Slicer Wiki - User contributions [en]

Documentation/4.5/Acknowledgments

2016-10-10T06:56:47Z

Kikinis: /* Major Contributors */

{{documentation/acknowledgments-versionlist}}

{|
|rowspan="2"|__TOC__
|rowspan="2" style="width: 10%"|
| class="toc" style="padding: 15px" align="left"|<h2> Citing Slicer</h2>
{{:{{FULLPAGENAME}}/CitingSlicer}}
|-
|| 
|}

Slicer is made possible through contributions from an international community of scientists from a multitude of fields, including engineering and biomedicine. The following sections give credit to some of the major contributors to the 3D Slicer core effort. Each 3D Slicer extension has a separate acknowledgements page with information specific to that extension.

==Major Contributors==
*Ron Kikinis: Principal Investigator
*Steve Pieper: Chief Architect
*Jean-Christophe Fillion-Robin: Lead Developer
*Nicole Aucoin
*Stephen Aylward
*Andrey Fedorov
*Noby Hata
*Hans Johnson
*Tina Kapur
*Andras Lasso
*Jim Miller
*Sonia Pujol: Director of Training
*Junichi Tokuda
*Lauren O'Donnell

==Groups Contributing to the Core Engineering of Slicer in a Major Way==
*SPL: Ron Kikinis, Nicole Aucoin, Lauren O'Donnell, Andrey Fedorov, Isaiah Norton, Sonia Pujol, Noby Hata, Junichi Tokuda
*Isomics: Steve Pieper, Alex Yarmarkovich
*Kitware: Jean-Christophe Fillion-Robin, Julien Finet, Will Schroeder, Stephen Aylward
*U Iowa: Hans Johnson
*GE: Jim Miller
*Perk Lab, Queen's University: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinger

== Funding Sources ==
Many of the activities around the Slicer effort are made possible through funding from public and private sources. The National Institutes of Health of the USA is a major contributor through a variety of competetive grants and contracts.
=== Grants ===
{| class="wikitable sortable"
|-
! '''Project Name''' || '''Grant Number and NIH Link''' || '''Title (and Project Page''') || '''Grant PIs''' || '''Start Date''' || '''End Date'''
|-
| CMF || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8576556&icde=18353487 1R01DE024450] || Quantification Of 3D Bony Changes In Temporomandibular Joint Osteoarthritis || Cevidanes, Lucia || 2013-09-10 || 2017-08-31
|-
| Craniosynostosis || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8778815&icde=27036063&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASCIMAGE-GUIDED 1R41HD081712] || Image-Guided Planning System For Skull Correction In Children With Craniosynostos || Linguraru, Marius George || 2014-09-26 || 2016-08-31
|-
| DiffusionMRI || [https://projectreporter.nih.gov/project_info_details.cfm?aid=8855115&icde=27026518 2P41EB015898] || Image Guided Therapy Center || Tempany, Clare M || 2004-04-01 || 2020-06-30
|-
| DiffusionMRI || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8971083&icde=27026834 1U01CA199459] || Open Source Diffusion Mri Technology For Brain Cancer Research || O'Donnell, Lauren Jean || 2015-09-22 || 2018-07-31
|-
| DiffusionMRI || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8890837&icde=27036647&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 5P41EB015902] || Neuroimaging Analysis Center (Nac) || Kikinis, Ron || 2013-08-01 || 2018-05-31
|-
| Duke Prostate Registration || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8905274&icde=27036277&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R41CA196565] || Prostate Cancer Assessment Via Integrated 3D Arfi Elasticity Imaging And Multi-Parametric Mri || Palmeri, Mark L. || 2015-04-01 || 2015-04-01
|-
| DWI || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8817256&icde=27036729&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01CA160902] || Advancement And Validation Of Prostate Diffusion And Spectroscopic Mri || Maier, Stephan E || 2012-04-01 || 2018-02-28
|-
| HD_FMRI_DWI || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8462829&icde=27164863&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1U01NS082083] || Functional Connectivity in Premanifest Huntington’s Disease || Rao, Stephen Mark || 2012-09-26 || 2015-08-31
|-
| HD_GENETICS || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8596213&icde=27164895&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1U01NS082074] || Imaging and Genetics in Huntington's Disease || Calhoun/Turner || 2013-07-01 || 2016-06-30
|-
| HD_KIDS || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8900362&icde=27164764&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 5R01NS055903] || Growth and Development of the Striatum in Huntington's Disease || Nopoulos, Peggy || 2009-03-01 || 2018-07-31
|-
| HD_PET || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8529927&icde=27164835&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1U01NS083173] || Brain Network Imaging: A Novel Biomarker for Preclinical Huntington’s Disease || Feigin, Andrew || 2013-07-01 || 2016-06-30
|-
| HD_PREDICT || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8338456&icde=27164778&ddparam=&ddvalue=&ddsub=&cr=4&csb=default&cs=ASC 5R01NS040068] || Neurobiological Predictors of Huntington's Disease (PREDICT-HD) || Paulsen, Jane || 2000-08-01 || 2016-08-31
|-
| HD_SHAPEANALSS || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8462842&icde=27164806&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1U01NS082086] || 4D Shape Analysis for Modeling Spatiotemporal Change Trajectories in Huntington’s || Gerig, Guido || 2012-09-28 || 2018-08-31
|-
| HD_TRAJECTORY || NA || Developing a Robust Segmentation Pipeline That Allows for Consistent Trajectory Estimation of HD Gene Positive Individuals Across Multiple Longitudinal MRI Sites || Kim, Eun Young || 2014-11-01 || 2016-10-31
|-
| HD_WHITEMATTER || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8652000&icde=27164795&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1U01NS083223] || Characterization of White Matter in Huntington’s Disease Using Diffusion MRI || Westin, Carl-Fredrik || 2014-01-01 || 2015-12-31
|-
| NIRView (Dartmouth) || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8828624&icde=27036841&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 5R01CA184354] || Mri Fluorescence Tomography For Quantifying Tumor Receptor Concentration In Vivo || Davis, Scott C. || 2014-04-01 || 2019-02-28
|-
| OrthognathicTrac || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8710950&icde=27036891 1R43DE024334] || Real-Time Image Guidance For Improved Orthognathic Surgery || Enquobahrie, Andinet A. || 2014-08-05 || 2016-07-31
|-
| PediatricRadiologicDecisionSupport || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329 1R01EB014947] || Mi2B2 Enabled Pediatric Radiological Decision Support || Murphy, Shawn N || 2012-08-01 || 2016-07-31
|-
| PET-CT guided needle biopsy || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8863934&icde=27037113&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 3R42CA153488] || Improving Liver Lesion Biopsy In The Ct Suite Through Fusion With Pet Images || Cleary, Kevin R. || 2012-09-01 || 2016-08-01
|-
| PET/CT Calibration Phantom || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8979242&icde=27036988&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 2R42CA167907] || Calibrated Methods For Quantitative Pet/Ct Imaging Phase Ii || Kinahan, Paul E || 2012-05-01 || 2017-07-31
|-
| PET/CT Calibration Phantom || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8979242&icde=27036988&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R42CA167907] || Calibrated Methods For Quantitative Pet/Ct Imaging Phase Ii || Kinahan, Paul E. || 2012-05-01 || 2017-07-01
|-
| ProstateBRP || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8906771&icde=27026518 5R01CA111288 ] || Enabling Technologies For Mri-Guided Prostate Interventions || Tempany, Clare M. || 2004-12-01 || 2016-07-01
|-
| ProstateQIN || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8707214&icde=27026645 5U01CA151261] || Quantitative Mri Of Prostate Cancer As A Biomarker And Guide For Treatment || Fennessy, Fiona || 2010-09-01 || 2016-07-01
|-
| QIICR || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8911287&icde=27026906 U24 CA180918] || [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] || Ron Kikinis, Andrey Fedorov || 2013-09-04 || 2018-08-31
|-
| Slicer-Radiomics-U01 || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8799943&icde=27026470 1U01CA190234] || Genotype And Imaging Phenotype Biomarkers In Lung Cancer || Aerts, Hugo || 2015-01-01 || 2019-12-01
|-
| Slicer-Radiomics-U24 || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8875289&icde=27050248 U24CA194354] || Quantitative Radiomics System Decoding the Tumor Phenotype || Aerts, Hugo || 2015-04-01 || 2020-03-31
|-
| Slicer-RT || NA || Cancer Care Ontario Applied Cancer Research Unit, Canada || Gabor Fichtinger, PerkLab, Queen's University || 2011-01-01 || 2016-12-31
|-
| Slicer-RT || NA || [http://ocairo.technainstitute.com/ Ontario Consortium for Adaptive Interventions in Radiation Oncology, Canada] || David Jaffray, Princess Margaret Hospital, Toronto || 2011-01-01 || 2016-12-31
|-
| Slicer-RT || NA || Cancer Care Ontario Research Chair, Canada || Gabor Fichtinger, PerkLab, Queen's University || 2010-01-01 || 2015-12-31
|-
| TubeTK || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8384153&icde=27037397&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1R01CA170665] || [http://tubetk.org Micro-Tumor Detection By Quantifying Tumor-Induced Vascular Abnormalities] || Dayton, Paul A. || 2012-09-01 || 2016-06-01
|-
| TubeTK || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8472102&icde=27037328&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1R43EB016621] || [http://tubetk.org In-Field Fast Procedure Support And Automation] || Aylward, Stephen R. || 2013-05-01 || 2015-04-01
|-
| TubeTK || [https://projectreporter.nih.gov/project_info_description.cfm?aid=8453963&icde=27037364&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC 1R41NS081792] || [http://tubetk.org Multimodality Image-Based Assessment System For Traumatic Brain Injury] || Aylward, Stephen R. || 2013-01-01 || 2014-12-01
|}

For more information on how this table was created, see [[Documentation/Nightly/Acknowledgments/Grants|this page]].

{{:{{FULLPAGENAME}}/CommercialPartners}}

{{:{{FULLPAGENAME}}/CommercialProducts}}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:20:10Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


3D Slicer
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
{| class="wikitable"
| [[image:Load-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/LoadingData| To add data, just drag and drop]]
| [[image:Save-Icon-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/SavingData| To save data, select the save icon]]
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|100 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|100px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|100 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|100px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|100px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|100 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:17:55Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


3D Slicer
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
{| class="wikitable"
| [[image:Load-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/LoadingData| To add data, just drag and drop]]
| [[image:Save-Icon-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/SavingData| To save data, select the save icon]]
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|100 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|100px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|100 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|100px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|100px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|100 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:17:19Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


3D Slicer
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
{| class="wikitable"
| [[image:Load-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/LoadingData| To add data, just drag and drop]]
| [[image:Save-Icon-2016-08-11.png|100px|link=Documentation/Nightly/SlicerApplication/SavingData| To save data, select the save icon]]
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|100 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|100px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|100 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|100px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|100px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|100 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|100px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:14:27Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
{| class="wikitable"
| [[image:Load-2016-08-11.png|180px|link=Documentation/Nightly/SlicerApplication/LoadingData| To add data, just drag and drop]]
| [[image:Save-Icon-2016-08-11.png|180px|link=Documentation/Nightly/SlicerApplication/SavingData| To save data, select the save icon]]
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:13:53Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
| [[image:Load-2016-08-11.png|180px|link=Documentation/Nightly/SlicerApplication/LoadingData| To add data, just drag and drop]]
| [[image:Save-Icon-2016-08-11.png|180px|link=Documentation/Nightly/SlicerApplication/SavingData| To save data, select the save icon]]
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

File:Save-Icon-2016-08-11.png

2016-08-11T14:13:18Z

Kikinis:

Documentation/Nightly/SlicerApplication/LoadingData

2016-08-11T14:02:44Z

Kikinis:

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/slicerapplication-header}}


=Read this first=
In most cases, "drag and drop" works as a way for loading data.

=Introduction=
Slicer can load a large variety of data in multiple ways. For DICOM data, please refer to the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module documentation. For almost everything else (including scenes), you can use the '''Add Data''' dialogue. For a listing of supported data formats see [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|this list]]. Please note that some of the formats listed are only partially supported.

For some of the more complicated formats (DWI in particular) it is recommended to first convert the DICOM data into the <code>nrrd</code> format using the [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOM to nrrd converter]] and then to load the nrrd file into Slicer. Many vendors are using non standard ways to describe their DWI data in the DICOM headers. The DICOM to nrrd documentation contains a listing of specific formats that have been debugged and tested.

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Add Data| Add Data ]]
|[[#Add DICOM Data| Add DICOM Data ]]
|[[#Misc.| Misc. ]]
|}

=Add Data=
The '''Add Data''' dialogue allows you to load virtually any type of data that Slicer can handle. It should be used as the default way of loading data, with the exception of DICOM, which has its own interface. Data is added to the existing scene.
<gallery widths="300px" heights="200px" perrow="2">
image:SlicerApplication-AddData-Empty.png|[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts|CTRL-A]] (Command-A on Mac) is an application-wide key combination for bringing up the Add Data dialogue.
image:SlicerApplication-FileAddData-4.4.png|File/Add Data contains another link to bring up this dialogue
image:SlicerApplication-AddData-SlicerWelcome-mj.png|Shortcuts to the dialogue are in the Load/Save toolbar and in the [[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome]] module
image:DragNDrop_Slicer.png|'''Drag & Drop''' multiple files (e.g. data, scenes etc.) and folders on the application will bring up the Add Data dialogue with the corresponding documents.
</gallery>

==="Add Data" Functionality===
*The '''Choose Directory to Add''' button adds all files inside the selected directory to the file list.
*The '''[[#"Choose" File Dialogue|Choose Files(s) to Add]]''' button adds all selected files to the file list.
*The '''[[#Show Options|Show Options]]''' checkbox shows/hides the option column which controls properties assigned to an object at loading time. Here you can identify a file as a label map or a streamline.
*The '''Reset''' button clears the entire list of files to load.
*The '''OK''' button loads all datasets in the list, and
*The '''Cancel''' button aborts the entire load.

==="Choose" File Dialogue===
<gallery widths="300px" heights="200px">
image:SlicerApplication-AddData-ChooseFiles.png|After clicking on the “Choose Files to Add” button, a new File Dialogue opens. It is possible to select multiple files using '''CTRL-click''' and multiple contiguous files with '''SHIFT-click'''.
image:SlicerApplication-AddData-ChooseFiles.png|Selecting a <code>.mrml</code> file will '''add''' the scene. When loaded, it will load all the objects contained in that scene. It is not necessary to individually select those files.
</Gallery>

===Show Options===
<gallery widths="350px" heights="200px">
image:SlicerApplication-AddData-SelectedFiles.png|Once the files are selected in the '''Choose File(s)''' dialogue, they are listed in the '''Add Data''' dialogue.
image:SlicerApplication-AddData-ChangeType.png|You can review the selected files, and ensure that they were properly identified before loading. The checkbox in the '''File''' column controls whether to load the file or not. This is useful if you change your mind about which files to load. The '''Description''' column shows the type of file automatically detected.
It is used to select the reader which loads a file. Some file extensions (e.g. <code>.vtk</code>) can contain different types, e.g. ''Volumes'', ''Models'' or ''Fiber bundles''. You must ensure the correct type is selected.
image:SlicerApplication-AddData-ShowOptions.png|Some objects (e.g. ''Volumes'' or ''Scalar Overlay'') can take additional specifications before loading Checking the '''Show Options''' box results in the display of additional columns containing loading options, if any.
</Gallery>

=Add DICOM Data=
Beginning with Slicer 4.0, Slicer holds DICOM data in a local data base. DICOM data can be imported from disk or retrieved from a PACS system (after proper setup).
* For more information about this module, please refer to the [[Documentation/{{documentation/version}}/Modules/DICOM|'''DICOM''']] module documentation.
<gallery widths="550px" heights="200px">
Image:DicomModule-2012-02-21.png|The Dicom Module uses a pop-up to provide information about the selected data set.
Image:LoadSaveToolbar-mj.png| Shortcuts to the dialogue are in the Load/Save toolbar and in the Welcome module
</Gallery>

=Misc.=
==Add Sample Data==
This module downloads a number of sample data sets from the internet. These data sets can be used for testing of slicer capabilities.
* For more information about this module, please refer to the [[Documentation/{{documentation/version}}/Modules/SampleData|'''Sample Data Module''']] documentation.
<gallery widths="350px" heights="200px">
Image:SampleData2012-02-21.png|The Sample Data Module allows downloading of sample data from a webserver.
</Gallery>

==Favorites==
In order to quickly navigate to particular locations in your file system, it is possible to define shortcuts, also known as '''Favorites'''.
<gallery widths="350px" heights="200px">
Image:SlicerApplication-Favorites.png|Favorites are visible in the left column of the "File Dialogue"
Image:SlicerApplication-Favorites-Add.png|Drag and drop from the list of folders on the right in order to create a new Favorite
</Gallery>

=Information for Developers=
Consider reading the [[Documentation/{{documentation/version}}/Developers/IO|Developers/IO]] page for information about programmatically loading and writing files.


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T14:01:01Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
| [[image:Load-2016-08-11.png|180px|link=Documentation/Nightly/SlicerApplication/LoadingData| loading data]]
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

File:Load-2016-08-11.png

2016-08-11T13:56:57Z

Kikinis:

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T13:47:09Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [http://slicerdmri.github.io/ Interactive tractography using diffusion MRI data]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-11T13:42:17Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Fiducial-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Ruler-2016-08-11.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

File:Fiducial-2016-08-11.png

2016-08-11T13:41:51Z

Kikinis:

File:Ruler-2016-08-11.png

2016-08-11T13:40:03Z

Kikinis:

Documentation/Nightly/2016-User-Manual-Discussion

2016-08-04T16:56:48Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]].


|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T17:25:02Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor-panel.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

CitingSlicer

2016-07-29T17:23:23Z

Kikinis: /* Individual Modules */

=3D Slicer as a Platform=
To acknowledge 3D Slicer as a platform, please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates 3D Slicer:

* Slicer 4
** Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.

* Slicer 3
**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.

* Slicer 2
** Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
** Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

=Individual Modules=
To acknowledge individual modules

<gallery widths="280px" heights="280px" >
File:Acknowledgement-tab.png|Each module has an acknowledgment tab in the top section. Information about contributors and funding source can be found there.
File:Help-tab.png|Additional information (including information about the underlying publications) can be typically found on the manual pages accessible through the help tab in the top section
</gallery>

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:45:48Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| [[Image:VolumeRendering-CTA-2011.png|180 px|link=Documentation/Nightly/Modules/VolumeRendering | Volume rendering]]
|-
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:41:33Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|180 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Markups| Fiducials]]
| [[Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|180px|link=Documentation/Nightly/Modules/Annotations| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:33:24Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]]
| [[link to the linear measurements page| Linear Measurements]]
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:30:57Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|180 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|180px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|180 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|180px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|180px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:25:58Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----
*Data Input and Output
*Data fusion
*Visualization
*Segmentation
*Measurements

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|60px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|60px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:22:14Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|60px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|60px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography using diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:16:24Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| [[image:WindowLevelEffectScreenShot.png|60px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|60px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T13:15:36Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| [[image:Editor.png|60px|link=https://www.youtube.com/watch?v=MKLWzD0PiIc| Interactive Segmentation (at 14 minutes)]]
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|60px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T12:27:57Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


=3D Slicer=
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
 
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px|link=Documentation/Nightly/Modules/Transforms|Interactive registration]]
| [[Image:Grid3dVolume.png|60px|link=https://www.youtube.com/watch?v=kZUAfR0mqqI| Demo of the transforms display feature]]
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary|Registration library]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T12:11:48Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
3D Slicer
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-Training: Tutorials and sample data]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T11:49:26Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
3D Slicer
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* How to [[CitingSlicer|cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/Training

2016-07-29T11:47:59Z

Kikinis: /* Introduction: Slicer {{documentation/version}} Tutorials */

<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 the Slicer4 Training Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''

* Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.

__TOC__

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome_Tutorial_SoniaPujol_2013.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*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 version 4.0
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
|
*The [[media:Slicer4minute_SoniaPujol_2013.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*Modules: Welcome to Slicer, Models
*Based on: 3D Slicer version 4.4
*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]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.pdf Data loading and 3D visualization] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
*Author: Sonia Pujol, Ph.D.
*Modules: Welcome to Slicer, Sample Data, Models.
*Audience: End-users
*Based on: 3D Slicer version 4.4
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media: Slicer4_ProgrammingTutorial_SPujol-SPieper_slicer4.4.pdf‎| Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*Based on: 3D Slicer version 4.4
*The [[Media:HelloPython_Slicer4.4.zip| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]

==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|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/b/b2/DiffusionMRIanalysis_Tutorial_SoniaPujol_UNC2015.pdf Diffusion Tensor Imaging Tutorial] course guides through 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 4.4
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/3/30/WhiteMatterExplorationTutorial_SoniaPujol_UNC2015.pdf Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.4
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_SoniaPujol.pdf‎ |3D Visualization of DICOM images for Radiology Applications]] 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 4.3.1_06.29.2014
*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|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/c/c9/QuantitativeImaging_SoniaPujol_RSNA2014_Dec2.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 4.4
*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 3D Printing ==

{|width="100%"
|
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D printing tutorial]'' shows how to prepare 3D Slicer data for 3D printing.
* Authors: Nabgha Farhat, MSc
* Audience: Users and developers interested in 3D printing
|align="right"|[[Image:3DPrinting_tutorial.png|250px]]
|}

== Slicer4 Image Registration ==

{|width="100%"
|
* The [http://www.na-mic.org/Wiki/images/8/8c/RegistrationTutorial_SoniaPujol_UNC2015.pdf Slicer 4 Image 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]]
|}

See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].

== 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]]
|}

== Other ==

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

=Summer 2014 Tutorial contest=

==Cardiac Agatston Tutorial==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf Cardiac Agatston Scoring Tutorial]
*Authors: Jessica Forbes, Hans Johnson, University of Iowa
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
|}

==CMR Toolkit LA workflow==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf CMR Toolkit LA Workflow Tutorial]
*Authors: Salma Bengali, Josh Cates, University of Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
|align="right"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
|}

=Summer 2013 Tutorial contest=

==Cardiac MRI Toolkit==
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

==HelloCLI==
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
|align="right"|
[[Image:Cli_icon.png|300px]]
|}

==SlicerRT==
{|width="100%"
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
*Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
|}

==DTIPrep==
{|width="100%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
|}

= Summer 2012 Tutorial contest =

==Automatic Left Atrial Scar Segmenter ==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
|}

==Qualitative and quantitative comparison of two RT dose distributions==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
[[Image:PlastimatchDose.png|250px]]
|}

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
|}

==WebGL Export==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
[[Image:WebGLExport.png|250px]]
|}

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink.png|250px]]
|}

=Additional resources =
{|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]]
|}
 
----
 
{|width="100%"
|
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

= External Resources =

== Using the Editor ==

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]

== Team Contributions ==
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]

Documentation/Nightly/Training

2016-07-29T11:47:06Z

Kikinis:

<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 the Slicer4 Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''

* Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.

__TOC__

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome_Tutorial_SoniaPujol_2013.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*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 version 4.0
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
|
*The [[media:Slicer4minute_SoniaPujol_2013.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*Modules: Welcome to Slicer, Models
*Based on: 3D Slicer version 4.4
*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]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.pdf Data loading and 3D visualization] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
*Author: Sonia Pujol, Ph.D.
*Modules: Welcome to Slicer, Sample Data, Models.
*Audience: End-users
*Based on: 3D Slicer version 4.4
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media: Slicer4_ProgrammingTutorial_SPujol-SPieper_slicer4.4.pdf‎| Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*Based on: 3D Slicer version 4.4
*The [[Media:HelloPython_Slicer4.4.zip| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]

==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|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/b/b2/DiffusionMRIanalysis_Tutorial_SoniaPujol_UNC2015.pdf Diffusion Tensor Imaging Tutorial] course guides through 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 4.4
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/3/30/WhiteMatterExplorationTutorial_SoniaPujol_UNC2015.pdf Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.4
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_SoniaPujol.pdf‎ |3D Visualization of DICOM images for Radiology Applications]] 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 4.3.1_06.29.2014
*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|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/c/c9/QuantitativeImaging_SoniaPujol_RSNA2014_Dec2.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 4.4
*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 3D Printing ==

{|width="100%"
|
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D printing tutorial]'' shows how to prepare 3D Slicer data for 3D printing.
* Authors: Nabgha Farhat, MSc
* Audience: Users and developers interested in 3D printing
|align="right"|[[Image:3DPrinting_tutorial.png|250px]]
|}

== Slicer4 Image Registration ==

{|width="100%"
|
* The [http://www.na-mic.org/Wiki/images/8/8c/RegistrationTutorial_SoniaPujol_UNC2015.pdf Slicer 4 Image 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]]
|}

See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].

== 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]]
|}

== Other ==

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

=Summer 2014 Tutorial contest=

==Cardiac Agatston Tutorial==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf Cardiac Agatston Scoring Tutorial]
*Authors: Jessica Forbes, Hans Johnson, University of Iowa
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
|}

==CMR Toolkit LA workflow==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf CMR Toolkit LA Workflow Tutorial]
*Authors: Salma Bengali, Josh Cates, University of Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
|align="right"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
|}

=Summer 2013 Tutorial contest=

==Cardiac MRI Toolkit==
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

==HelloCLI==
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
|align="right"|
[[Image:Cli_icon.png|300px]]
|}

==SlicerRT==
{|width="100%"
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
*Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
|}

==DTIPrep==
{|width="100%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
|}

= Summer 2012 Tutorial contest =

==Automatic Left Atrial Scar Segmenter ==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
|}

==Qualitative and quantitative comparison of two RT dose distributions==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
[[Image:PlastimatchDose.png|250px]]
|}

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
|}

==WebGL Export==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
[[Image:WebGLExport.png|250px]]
|}

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink.png|250px]]
|}

=Additional resources =
{|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]]
|}
 
----
 
{|width="100%"
|
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

= External Resources =

== Using the Editor ==

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]

== Team Contributions ==
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]

Documentation/Nightly/Training

2016-07-29T11:46:22Z

Kikinis:

<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 the Slicer4 Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''

{{documentation/banner|text=Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.}}

__TOC__

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome_Tutorial_SoniaPujol_2013.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*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 version 4.0
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
|
*The [[media:Slicer4minute_SoniaPujol_2013.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*Modules: Welcome to Slicer, Models
*Based on: 3D Slicer version 4.4
*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]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
|
*The [http://www.na-mic.org/Wiki/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.pdf Data loading and 3D visualization] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
*Author: Sonia Pujol, Ph.D.
*Modules: Welcome to Slicer, Sample Data, Models.
*Audience: End-users
*Based on: 3D Slicer version 4.4
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media: Slicer4_ProgrammingTutorial_SPujol-SPieper_slicer4.4.pdf‎| Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*Based on: 3D Slicer version 4.4
*The [[Media:HelloPython_Slicer4.4.zip| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]

==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|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/b/b2/DiffusionMRIanalysis_Tutorial_SoniaPujol_UNC2015.pdf Diffusion Tensor Imaging Tutorial] course guides through 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 4.4
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/3/30/WhiteMatterExplorationTutorial_SoniaPujol_UNC2015.pdf Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.4
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_SoniaPujol.pdf‎ |3D Visualization of DICOM images for Radiology Applications]] 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 4.3.1_06.29.2014
*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|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
|
*The [http://wiki.na-mic.org/Wiki/images/c/c9/QuantitativeImaging_SoniaPujol_RSNA2014_Dec2.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 4.4
*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 3D Printing ==

{|width="100%"
|
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D printing tutorial]'' shows how to prepare 3D Slicer data for 3D printing.
* Authors: Nabgha Farhat, MSc
* Audience: Users and developers interested in 3D printing
|align="right"|[[Image:3DPrinting_tutorial.png|250px]]
|}

== Slicer4 Image Registration ==

{|width="100%"
|
* The [http://www.na-mic.org/Wiki/images/8/8c/RegistrationTutorial_SoniaPujol_UNC2015.pdf Slicer 4 Image 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]]
|}

See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].

== 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]]
|}

== Other ==

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

=Summer 2014 Tutorial contest=

==Cardiac Agatston Tutorial==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf Cardiac Agatston Scoring Tutorial]
*Authors: Jessica Forbes, Hans Johnson, University of Iowa
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
|}

==CMR Toolkit LA workflow==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf CMR Toolkit LA Workflow Tutorial]
*Authors: Salma Bengali, Josh Cates, University of Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
|align="right"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
|}

=Summer 2013 Tutorial contest=

==Cardiac MRI Toolkit==
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

==HelloCLI==
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
|align="right"|
[[Image:Cli_icon.png|300px]]
|}

==SlicerRT==
{|width="100%"
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
*Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
|}

==DTIPrep==
{|width="100%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
|}

= Summer 2012 Tutorial contest =

==Automatic Left Atrial Scar Segmenter ==
{|width="100%"
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
|}

==Qualitative and quantitative comparison of two RT dose distributions==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
[[Image:PlastimatchDose.png|250px]]
|}

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
|}

==WebGL Export==
{|width="100%"
|
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
[[Image:WebGLExport.png|250px]]
|}

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink.png|250px]]
|}

=Additional resources =
{|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]]
|}
 
----
 
{|width="100%"
|
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

= External Resources =

== Using the Editor ==

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]

== Team Contributions ==
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T11:44:24Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
3D Slicer
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-29T11:43:44Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
 
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-26T15:23:52Z

Kikinis:

<noinclude></noinclude>
__NOTOC__


{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-26T15:07:42Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|

|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|

----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}

* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-26T14:20:32Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|

----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}
|}

Documentation/Nightly/SlicerApplication/ApplicationSettings

2016-07-22T21:09:20Z

Kikinis:

<noinclude>{{documentation/versioncheck}}</noinclude>
=Overview=

The application setting dialog will allow the user to customize application behavior.

After starting Slicer, it can be accessed clicking on menu <code>Edit -> Application Settings</code>

=Panels=
==General==
{|
|
|valign="top"|[[Image:GeneralSettings.png|thumb|400px|General settings panel]]
|}
==Modules==
{|
|
===Skip Loading of===
Select which [[Documentation/{{documentation/version}}/Developers/Modules|type of modules]] to not load at startup. It is also possible to start slicer by temporarily disabling those modules (not saved in settings) by passing the arguments in the command line.

For example <code>$ .\Slicer.exe --disable-cli-modules</code> will start Slicer without any CLI loaded.

===Prefer Executable CLIs===
Use the executable version of a CLI instead of its shared version. CLI modules typically come in 2 forms, as shared (dll)and as executable (exe). By default, if there is a shared version, it is the one loaded by Slicer, ignoring the executable version. Loading a shared runs the module faster but increases the memory consumption. For some configurations (e.g. Windows 32b), memory is critical. Toggling this option to ON skips the loading of shared CLIs and loads executable version of CLIs instead. If there is no executable for a given CLI, the shared version is used.

===Show hidden modules===
Some modules don't have a user interface, they are hidden from the module's list. For debugging purpose, it is possible to force their display

===Temporary directory===
Directory where modules can store their temporary outputs if needed.

===Additional module paths===
List of directories scanned at startup to load additional modules. Any CLI, Loadable or scripted modules located in these paths will be loaded. Extensions are listed in the list, to remove an extension, use the Extension Manager instead.

===Modules===
List of modules loaded, ignored or failed to load in Slicer. An unchecked checkbox indicates that module should not be loaded (ignored) next time Slicer starts. A text color code is used to describe the state of each module:
** Black: module successfully loaded in Slicer
** Gray: module not loaded because it has been ignored (unchecked)
** Red: module failed to load. There are multiple reasons why a module can fail to load. Look at startup [[Documentation/{{documentation/version}}/SlicerApplication/ErrorLog|log outputs]] to have more informations.
If a module is not loaded in Slicer (ignored or failed), all dependent modules won't be loaded. You can verify the dependencies of a module in the tooltip of the module.

You can filter the list of modules by untoggling in the advanced (>>) panel the "To Load", "To Ignore", "Loaded", "Ignored" and "Failed" buttons.

===Home===
Module that is shown when Slicer starts up.

===Favorites===
List of modules that appear in the Favorites toolbar.
[[Image:FavoritesToolbar.png|Favorites toolbar]]
To add a module, drag&drop it from the ''Modules'' list above. Then use the advanced panel (>>) to reorganize/delete the modules within the toolbar.
|valign="top"|[[Image:ModulesSettings.png|thumb|400px|Modules settings panel]]
|}
==Extensions==
{|
|
|valign="top"|[[Image:ExtensionsSettings.png|thumb|400px|Extensions settings panel]]
|}
==Cache==
{|
|
|valign="top"|[[Image:CacheSettings.png|thumb|400px|Cache settings panel]]
|}
==Python==
{|
|
|valign="top"|[[Image:PythonSettings.png|thumb|400px|Python settings panel]]
|}
==Units==
{|
|
|valign="top"|[[Image:UnitsSettings.png|thumb|400px|Units settins panel]]
|}

==Volume Rendering==
{|
|
|valign="top"|[[Image:VolumeRenderingSettings.png|thumb|400px|Volume Rendering settings panel]]
|}
== Others ==
Extensions can also add their own settings panel.

= Information for Advanced Users =
Settings are stored in an *.ini file located:
* Windows: C:\Users\USERNAME\AppData\Roaming\NA-MIC\Slicer.ini
* Linux: ~/.config/NA-MIC/Slicer.ini
* Mac: ~/.config/www.na-mic.org/Slicer.ini
Deleting the file restores all the settings to default.

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-22T18:56:30Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]]
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-22T18:54:00Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Overview|settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/4.5/SlicerApplication/ApplicationSettings

2016-07-22T18:52:07Z

Kikinis: /* Overview */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Overview=

The "application setting" dialog can be reached from the edit pull-down menu at the right top of the screen. A pop-up window will allow the user to customize application behavior.

After starting Slicer, it can be accessed by clicking on menu <code>Edit -> Application Settings</code>

=Panels=
==General==
{|
|
|valign="top"|[[Image:GeneralSettings.png|thumb|400px|General settings panel]]
|}
==Modules==
{|
|
===Skip Loading of===
Select which [[Documentation/{{documentation/version}}/Developers/Modules|type of modules]] to not load at startup. It is also possible to start slicer by temporarily disabling those modules (not saved in settings) by passing the arguments in the command line.

For example <code>$ .\Slicer.exe --disable-cli-modules</code> will start Slicer without any CLI loaded.

===Prefer Executable CLIs===
Use the executable version of a CLI instead of its shared version. CLI modules typically come in 2 forms, as shared (dll)and as executable (exe). By default, if there is a shared version, it is the one loaded by Slicer, ignoring the executable version. Loading a shared runs the module faster but increases the memory consumption. For some configurations (e.g. Windows 32b), memory is critical. Toggling this option to ON skips the loading of shared CLIs and loads executable version of CLIs instead. If there is no executable for a given CLI, the shared version is used.

===Show hidden modules===
Some modules don't have a user interface, they are hidden from the module's list. For debugging purpose, it is possible to force their display

===Temporary directory===
Directory where modules can store their temporary outputs if needed.

===Additional module paths===
List of directories scanned at startup to load additional modules. Any CLI, Loadable or scripted modules located in these paths will be loaded. Extensions are listed in the list, to remove an extension, use the Extension Manager instead.

===Modules===
List of modules loaded, ignored or failed to load in Slicer. An unchecked checkbox indicates that module should not be loaded (ignored) next time Slicer starts. A text color code is used to describe the state of each module:
** Black: module successfully loaded in Slicer
** Gray: module not loaded because it has been ignored (unchecked)
** Red: module failed to load. There are multiple reasons why a module can fail to load. Look at startup [[Documentation/{{documentation/version}}/SlicerApplication/ErrorLog|log outputs]] to have more informations.
If a module is not loaded in Slicer (ignored or failed), all dependent modules won't be loaded. You can verify the dependencies of a module in the tooltip of the module.

You can filter the list of modules by untoggling in the advanced (>>) panel the "To Load", "To Ignore", "Loaded", "Ignored" and "Failed" buttons.

===Home===
Module that is shown when Slicer starts up.

===Favorites===
List of modules that appear in the Favorites toolbar.
[[Image:FavoritesToolbar.png|Favorites toolbar]]
To add a module, drag&drop it from the ''Modules'' list above. Then use the advanced panel (>>) to reorganize/delete the modules within the toolbar.
|valign="top"|[[Image:ModulesSettings.png|thumb|400px|Modules settings panel]]
|}
==Extensions==
{|
|
|valign="top"|[[Image:ExtensionsSettings.png|thumb|400px|Extensions settings panel]]
|}
==Cache==
{|
|
|valign="top"|[[Image:CacheSettings.png|thumb|400px|Cache settings panel]]
|}
==Python==
{|
|
|valign="top"|[[Image:PythonSettings.png|thumb|400px|Python settings panel]]
|}
==Units==
{|
|
|valign="top"|[[Image:UnitsSettings.png|thumb|400px|Units settins panel]]
|}

==Volume Rendering==
{|
|
|valign="top"|[[Image:VolumeRenderingSettings.png|thumb|400px|Volume Rendering settings panel]]
|}
== Others ==
Extensions can also add their own settings panel.

= Information for Advanced Users =
Settings are stored in an *.ini file located:
* Windows: C:\Users\USERNAME\AppData\Roaming\NA-MIC\Slicer.ini
* Linux: ~/.config/NA-MIC/Slicer.ini
* Mac: ~/.config/www.na-mic.org/Slicer.ini
Deleting the file restores all the settings to default.

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-22T18:46:13Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Learn how to use 3D Slicer]]
* [[FAQ|Frequently asked questions]]
* [http://slicer-users.65878.n3.nabble.com/ Search users mailing list] / [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Sign-up]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite 3D Slicer and individual 3D Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT | Slicer IGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/{{documentation/version}}/SlicerApplication/LookupTables | Slicer Lookup Tables]]
* [[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]
* [[Documentation/{{documentation/version}}/SlicerApplication/QtTesting | QtTesting - Easy way to record and play macros]]

----
Documentation in other languages 
----
{{:Documentation/{{documentation/version}}/Lang/ES}}

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

CitingSlicer

2016-07-22T18:36:21Z

Kikinis:

=3D Slicer as a Platform=
To acknowledge 3D Slicer as a platform, please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates 3D Slicer:

* Slicer 4
** Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.

* Slicer 3
**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.

* Slicer 2
** Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
** Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

=Individual Modules=
To acknowledge individual modules

* Each module has an acknowledgment tab in the top section. Information about contributors and funding source can be found there.
* Additional information (including information about the underlying publications) can be typically found on the manual pages accessible through the help tab in the top section

CitingSlicer

2016-07-22T18:35:12Z

Kikinis:

To acknowledge 3D Slicer as a platform, please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates 3D Slicer:

* Slicer 4
** Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.

* Slicer 3
**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.

* Slicer 2
** Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
** Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

To acknowledge individual modules

* Each module has an acknowledgment tab in the top section. Information about contributors and funding source can be found there.
* Additional information (including information about the underlying publications) can be typically found on the manual pages accessible through the help tab in the top section

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-21T14:34:12Z

Kikinis:

<noinclude></noinclude>
__NOTOC__
{{documentation/versionlist}}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/{{documentation/version}}/Training|Self-training]]
* [[FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [[Documentation/{{documentation/version}}/Report_a_problem|Report a problem or request a feature ]]
* How to [[CitingSlicer|Cite Slicer and individual Slicer Modules]]
----
----
The Basics
----
* [[Documentation/{{documentation/version}}/SlicerApplication/Installation|Installation]]
* A [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|tour through the main window of 3D Slicer]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Layouts]], [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#3D_Viewer|3D Viewers]], and [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Slice_Viewers|Slice Viewers]]
* [[Documentation/{{documentation/version}}/SlicerApplication/MouseandKeyboardShortcuts|Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration|Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-20T14:49:10Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [https://www.slicer.org/pages/LicenseText here] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/4.5/Training|Self-training]]
* [[FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Report_a_problem Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]
----
----
The Basics
----
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/Installation Installation]
* A [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MainApplicationGUI tour through the main window of 3D Slicer]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Layouts Layouts], [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#3D_Viewer 3D Viewers], and [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers Slice Viewers]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MouseandKeyboardShortcuts Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/HardwareConfiguration Hardware requirements]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-20T14:37:59Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [[Link to License|here]] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/4.5/Training|Self-training]]
* [[FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Report_a_problem Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]
----
----
The Basics
----
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/Installation Installation]
* A [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MainApplicationGUI tour through the main window of 3D Slicer]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Layouts Layouts], [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#3D_Viewer 3D Viewers], and [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers Slice Viewers]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MouseandKeyboardShortcuts Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/HardwareConfiguration Hardware requirements]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-20T14:36:32Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [[Link to License|here]] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/4.5/Training|Self-training]]
* [[FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Report_a_problem Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]
----
----
The Basics
----
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/Installation Installation]
* A [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MainApplicationGUI tour through the main window of 3D Slicer]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Layouts Layouts] and [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/MainApplicationGUI#Slice_Viewers slice viewers]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MouseandKeyboardShortcuts Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/HardwareConfiguration Hardware requirements]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-20T14:31:48Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [[Link to License|here]] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ New_users|Getting started]]
* [[ Documentation/4.5/Training|Self-training]]
* [[FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Report_a_problem Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]
----
----
The Basics
----
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/Installation Installation]
* A [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MainApplicationGUI tour through the main window of 3D Slicer]
* [[Link to the proper page| Layouts and viewers]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/MouseandKeyboardShortcuts Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/SlicerApplication/HardwareConfiguration Hardware requirements]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Functions
----

{| class="wikitable"
|
| Data IO and Organization
|-
| [[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| link=Link to Editor module |Interactive segmentation]]
| Interactive and Automated Segmentation
|-
| [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]]
| Interactive and Automated Registration
|-
| [[Image:SlicerRegistrationLibrary_Ad.png|80px|link=Documentation/Nightly/Registration/RegistrationLibrary]]
| Registration library
|-
| [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]]
| Volume rendering
|-
| [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]
| Measurements and Quantification
|}

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-03T12:42:09Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [[Link to License|here]] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Designed for biomedical research
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ link to Training pages|Self-training]]
* [[link to FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [[Link to report a problem page|Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]]
----
----
The Basics
----
* A [[Link to the proper page| tour through the main window of 3D Slicer]]
* [[Link to the proper page| Layouts and viewers]]
* [[Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [[Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Modules
----

[[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| Link= Link to Editor module |Interactive segmentation]] Interactive segmentation, [[link to the proper page|and addtional effects]]
 [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]] Interactive registration
 [[Image:Grid3dVolume.png|60 px| Link to the brainsfit page| Automated]] Automated registration
 [[Image:SlicerRegistrationLibrary_Ad.png|80px|link to the proper page| Registration Solutions library]] Registration library
 [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]] Volume rendering
 [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions

Documentation/Nightly/2016-User-Manual-Discussion

2016-07-03T12:37:59Z

Kikinis:

__NOTOC__
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="50%"|
! |
! width="50%"|
|-
|valign="top"|
----
3D Slicer
----
* Analysis and visualization of medical images
* Image guided therapy research, device interfaces.
* Extensible, free, open source. See [[Link to License|here]] for the license

|bgcolor="#CCCCCC"|
|valign="top"|
----
Highlights
----
* Multi organ capability: from head to toe.
* Multi-modality imaging: MRI, CT, US, nuclear medicine, and microscopy.
|}

{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"
|-
! width="33%"|
! |
! width="33%"|
! |
! width="33%"|
|-
|valign="top"|
----
Where to start ?
----
* [[ link to Training pages|Information on how to use 3D Slicer]]
* [[link to FAQ|Frequently asked questions]]
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users of 3D Slicer] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] [http://slicer-users.65878.n3.nabble.com/ Search the mailing list archives]
* [[Link to report a problem page|Report a problem or request a feature (edit that page accordingly, aimed at end users, not developers)]]
----
----
The Basics
----
* A [[Link to the proper page| tour through the main window of 3D Slicer]]
* [[Link to the proper page| Layouts and viewers]]
* [[Mouse Buttons, "Hot-keys" and Keyboard Shortcuts]]
* Where to modify [[settings]] and where they are [[stored]] (refers to the Edit/Appplication Settings pop up panel)
* [[Hardware requirements]]
* [[Link to portal page about loading data|Loading]], [[Saving data]] and [[listing of supported data formats]].

|bgcolor="#CCCCCC"|
|valign="top"|
----
Core Modules
----

[[Image:2016-07-03-Interactive-Editor-Icon.png|60 px| Link= Link to Editor module |Interactive segmentation]] Interactive segmentation, [[link to the proper page|and addtional effects]]
 [[Image:2016-07-03-Transforms-Module-Icon.png|60 px| Link= Link to Transforms module |Interactive]] Interactive registration
 [[Image:Grid3dVolume.png|60 px| Link to the brainsfit page| Automated]] Automated registration
 [[Image:SlicerRegistrationLibrary_Ad.png|80px|link to the proper page| Registration Solutions library]] Registration library
 [[Image:2016-07-03-Volume-Rendering-Icon.png|60 px| Link= Link to Volume rendering module | Volume rendering]] Volume rendering
 [[Link to the fiducials page | Fiducials]] and [[link to the linear measurements page| Linear Measurements]]

----
Advanced Topics
----
* [[Link to the proper page | Interactive tractography of diffusion MRI data]]
* [[Link to the proper page | Slicer IGT]]
* [[Link to the proper page | Slicer RT]]

|bgcolor="#CCCCCC"|
|valign="top"|
----
Miscellaneous
----
* [[Documentation/Nightly/Developers | Information for Software Developers]]
* [[Slicer4:VisualBlog|Visual blog: A set of screenshots showing Slicer in action.]]
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes: Platform specific issues and considerations]]
* [[Documentation/{{documentation/version}}/Announcements|Announcements]] & [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* Slicer Lookup Tables
* Setting up and using stereoscopic viewing
* QtTesting - Easy way to record and play macros

----
Documentation in other languages 
----
* [[Link to the appropriate language page | Español]]

|}
* [[search box right here|Search for a module in this version of Slicer (including extensions)]]
* Listing in two columns:
** Alphabetic list of modules
** Alphabetic list of extensions