

Update to python scripts have been done leveraging the CLI provided by https://python-future.org by (1) iteratively applying each one of the associates "fixes", (2) reviewing associated changes and (3) updating as needed.

Updates specific to extensions are discussed in [[Documentation/Nightly/Developers/Tutorials/MigrationGuide#Slicer_5.0:_Python2_to_Python3]]

====Interactor styles====

Limitations of VTK widgets (editable points, lines, curves, etc.) prevented Slicer from having sophisticated user interaction in slice and 3D views. In Slicer5, we replaced VTK widgets with MRML widgets. These widgets are still VTK-based and somewhat similar to VTK widgets, but they operate directly on MRML nodes, they use direct method calls between widgets and their representation, and they use a more efficient and flexible event processing. Instead of hardcoding how viewers behave in response to interaction (mouse move, button click, keyboard, ...) events in an interactor style, all these events are translated to actions and performed in a MRML widget. Most modules are not expected to observe interactor events or styles directly, but if they did, then they may need to be updated accordingly.

*vtkSliceViewInteractorStyle renamed to vtkMRMLSliceDViewInteractorStyle to reflect that it uses MRML classes directly.
*vtkThreeDViewInteractorStyle renamed to vtkMRMLThreeDViewInteractorStyle to reflect that it uses MRML classes directly.

====slicer.util functions====

*slicer.util.loadVolume (and other node load functions) now return the loaded node instead of a True/False flag. In case of an error, a RuntimeError exception is thrown.
**Old way of loading a node and get it in a variable: <code>volumeNode = slicer.util.loadVolume('path/to/volume.nrrd', returnNode=True)[1]</code>
**New way of loading a node and get it in a variable: <code>volumeNode = slicer.util.loadVolume('path/to/volume.nrrd')</code>

====Markups====

*<tt>vtkCommand::Modified</tt> events are no longer invoked when control points are added/removed/modified to improve performance. Modules that need to know If a point position is modified need to add observers to <tt>vtkMRMLMarkupsNode::PointAddedEvent</tt>, <tt>vtkMRMLMarkupsNode::PointRemovedEvent</tt>, <tt>vtkMRMLMarkupsNode::PointModifiedEvent</tt> events. See example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#get-a-notification-if-a-markup-point-position-is-modified Script repository].
*<tt>vtkMRMLMarkupsNode::MarkupAddedEvent</tt> is renamed to <tt>PointPositionDefinedEvent</tt>. There is a similar event, <tt>vtkMRMLMarkupsNode::PointAddedEvent</tt>, which is called even when preview point is created.
*<tt>vtkMRMLMarkupsNode::MarkupRemovedEvent</tt> is renamed to <tt>vtkMRMLMarkupsNode::PointPositionUndefinedEvent</tt>. There is a similar event, <tt>vtkMRMLMarkupsNode::PointRemovedEvent</tt>, which is called even when preview point is removed.
*<tt>vtkMRMLMarkupsNode::NthMarkupModifiedEvent</tt> is replaced by <tt>vtkMRMLMarkupsNode::PointModifiedEvent</tt>
*During placement of markups, a preview markup point is created. If number of already placed markup points needs to be determined then <code>GetNumberOfDefinedControlPoints()</code> method can be used.
*<tt>GetDefaultMarkups...()</tt> and <tt>SetDefaultMarkups...()</tt> methods are removed. Instead default display node can be accessed by <tt>GetDefaultMarkupsDisplayNode()</tt> method and default values can be get/set in that class.
*<tt>vtkMRMLMarkupsNode::GetNthMarkupSelected()</tt> is replaced by <tt>GetNthControlPointSelected()</tt>
*<tt>vtkMRMLMarkupsNode::PointPositionDefinedEvent</tt> event is added. This event is invoked whenever position is defined for a new point.
*<tt>vtkMRMLMarkupsNode::PointPositionUndefinedEvent</tt> event is added. This event is invoked whenever point with defined position is removed (point is deleted or its position gets undefined).
*For more details, see [{{doxygen-class-url|vtkMRMLMarkupsNode}} vtkMRMLMarkupsNode]

====Segmentations====

Binary labelmap segmentations can now be represented as shared labelmaps.
The previous implementation of binary labelmaps was performance intensive as each labelmap was represented using a separate vtkDataObject.
Visualizing and editing segmentations that contained a large number of segments could cause performance issues, due to the large number of vtkActors required, as well as calculating masks and overwriting other segments when editing.

By default, newly created segments will now be contained on the same layer.
Segments will only be separated into multiple layers if the user creates an overlapping segment when editing.

Segments are now saved as a 4D volume with shared 3D layers.
For a segmentation that only uses one layer, the resulting image is a 3D volume.
Before saving, the labelmaps will be collapsed into as few layers as possible.

*seg.nrrd files now contain two additional attributes for each segment: SegmentX_LabelValue and SegmentX_Layer
*The label value of a segment can be found using vtkSegment::GetLabelValue()
*Whether or not a segment is shared can be found using vtkSegmentation::IsSharedBinaryLabelmap()
*The other segments sharing the same labelmap can be found using vtkSegmentation::GetSegmentIDsSharingBinaryLabelmapRepresentation()
*Segment editor effects should generally use modifySelectedSegmentByLabelmap rather than SetBinaryLabelmapToSegment to manage layer separation
*Conversion rules now call PreConvert() and PostConvert() before and after conversion to perform pre and post processing steps on the segmentation as a whole
*The function signature for vtkSegmentationConverterRule::Convert now accepts a vtkSegment rather than two vtkDataObjects
*slicer.util.arrayFromSegment has been deprecated. slicer.util.arrayFromSegmentBinaryLabelmap and slicer.util.arrayFromSegmentInternalBinaryLabelmap can be used instead

=====Erase the contents of a single segment=====

<pre>
segmentation = segmentationNode.GetSegmentation()
segmentation.ClearSegment(segmentId)
</pre>

=====Set labelmap in a segment=====

Directly, bypassing masking settings:

<pre>
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(orientedImageDataToSet, segmentationNode, segmentId)
</pre>

=====Move a segment from a shared labelmap to a separate layer=====

<pre>
segmentation = segmentationNode.GetSegmentation()
segmentation.SeparateSegmentLabelmap(segmentId)
</pre>

=====Combine all binary labelmaps to as few layers as possible=====

<pre>
segmentation = segmentationNode.GetSegmentation()
segmentation.CollapseBinaryLabelmaps(forceToSingleLayer=false)
</pre>

Get a read-only labelmap for a single segment:

<pre>
labelmap = slicer.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapRepresentation(segmentId, labelmap)
</pre>

(similarly, use GetClosedSurfaceRepresentation with an additional vtk.vtkPolyData parameter to get a read-only surface mesh)

or

<pre>
labelmapNumpyArray = slicer.util.arrayFromSegmentBinaryLabelmap(segmentationNode, segmentId)
</pre>

=====Get a modifiable shared labelmap=====

<pre>
labelmap = slicer.vtkOrientedImageData()
segmentationNode.GetBinaryLabelmapInternalRepresentation(segmentId, labelmap)
</pre>

(similarly, use GetClosedSurfaceInternalRepresentation to get a modifiable surface mesh)

or

<pre>
labelmapNumpyArray = slicer.util.arrayFromSegmentInternalBinaryLabelmap(segmentationNode, segmentId)
</pre>

=====Export segments to models=====

Model hierarchies no longer exist in Slicer5, but instead various kinds of hierarchies are now replaced by "subject hierarchy", which can accommodate any node types in a single hierarchy. Accordingly, `ExportSegmentsToModelHierarchy`, `ExportAllSegmentsToModelHierarchy`, etc. are replaced by `ExportSegmentsToModels`, `ExportAllSegmentsToModels`, which take a subject hierarchy folder item ID as input.
Documentation/Nightly
See code example in [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#export-model-nodes-from-segmentation-node Script repository].

=====Smoothing effect=====

In Slicer-4.11 version before October 29, 2020 (and earlier versions), Gaussian smoothing method's Standard deviation parameter ("GaussianStandardDeviationMm") was interpreted in pixels, while on the user interface and code it was claimed to be in physical units (millimeter). The problem was fixed and now the parameter is in millimeter.

====Volume rendering====

vtkMRMLVolumeRenderingDisplayNode::SetAndObserveVolumeNodeID method was removed, as display node base class already maintains a pointer to the displayed (volume) node. To associate a volume display node with a volume node, call <pre>volumeNode->AddAndObserveDisplayNodeID(volumeRenderingDisplayNode->GetID());</pre> after both nodes are added to the scene.

====Extract skeleton====

Command-line arguments of the module have been updated:
- output image is now optional, therefore the output image file name must be specified using "--outputImage" argument
- output image centerline voxel value is set to 255 (instead of 1) to make it easier to apply image processing operations on it (values can be interpolated between 0 and 255, while there are no integer values between 0 and 1)
- "--dontPrune" is renamed to "--fullTree" for clarity
- centerline curve is saved in mrk.json format

==== MRML node copy API improvements ====

Slicer-4.10 and earlier had a single Copy() method, which had limitations:
- usually implemented deep copy (but sometimes bulk data was just shallow-copied): problem, because for quick browsing of sequences, we need shallow-copy (to avoid copying bulk data, such as vtkImageData)
- copied all node properties (except node ID and scene): this required workarounds, whenever we wanted to copy only the content of nodes (but for example keeping node references or node name intact)

In Slicer-4.11, these limitations are addressed, by implementing a ''CopyContent(vtkMRMLNode* node, bool deepCopy=true)'' method which allows choosing between deep/shallow copy (create an independent copy of bulk data or pass bulk data pointer) and does not copy node ID, Scene, Name, SingletonTag, HideFromEditors, AddToScene, UndoEnabled, and node references.

To make it easier to introduce this new method into existing classes, helper macros are implemented.

If a class implements CopyContent method then the developer must make sure that CopyContent and HasCopyContent methods are implemented in all parent classes by adding vtkMRMLCopyContentMacro(ClassName) or vtkMRMLCopyContentDefaultMacro(ClassName) to the class headers. vtkMRMLCopyContentDefaultMacro should be used when the class does not have any additional properties (only those that parent classes already copy). CopyContent must be implemented by calling CopyContent of the parent class, and then copy node properties added in he class (preferable using shallow copy for large data, if deepCopy argument was set to false).

If HasCopyContent macro is not added to a class then it cannot be recorded or replayed in Sequences module.

==== Removed classes ====

Classes removed due to removing legacy Editor module:
* vtkITKNewOtsuThresholdImageFilter is replaced by vtkITKImageThresholdCalculator
* vtkITKGrowCutSegmentationImageFilter is replaced by vtkImageGrowCutSegment (it will be replaced by the ITK implementation https://github.com/Slicer/Slicer/pull/5807)
* vtkITKTimeSeriesDatabase was removed, it was an incomplete class, not used anywhere
* vtkITKWandImageFilter was removed, vtkImageThresholdConnectivity (in VTK) can be used instead
* vtkImageConnectivity was removed, vtkImageThresholdConnectivity (in VTK) can be used instead
* vtkImageErode was removed, vtkImageDilateErode3D (in VTK) can be used instead
* vtkImageLabelChange was removed, vtkImageThreshold (in VTK) can be used instead
* vtkImageSlicePaint was replaced by logic built into qSlicerSegmentEditorPaintEffect
* vtkImageStash is replaced by vtkSegmentationHistory
* vtkPichonFastMarching moved to SegmentEditorExtraEffects extension (https://github.com/lassoan/SlicerSegmentEditorExtraEffects)

Classes removed due to removing Charts and DoubleArrays modules:
* vtkMRMLChartNode is replaced by vtkMRMLPlotNode
* vtkMRMLChartViewNode is replaced by vtkMRMLPlotViewNode
* vtkMRMLDoubleArrayNode is replaced by vtkMRMLTableNode (can store any number of columns, not just two)
* vtkMRMLDoubleArrayStorageNode is replaced by vtkMRMLTableStorageNode
* qMRMLChartView is replaced by qMRMLPlotView
* qMRMLChartViewControllerWidget is replaced by qMRMLPlotViewControllerWidget
* qMRMLChartWidget is replaced by qMRMLPlotWidget

===Slicer 5.0: Fiducial List was renamed to Point List===

To simplify terms used in Slicer, "Fiducial List" term was renamed to "Point List" on the user interface.
The term in the API has not been changed to preserve backward compatibility.

See discussion of the topic [https://discourse.slicer.org/t/delete-control-point-delete-fiducial-pop-up-confirm-box/20430/18 here].

===Slicer 5.0: SliceIntersectionVisibility was moved from vtkMRMLSliceCompositeNode to vtkMRMLSliceDisplayNode===

SliceIntersectionVisibility property (that controls if intersections of other slices should be displayed in the slice view) was stored in vtkMRMLSliceCompositeNode. This was not a good choice because the composite node stores what image layers should be displayed in the slice view and how (what opacity, what blending method, etc.). The property was kept in that class for a long time to preserve backward compatibility, but when interactive slice intersection feature was added and additional properties had to be added that control appearance and behavior of slice intersections, this property was moved into the new vtkMRMLSliceDisplayNode node type and renamed to IntersectingSlicesVisibility.

Scripts that previously used SliceIntersectionVisibility property will now fail with this error:

AttributeError: 'MRMLCore.vtkMRMLSliceCompositeNode' object has no attribute 'SetSliceIntersectionVisibility'

Those failing scripts can be updated with this example in the script repository: https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#turn-on-slice-intersections

===Slicer 5.0: SlicerPython was removed. Use PythonSlicer instead===

Error message:

<pre>
SlicerPython executable is obsolete and will be removed. Use PythonSlicer executable instead.
For more details, see https://github.com/Slicer/Slicer/issues/4843
</pre>

Solution:

Use <tt>PythonSlicer</tt> instead of <tt>SlicerPython</tt>

Background:

Python IDEs (specifically PyCharm, but potentially others) only recognize <tt>Python*.exe</tt> files as Python interpreters.

To allow using Slicer's Python interpreter in these IDEs, we had to add <tt>PythonSlicer</tt>, but kept <tt>SlicerPython</tt> around for not immediately breaking things.

This redundancy is confusing for users that we could resolve by simply removing SlicerPython for Slicer5.

References:

https://github.com/Slicer/Slicer/issues/4843

===Slicer 5.0: Application must be installed in writable location to install extensions===

Extensions are now installed in the application home folder because Python packages are installed there anyway, so the application home folder has to be writable (or Slicer has to be run as admin when you install extensions). It also allows making Slicer fully portable - see details [https://discourse.slicer.org/t/slicer-is-now-fully-portable/15410 here].

If you want to allow any user to install extensions without admin rights and you only need to use extensions that don’t install Python packages at runtime then you can specify a custom extension install path folder in Slicer-NNN.ini file or revert to the old behavior of Slicer by specifying <code>Slicer_STORE_SETTINGS_IN_APPLICATION_HOME_DIR:BOOL=OFF</code> when configuring your Slicer build.

===Slicer 5.0: Models are saved in LPS coordinate system by default===

While Slicer uses RAS coordinate system internally, images, transforms, and markups files are stored in LPS coordinate system, because DICOM and all medical image computing software (maybe except a few very old ones) uses LPS coordinate system in files.

However, Slicer has been still using its internal RAS coordinate system in mesh files (STL, VTK, VTP, OBJ, PLY), which caused issues when interfacing with third-party software.

From Slicer-4.11.0-2020-02-26 (revision 28794) models are saved in LPS coordinate system, and mesh files assumed to be in LPS coordinate system by default (if no other coordinate system specified in the file).

Slicer started embedding coordinate system name in mesh files a few years ago (see <code>SPACE=RAS</code> in the file header), so all the files that Slicer saved in recent years will load correctly and any scene files created with any version of Slicer will also load the models with correct orientation, too.

Manual setting of coordinate system (in Add data dialog / Options column) is only needed when loading a mesh file without a scene that were created by Slicer-4.6 (2017-09-27) and earlier; and obj files created by Slicer-4.6 and Slicer-4.8 (between 2016-10-11 and 2018-03-26), or files are created by third-party software in RAS coordinate system.

If you encounter orientation issues when loading a model file, you have the following options:

*Option A: Specify the coordinate system when you open the model file. In “Add data” dialog, click “Show Options” and then choose “RAS” as coordinate system.
*Option B: Update the third-party software that generate the mesh to save coordinates in LPS coordinate system instead of RAS coordinate system. Conversion is simple inverting the sign of the first two coordinates.
*Option C: Write <code>SPACE=RAS</code> in the comment/description field in the mesh file (for STL, OBJ, PLY, VTK file; for VTP files, add in the first value of a vtkStringArray field array named <code>SPACE</code>) to indicate that the values are stored in RAS coordinate system. This option is useful if coordinates have to be stored in RAS coordinate system (for example, for compatibility with other software). See implementation example [https://github.com/Slicer/SlicerGitSVNArchive/blob/c0829f596f0ea661e0c5484056bd1374a3d22958/Libs/MRML/Core/vtkMRMLModelStorageNode.cxx#L421-L647 here].

See more information, discussion of this topic on the [https://discourse.slicer.org/t/model-files-are-now-saved-in-lps-coordinate-system/10446 Slicer forum].

===Slicer 5.0: CLI module descriptor XML files assume LPS coordinate system by default===

If [[Documentation/Nightly/Developers/SlicerExecutionModel|SlicerExecutionModel]] descriptor XML file of a CLI module does not specify coordinate system for a point, pointfile, or region element then the coordinate system is assumed to be "lps". To preserve previous behavior and use "ras" coordinate system instead, add '''coordinateSystem="ras"''' to the element.

===Slicer 5.0: Sequences extension has been merged into Slicer core===

Sequences extension has been merged into Slicer core, therefore extensions do not need to depend on Sequences extension anymore.

SequenceBrowser module has been merged into Sequences module, therefore previous code that used SequenceBrowser module now should use Sequences module instead.

===Slicer 5.0: FreeSurfer support has been removed from Slicer core===
The loading of FreeSurfer models and scalar overlays, as well as the FreeSurfer-specific color nodes, have been moved to the new [https://github.com/PerkLab/SlicerFreeSurfer SlicerFreeSurfer] extension. Tutorials on how to use the FreeSurfer Importer module to load multiple files at once can be found on the [https://github.com/PerkLab/SlicerFreeSurfer/wiki/Tutorials SlicerFreeSurfer tutorial page].

===Slicer 5.0: Removed Editor module===

The legacy Editor module has been deprecated since about 2017 and got removed in November 2021. It is replaced by the much improved Segment Editor module.

===Slicer 5.0: Removed Charts and DoubleArrays module===

Charts and DoubleArrays module have been deprecated since about 2018 and got removed in November 2021. They are replaced by Plots and Tables modules.

'''Example of commits'''
* [https://github.com/SlicerRt/SlicerRT/commit/8f9155f94399be71e747d3d45b1f6c4152caa139 SlicerRT@8f9155f94] ENH: Update DVH module to use plots infrastructure instead of charts

===Slicer 5.0 : Avoid typedef of anonymous structure===

Due to a recent (but retroactive) C++ rule change, only sufficiently C-compatible classes are permitted to be given a typedef name for linkage purposes. Add an <tt>enabled-by-default</tt> warning for these cases, and rephrase our existing error for the case where we encounter the <tt>typedef</tt> name for linkage after we've already computed and used a wrong linkage in terms of the new rule.

To fix warning message similar to:

<pre>
Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:95:17:
warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct
^
ColumnInfo
Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:99:5:
note: type is not C-compatible due to this default member initializer
int ScalarType = VTK_STRING;
^~~~~~~~~~~~~~
Slicer/Libs/MRML/Core/vtkMRMLTableStorageNode.h:102:5:
note: type is given name 'ColumnInfo' for linkage purposes by this typedef declaration
} ColumnInfo;
^
For consistency, Use 'using' to a named structure definintion for all
structures.
</pre>

Replace code like this:

<pre>
typedef struct
{
std::string ColumnName;
std::vector<vtkAbstractArray*> RawComponentArrays;
int ScalarType = VTK_STRING;
std::vector<std::string> ComponentNames;
std::string NullValueString;
} ColumnInfo;
</pre>

By this:

<pre>
struct StructColumnInfo
{
std::string ColumnName;
std::vector<vtkAbstractArray*> RawComponentArrays;
int ScalarType = VTK_STRING;
std::vector<std::string> ComponentNames;
std::string NullValueString;
};
using ColumnInfo = struct StructColumnInfo;
</pre>

References:

https://reviews.llvm.org/D74103

===Slicer 5.0 : Temporary path===

Temporary path was stored redundantly application settings (Slicer.ini) in two keys: <code>Modules/TemporaryDirectory</code> and <code>TemporaryPath</code>. <code>Modules/TemporaryDirectory</code> overwrote <code>TemporaryPath</code> at startup, but when temporary path was set via the <code>slicer.app.temporaryPath</code> then it was only written to <code>TemporaryPath</code>.

Changed behavior so that only <code>TemporaryPath</code> is used. <code>Modules/TemporaryDirectory</code> is ignored.

To ensure that temporary path is always writable, it as checked at startup that a file can be created in temporary path and if this check fails then temporary path is reset to default (<code>QDir::tempPath()</code>).

===Slicer 5.0 : Always prefer executable CLIs===

Previously, if a CLI module was available both as an executable and a shared library, then PreferExecutableCLI application setting was used to determine which one is used. Now always CLIs are always executed in an external process (if an executable is available). Reasons are described in this issue: https://github.com/Slicer/Slicer/issues/4893. The application setting is no more displayed in the GUI and any setting specified in earlier Slicer versions is ignored.

===Slicer 5.0 : SlicerApp-real is a console application on Windows===

Previously, the application (SlicerApp-real.exe) was built as a GUI application (without console) on Windows, to avoid displaying a terminal window when starting the application. This had the drawback that the Slicer application did not have standard input/output that could be displayed or redirected (for example, for capturing into a file). SlicerApp-real has always been a console application on Linux and macOS, therefore this change makes the software behavior more consistent across platforms.

SlicerApp-real.exe is now built as a console application (see [https://github.com/Slicer/Slicer/issues/2934 #2934]). Displaying of a terminal window is prevented by using a launcher (Slicer.exe) that is built as a GUI application and it starts Slicer with the standard input and outputs redirected.

To display console output: https://slicer.readthedocs.io/en/latest/developer_guide/debugging/overview.html#console-output-on-windows

To launch a command-line terminal using <code>subprocess.Popen</code> that shows a new terminal, specify <code>creationflags=subprocess.CREATE_NEW_CONSOLE</code> argument.

===Slicer 4.11: Variable CMAKE_DEFAULT_BUILD_TYPE renamed to Slicer_DEFAULT_BUILD_TYPE===

Setting the default build type for single config generator may be done setting <tt>Slicer_DEFAULT_BUILD_TYPE</tt> instead of <tt>CMAKE_DEFAULT_BUILD_TYPE</tt>.

Error message similar to:

<pre>
CMake Error:
Generator

Visual Studio 15 2017

does not support variable

CMAKE_DEFAULT_BUILD_TYPE

but it has been specified.
</pre>

References:

https://github.com/Slicer/Slicer/pull/4799

===Slicer 4.11: teem python module renamed to vtkTeem, explicit import required===

*Since the module provides VTK classes interfacing with "teem", the name is now representative of the class it contains.
*<tt>vtkTeem</tt> classes are expected to be used by explicitly importing the module.

Replace code like this:

<pre>
import teem

class CalculateTensorScalars(object):
def __init__(self):
self.dti_math = teem.vtkDiffusionTensorMathematics()
</pre>

By this:

<pre>
import vtkTeem

class CalculateTensorScalars(object):
def __init__(self):
self.dti_math = vtkTeem.vtkDiffusionTensorMathematics()
</pre>

===Slicer 4.11: Display window/level (brightness/contrast) adjustment===

*A new "Window/level" mouse interaction mode was introduced. Volume display window/level can only be changed if this mode is activated by clicking the corresponding button in the toolbar. The new mouse mode prevents accidental modification of volume window/level (when for example the user accidentally clicked too far from a markup) and it also allows more sophisticated window/level adjustments.
*New region-based auto window/level feature added: activate "Window/level" mouse mode and use Ctrl + left-click-and-drag to highlight a region and optimize window/level for that (pressing Escape or right-click cancels the operation).
*Auto window/level reset: activate "Window/level" mouse mode and double-click the left mouse button.
*Improved auto window/level algorithm to prevent too bright display of images. Window/level is set to display values between 0.1th and 99.9th percentile of gray levels. See details here: https://discourse.slicer.org/t/feedback-requested-how-to-improve-mouse-interaction-in-views/6420.
*Removed class <tt>vtkImageBimodalAnalysis</tt>

===Slicer 4.10: Registration of runTest function done in ScriptedLoadableModule base class===

Following [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=27617 r27617]:

*the <code>ScriptedLoadableModule</code> class takes care of registering the <code>runTest</code> function.
*the <code>runTest</code> function expects <code>msec</code> keyword argument.

Error message similar to:

<pre>
Traceback (most recent call last):
File "/path/to/Slicer-SuperBuild/Slicer-build/bin/Python/slicer/ScriptedLoadableModule.py", line 205, in onReloadAndTest
test(msec=int(slicer.app.userSettings().value("Developer/SelfTestDisplayMessageDelay")), **kwargs)
TypeError: runTest() got an unexpected keyword argument 'msec'
Reload and Test: Exception!

runTest() got an unexpected keyword argument 'msec'
</pre>

Replace code like this:

<pre>
class sceneImport2428(ScriptedLoadableModule):
[...]
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
parent.title = "..."
[...]
parent.acknowledgementText = "..."
self.parent = parent

# Add this test to the SelfTest module's list for discovery when the module
# is created. Since this module may be discovered before SelfTests itself,
# create the list if it doesn't already exist.
try:
slicer.selfTests
except AttributeError:
slicer.selfTests = {}
slicer.selfTests['sceneImport2428'] = self.runTest

def runTest(self):
tester = sceneImport2428Test()
tester.runTest()

[...]
</pre>

By this:

<pre>
class sceneImport2428(ScriptedLoadableModule):
[...]
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
parent.title = "..."
[...]
parent.acknowledgementText = "..."

[...]
</pre>

===Slicer 4.9: Update of VTK version from 9.0 to 8.2===

Following [https://github.com/Kitware/VTK/commit/b703d78be3ffd8ae69c319afa0230097ff270f26 kitware/VTK@b703d78be], VTK has updated to use version number 8.2 instead of 9.0. This was discussed in on the VTK mailing list in http://vtk.1045678.n5.nabble.com/Discussion-OK-to-change-VTK-s-version-number-from-9-0-to-8-2-tt5748702.html

At first, this VTK commit and its companion [https://github.com/Kitware/VTK/commit/8a00b357e84eec695bda049216f30f2b76d80855 kitware/VTK@8a00b357e] were both reverted from the [https://github.com/Slicer/VTK/ Slicer/VTK] fork. Then, since having the corresponding changes reverted in VTK was not possible, it was decided to also update Slicer. This was done in the following commits:

*[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=27472 r27472]: COMP: Update c++ classes to support building against VTK >= 9 and VTK >= 8.2
*[http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=27473 r27473]: COMP: Update VTK to include version change from 9.0 to 8.2. Fixes #4623

This means that code depending on VTK must also be updated to include similar fixes.

'''Replace this:'''
#if VTK_MAJOR_VERSION >= 9

'''By this:'''
#if VTK_MAJOR_VERSION >= 9 || (VTK_MAJOR_VERSION >= 8 && VTK_MINOR_VERSION >= 2)

and

'''Replace this:'''
#if VTK_MAJOR_VERSION < 9

'''By this:'''
#if VTK_MAJOR_VERSION <= 7 || (VTK_MAJOR_VERSION <= 8 && VTK_MINOR_VERSION <= 1)

===Slicer 4.9: ITK_LEGACY_REMOVE is now OFF===
In preparation to switch to ITK 5.0, we disable legacy functionality in ITK. This might affect some modules which rely on ITK. Take a look at [https://itk.org/migrationv4 ITK 4 migration guide] before [https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/ITK5MigrationGuide.md ITK 5 migration guide].

===Slicer 4.9: vtkMRMLPlotDataNode renamed to vtkMRMLPlotSeriesNode===
Plotting was improved in [https://github.com/Slicer/Slicer/commit/082edc40c this commit]

'''Replace this:'''

vtkMRMLPlotDataNode

'''By this:'''
vtkMRMLPlotSeriesNode

===Slicer 4.9: CMake: Module MIDAS not available===

The test infrastructure of your project should be updated to use [https://cmake.org/cmake/help/latest/module/ExternalData.html ExternalData] built-in CMake module
instead of the specific <tt>MIDAS</tt> module.

See EMSegment commit [http://viewvc.slicer.org/viewvc.cgi/Slicer3?view=revision&revision=17150 r17150] for an example of transition.

This means that instead of using <tt>midas_add_test</tt> with the <tt>MIDAS{path/to/file.ext.md5}</tt>
syntax for addressing the test data, the function [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_test ExternalData_add_target] is used by
specifying both <tt>DATA{path/to/file.ext}</tt> and a download target name.

'''Replace this:'''

midas_add_test(NAME test1 COMMAND ...)
midas_add_test(NAME test2 COMMAND ...)

'''By this:'''

ExternalData_add_test(EMSegmentData NAME test1 COMMAND ...)
ExternalData_add_test(EMSegmentData NAME test2 COMMAND ...)

[...]

ExternalData_add_target(EMSegmentData)

A key difference with the former approaches is that instead of adding two tests (one named
<tt><testName>_fetchData</tt> to downoad the data and one running the test command), only one
test is added but a common download target is added at the end using [https://cmake.org/cmake/help/latest/module/ExternalData.html#command:externaldata_add_target ExternalData_add_target]
function.

This means that test data can now be downloaded in parallel (and cached) at build time instead
of testing time.

===Slicer 4.9: CMake: Module SlicerMacroCheckExternalProjectDependency not available===

Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=26992 r26992], consider updating
your build system to use CMake module <code>ExternalProjectDependency</code>

===Slicer 4.9: CMake: Module SlicerMacroEmptyExternalProject not available===

Since the module was removed in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=26991 r26991]

'''Replace this:'''

<pre>
include(SlicerMacroEmptyExternalProject)

[...]

SlicerMacroEmptyExternalProject("${proj}" "${${proj}_DEPENDENCIES}")
</pre>

'''By this:'''

<pre>
include(ExternalProjectDependency)

[...]

ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})
</pre>

===Slicer 4.9: CMake: Module SlicerBlockSetCMakeOSXVariables not available===

Since it was renamed to <tt>SlicerInitializeOSXVariables</tt> in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=26982 r26982]

'''Replace this:'''

<pre>
include(SlicerBlockSetCMakeOSXVariables)
</pre>

'''By this:'''

<pre>
include(SlicerInitializeOSXVariables)
</pre>

===Slicer 4.9: Application: isRelease() function not available===

See [[#Slicer_4.8:_Application:_isRelease.28.29_function_not_available_or_deprecated]]

===Slicer 4.9: slicer.util.getNode() raises exception if node not found===

If slicer.util.getNode() is called and the node is not found then instead of just returning None (Slicer 4.8 behavior), the method now raises a MRMLNodeNotFoundException. This makes code debugging easier (the error is reported when it happens), and in general more consistent with Python conventions.

How to update existing code:

It is advisable to only use slicer.util.getNode in tests, or interactively in the Python console, as its behavior is somewhat unpredictable (it may either found a node by name or ID, and result of wildcard search is even less deterministic). In general, it is recommended to use the MRML scene's GetFirstNodeByName and GetNodeByID methods instead.

'''Replace this:'''

<pre>
n = slicer.util.getNode(nodeNameOrID)
</pre>

'''By one of these:'''

If node is to be found by name:
<pre>
n = slicer.mrmlScene.GetFirstNodeByName(nodeName)
</pre>

If node is to be found by ID:
<pre>
n = slicer.mrmlScene.GetNodeByID(nodeID)
</pre>

If node is to be found by name or ID (slower, less predictable, recommended for testing only):

<pre>
try:
n = slicer.util.getNode(nodeNameOrID)
except slicer.util.MRMLNodeNotFoundException:
n = None
</pre>

More information: https://github.com/Slicer/Slicer/commit/b63484af1b1b413f35396f8f7efb73e870448bd4

===Slicer 4.8: Application: isRelease() function not available or deprecated===

Error message similar to:

Missing/deprecated qSlicerCoreApplication::isRelease()

or

Missing/deprecated slicer.app.isRelease()

Solution:

Use <tt>qSlicerCoreApplication::releaseType() == "Stable"</tt>

Summary:

Prior to r26420, the variable <tt>Slicer_VERSION_TWEAK</tt> was used to check if a "stable release" was built. The variable value
was set by updating the sources and defining the variable to an integer greater or equal to 0. In other word, if the variable
evaluated to an empty string, a nighty or experimental build was being done, if it evaluated to an integer, a stable release build
was being done.

The approach had few issues:

*the name of the variable was confusing
*identifying a "stable release" only from a source tree revision was not enough. Indeed the environment defining a "release" is the one found on the build machines used to generate the installer.
*nightly build are also considered as release

To address this, the CMake variable <tt>Slicer_RELEASE_TYPE</tt> was introduced. As of 2017-10-04, it can be set to <tt>Experimental</tt>, <tt>Nightly</tt>
or <tt>Stable</tt> with <tt>Experimental</tt> being the value hard-coded in the source.

Identifying a build as "stable" is now explicitly done by setting <tt>Slicer_RELEASE_TYPE</tt> to <tt>Stable</tt> at configure time.

Also, since the concept of release types was introduced, the function <tt>isRelease()</tt> has been removed in favor of <tt>releaseType()</tt>.

References:

https://github.com/Slicer/Slicer/pull/354

===Slicer Python Module: modulewidget and others removed.===

 Summary
Python classes formerly in "slicer.moduledm", "slicer.modulelogic", "slicer.modulemrml"
and "slicer.modulewidget" are now directly available in the slicer module.

See example of change [https://github.com/QIICR/LongitudinalPETCT/pull/11 here].

Rational:

See comments in commit messages referenced blow.

References:

https://github.com/Slicer/Slicer/commit/628f83fe7a6f4e0710e306bcaf7c04b9e3e5e6bd

https://github.com/Slicer/Slicer/commit/9cb5668fde1abc8f0430a91ca37fc29277ceeb4e

===MRML: Slicer 4.6: Moved up vtkMRMLStorableNode in the MRML node hierarchy.===

Rational:

vtkMRMLStorableNode is not a children of vtkMRMLTransformable node anymore,
but directly a children of vtkMRMLNode.

This allows making a node storable without requiring it to be also
transformable. It is important for several node types (color maps, tables,
etc), which require separate storage node but are not transformable.

References:

*Changed introduced in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24891 r24891]

Error message similar to:

/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx: In member function ‘void vtkMRMLLongitudinalPETCTStudyNode::ObserveRegistrationTransform(bool)’:
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:478:28: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘GetParentTransformNode’
&& propNode->GetParentTransformNode()
^
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:480:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’
propNode->SetAndObserveTransformNodeID(
^
/tmp/LongitudinalPETCT/MRML/vtkMRMLLongitudinalPETCTStudyNode.cxx:503:23: error: ‘class vtkMRMLVolumePropertyNode’ has no member named ‘SetAndObserveTransformNodeID’
propNode->SetAndObserveTransformNodeID(NULL);
^

Solution:

Removes lines and/or refactor code

===MRML: Slicer 4.5: Introduction of vtkMRMLLabelMapVolumeNode===

Rational:

Before <tt>vtkMRMLScalarVolumeNode</tt> was used for both scalar and label map
volumes and the LabelMap custom MRML node attribute was used for
distinguishing between them (0=scalar; 1=label map volume).

This made conversion between labelmap/scalar volumes very easy but made
it difficult to customize behavior, display, processing of segmentation
information.

Now a new <tt>vtkMRMLLabelMapVolumeNode</tt> class is used for storing segmentation
information (still using <tt>vtkMRMLScalarVolume</tt> used as base class for backward
compatibility; but in the future the base class may be changed to reflect
that segmentation can be represented in various ways, not just as volumes).

Error message similar to:

error: ‘class vtkMRMLScalarVolumeNode’ has no member named ‘SetLabelMap’
outputVolumeNode->SetLabelMap(1);
^

Solution (part1: down cast to <tt>vtkMRMLLabelMapVolumeNode</tt>, remove call to <tt>SetLabelMap</tt>)

Replace lines like:

vtkMRMLNode* outputNode = d->OutputLabelVolumeMRMLNodeComboBox->currentNode();
vtkMRMLScalarVolumeNode* outputVolumeNode = vtkMRMLScalarVolumeNode::SafeDownCast(outputNode);
[...]
outputVolumeNode->SetLabelMap(1);

with:

vtkMRMLLabelMapVolumeNode* outputVolumeNode =
vtkMRMLLabelMapVolumeNode::SafeDownCast(d->OutputLabelVolumeMRMLNodeComboBox->currentNode());
[...]

Solution (part2: Update UI file):

Replace lines like:

<widget class="qMRMLNodeComboBox" name="InputLabelVolumeMRMLNodeComboBox">
<property name="nodeTypes">
<stringlist>
<string>vtkMRMLScalarVolumeNode</string>
</stringlist>
</property>
[...]
</widget>

with:

<widget class="qMRMLNodeComboBox" name="InputLabelVolumeMRMLNodeComboBox">
<property name="nodeTypes">
<stringlist>
<string>vtkMRMLLabelMapVolumeNode</string> <------------- Update Here
</stringlist>
</property>
[...]
</widget>

Solution (part3: Update node selector configuration):

Replace lines like:

nodeSelector.setNodeTypes(QStringList("vtkMRMLScalarVolumeNode"));
nodeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", "1");

with:

nodeSelector.setNodeTypes(QStringList("vtkMRMLLabelMapVolumeNode"));

References:

*https://www.slicer.org/wiki/Documentation/Labs/Segmentations#vtkMRMLLabelMapVolumeNode_integration* http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24291

===CLI: Slicer 4.3: Add ITKFactoryRegistration library centralizing ITK IO factory registration===

Rational:

Linking against <tt>ITKFactoryRegistration</tt> ensures that ITK IO factory are properly registered on all supported platforms.

Error message similar to:

Undefined symbols for architecture x86_64:
"itk::itkFactoryRegistration()", referenced from:
_main in ImageMakerTest.cxx.o
ld: symbol(s) not found for architecture x86_64

Solution:

Replace lines like:

target_link_libraries(${CLP}Test ${CLP}Lib)

with:

target_link_libraries(${CLP}Test ${CLP}Lib ${SlicerExecutionModel_EXTRA_EXECUTABLE_TARGET_LIBRARIES})

References:

*http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21592
*https://issues.slicer.org/view.php?id=2813