Slicer Wiki - User contributions [en]

Slicer3:3.6 Final Issues

2011-01-24T22:10:14Z

Taox: /* TODO: Issues to fix for the 3.6.3 patch release */

'''Notes:
* Include the [http://www.na-mic.org/Bug/ mantis] bug number in your svn commit messages
* Test your fixes in the slicer3 trunk - when you are sure they work, (1) move them to the Slicer-3-6 branch (2) move them from the TODO to the DONE category on this page
* The Slicer3 repository is in maintenance mode - please do not add new features. New modules should be added only as [http://www.slicer.org/slicerWiki/index.php/Slicer3:Extensions extensions].
'''

==TODO: Issues to fix for the 3.6.3 patch release==
''Fixes for these issues should be checked in to the Slicer-3-6 release branch by 3pm Eastern time on Thursday, Feb 3, 2011''

* Integrate SPECTRE plugin as an extension (Nicole)
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043] (Nicole)
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)
* Migrate MRML Node test fixes to the Slicer-3-6 release branch (Nicole)

* CompareView slice spacing issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim)
* BRAINSResample is not available as a shared library (C++ symbol name in .so) [http://www.na-mic.org/Bug/view.php?id=941 941] (Jim)
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)
* Compareviewer and crosshairs in Navigator mode: 4 compare viewers in wide screen mode (e.g. use [http://www.na-mic.org/Wiki/index.php/File:RSNA2010_fMRICase040Dataset.zip case 40] for data). text is not suppressed, display is slow. (Jim)

* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.3 (Steve)
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067] (Steve)
* Resample widget does not work properly in linked mode. In that situation, the slices should maintain the relative positions as the widget reorients them. (Steve)
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061] Steve)
* Label Grid should be off by default
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi)
* Remove bugs and simplify user interface of Extension manager: (Steve)
** uninstall does not work
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard
* Expose step size parameter for Endoscopy (Steve)
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).
** switching layouts loses observers on scene
** no way to filter display of models or volume rendering in different viewers

* Integrate Endoscopic layout. (Wendy)
* Clean up code for creating DataIO manager in Slicer (Wendy,Steve ?) [http://na-mic.org/Mantis/view.php?id=1033 1033]
** Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call
** commandlines currently cannot execute links to files with http address
* Maybe add DICOM support for XNAT xcat import. (Wendy)
* Data loading and FetchMI:
** http://na-mic.org/Mantis/view.php?id=1029 (working on the leaks)
** http://na-mic.org/Mantis/view.php?id=1028 (partly fixed: slicer will not try to load zero-length downloads. no checksum yet.)
** http://na-mic.org/Mantis/view.php?id=1027 (related to 1028, need input from Steve and Alex)

* Generate Robust MRI brain registration for EMSegmenter (Dominik)

* Include Atlas Creator (Daniel)

* Migrate EMSegment test fixes to the Slicer-3-6 release branch (Dominique)

* Migrate BRAINS test fixes to the Slicer-3-6 release branch (Hans)

=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064] (Alex)
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)
* Warning on unsaved data on scene close and exit (Alex)
* Status of fade slider is not captured by scenesnapshot (Alexy).
* Models Display UI cleanup (Alex)
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)
* multiple fiber tubes rendering performance (Alex)
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)
* Fixes to Camera/View handling (Alex & Wendy)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)
* Fix for passing parameters to command line modules from Luca
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)
* Setup node selector in LabelStatistics to allow label maps only (Andrey)
* CropVolume would not work anymore after scene is closed (Andrey)
* While in the volume rendering module, the render speed is slow while looking at a composited cross section. [http://www.na-mic.org/Bug/view.php?id=1052 1052]
* http://na-mic.org/Mantis/view.php?id=983 (fixed)
* Migrate DicomToNrrd fixes to the Slicer-3-6 release branch (Xiaodong)

==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==

* Create extensions for all versions of Slicer for the release (Steve)

=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)
* N4 module bug in histogram sharpening parameter passing (Andrey)
* Updated versions of BRAINS tools (Hans)
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)
* Editor tweaks:
** add search to the color selector box - color list dynamically filtered when typing in search box
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user) - color box remembers size selected by user
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access
** rename 'check points' to 'undo/redo'
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives). Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data. Also allows for compression in background thread so it does not get in the way of interactive use.
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)
* in the editor module compress saved label maps into stencils (Steve)
* Side-by-side and Widescreen compare view linking problems appear fixed.
* Ron requests default for crosshair to be navigator OFF
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now.
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services.
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
**add thumbnails to show effect of the transfer functions,
**remove unneeded ones, correct a typo.
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)
** Flickering has not been improved since 3.6.1.
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].

Modules:DicomToNRRD-3.6

2010-12-17T14:00:48Z

Taox: /* Supported DWI formats */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
DWI Dicom To NRRD

{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}

== General Information ==
===Module Type & Category===

Type: Command line module

Category: Converters

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao (with contribution from Vince Magnotta and Hans Johnson)
* Contact: taox @ research.ge.com

===Module Description===
This module converts diffusion weighted MR images in dicom series into Nrrd
format for analysis in Slicer. This program has been tested on only
a limited subset of DTI dicom formats available from Siemens, GE,
and Phillips scanners. Work in progress to support dicom multi-frame
data. The program parses dicom header to extract necessary
information about measurement frame, diffusion weighting directions,
b-values, etc, and write out a nrrd image.

== Usage ==

===Examples, Use cases & Tutorials===

This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer3 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

====Supported DWI formats====
*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Acheiva 2.6.3.4
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0
**DVMR 20.0M4
**DVMR 20.1

====Command Line Usage====
A command line example for running the module is:

d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr

===Quick Tour of Features and Use===

[[Image:DicomToNrrd-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
When this module is run from Slicer UI, simply select the directories for '''Input Dicom Data''' and '''Output Directory''', enter the filename (without path name, but '''with''' extension, such as '''mydti.nrrd''') in the '''Output Filename''' field, and press "Apply" button.

The module can also be run from command line to enable batch process. An example command line look like:

d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe
--inputDicomDirectory MyDicomDir
--outputDirectory /scratch/Diffusion
--outputVolume MyNrrdImage.nrrd

== Development==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known Bugs===

===Usability Issues===

Because different vendors used different private tags to store information related to diffusion weighting and documentation on how to interoperate this information is scarce, the current version support diffusion weighted images from GE, Siemens, and Philips scanners. For Siemens, both mosaic and split formats are supported. For Philips, both multi-slice and signal-slice formats are supported.

The current version also support non-diffusion weighted images from any vendors (that GDCM supports), in which case, the module acts as a dicom series to nrrd volume converter.

===Source Code and Documentation===

Source Code: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/DicomToNrrdConverter.cxx?view=markup DicomToNrrdConverter.cxx]

XML Description: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?view=markup DicomToNrrdConverter.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/Testing/DicomToNrrdConverterTest.cxx?rev=12979&view=log DicomToNrrdConverterTest.cxx]

<pre>
./lib/Slicer3/Plugins/DicomToNrrdConverter --help

USAGE:

./lib/Slicer3/Plugins/DicomToNrrdConverter [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--useIdentityMeaseurementFrame]
[--writeProtocolGradientsFile]
[--outputVolume <std::string>]
[--outputDirectory <std::string>]
[--inputDicomDirectory
<std::string>] [--] [--version]
[-h]

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--useIdentityMeaseurementFrame
Adjust all the gradients so that the measurement frame is an identity
matrix. (default: 0)

--writeProtocolGradientsFile
Write the protocol gradients to a file suffixed by '.txt' as they were
specified in the procol by multiplying each diffusion gradient
direction by the measurement frame. This file is for debugging
purposes only, the format is not fixed, and will likely change as
debugging of new dicom formats is necessary. (default: 0)

--outputVolume <std::string>
Output filename (.nhdr)

--outputDirectory <std::string>
Directory holding the output NRRD format

--inputDicomDirectory <std::string>
Directory holding Dicom series

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

Description: Converts diffusion weighted MR images in dicom series into
Nrrd format for analysis in Slicer. This program has been tested on only
a limited subset of DTI dicom formats available from Siemens, GE, and
Phillips scanners. Work in progress to support dicom multi-frame data.
The program parses dicom header to extract necessary information about
measurement frame, diffusion weighting directions, b-values, etc, and
write out a nrrd image. For non-diffusion weighted dicom images, it
loads in an entire dicom series and writes out a single dicom volume in
a .nhdr/.raw pair.

Author(s): Xiaodong Tao

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Additional support for DTI data produced on Philips scanners was
contributed by Vincent Magnotta and Hans Johnson at the University of
Iowa.
</pre>

==More Information==

===Acknowledgement===

Acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.

===References===

More information on Dicom format for diffusion weighted images on [http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI NA-MIC Wiki.]

Modules:DicomToNRRD-3.6

2010-12-09T19:58:38Z

Taox: /* Supported DWI formats */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
DWI Dicom To NRRD

{|
|[[Image:DWIDicomToNrrdGUI.png|thumb|280px|Screenshot of the UI]]
|}

== General Information ==
===Module Type & Category===

Type: Command line module

Category: Converters

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao (with contribution from Vince Magnotta and Hans Johnson)
* Contact: taox @ research.ge.com

===Module Description===
This module converts diffusion weighted MR images in dicom series into Nrrd
format for analysis in Slicer. This program has been tested on only
a limited subset of DTI dicom formats available from Siemens, GE,
and Phillips scanners. Work in progress to support dicom multi-frame
data. The program parses dicom header to extract necessary
information about measurement frame, diffusion weighting directions,
b-values, etc, and write out a nrrd image.

== Usage ==

===Examples, Use cases & Tutorials===

This module is typically used as the first step in diffusion weighted image analysis and tractography to convert diffusion weighted images in Dicom format into Nrrd format, which is recognized by Slicer3 as a legitimate diffusion weighted volume.

In the recent development, it is extended to act as a dicom series to nrrd file converted for non-diffusion-weighted images as well.

====Supported DWI formats====
*Philips scanner/software version combinations:
**Achieva 2.1.3.6
**Achieva 2.5.3.0
**Achieva 2.5.3.3
**Achieva 2.6.1.0
**Intera 2.1.3.6
**Intera 2.6.3.5
*Siemens
**Trio B13
**Trio B15
**Trio B17
**Verio B15V
*GE
**SIGNA HDx14.0
**SIGNA HDxt 15.0

====Command Line Usage====
A command line example for running the module is:

d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe --inputDicomDirectory MyDicomDir --outputVolume MyNrrdImage.nhdr

===Quick Tour of Features and Use===

[[Image:DicomToNrrd-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
When this module is run from Slicer UI, simply select the directories for '''Input Dicom Data''' and '''Output Directory''', enter the filename (without path name, but '''with''' extension, such as '''mydti.nrrd''') in the '''Output Filename''' field, and press "Apply" button.

The module can also be run from command line to enable batch process. An example command line look like:

d:\Builds\Slicer3\lib\Slicer3\Plugins\Release\DicomToNrrdConverter.exe
--inputDicomDirectory MyDicomDir
--outputDirectory /scratch/Diffusion
--outputVolume MyNrrdImage.nrrd

== Development==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known Bugs===

===Usability Issues===

Because different vendors used different private tags to store information related to diffusion weighting and documentation on how to interoperate this information is scarce, the current version support diffusion weighted images from GE, Siemens, and Philips scanners. For Siemens, both mosaic and split formats are supported. For Philips, both multi-slice and signal-slice formats are supported.

The current version also support non-diffusion weighted images from any vendors (that GDCM supports), in which case, the module acts as a dicom series to nrrd volume converter.

===Source Code and Documentation===

Source Code: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/DicomToNrrdConverter.cxx?view=markup DicomToNrrdConverter.cxx]

XML Description: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?view=markup DicomToNrrdConverter.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/DicomToNrrdConverter/Testing/DicomToNrrdConverterTest.cxx?rev=12979&view=log DicomToNrrdConverterTest.cxx]

<pre>
./lib/Slicer3/Plugins/DicomToNrrdConverter --help

USAGE:

./lib/Slicer3/Plugins/DicomToNrrdConverter [--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo]
[--useIdentityMeaseurementFrame]
[--writeProtocolGradientsFile]
[--outputVolume <std::string>]
[--outputDirectory <std::string>]
[--inputDicomDirectory
<std::string>] [--] [--version]
[-h]

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--useIdentityMeaseurementFrame
Adjust all the gradients so that the measurement frame is an identity
matrix. (default: 0)

--writeProtocolGradientsFile
Write the protocol gradients to a file suffixed by '.txt' as they were
specified in the procol by multiplying each diffusion gradient
direction by the measurement frame. This file is for debugging
purposes only, the format is not fixed, and will likely change as
debugging of new dicom formats is necessary. (default: 0)

--outputVolume <std::string>
Output filename (.nhdr)

--outputDirectory <std::string>
Directory holding the output NRRD format

--inputDicomDirectory <std::string>
Directory holding Dicom series

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

Description: Converts diffusion weighted MR images in dicom series into
Nrrd format for analysis in Slicer. This program has been tested on only
a limited subset of DTI dicom formats available from Siemens, GE, and
Phillips scanners. Work in progress to support dicom multi-frame data.
The program parses dicom header to extract necessary information about
measurement frame, diffusion weighting directions, b-values, etc, and
write out a nrrd image. For non-diffusion weighted dicom images, it
loads in an entire dicom series and writes out a single dicom volume in
a .nhdr/.raw pair.

Author(s): Xiaodong Tao

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Additional support for DTI data produced on Philips scanners was
contributed by Vincent Magnotta and Hans Johnson at the University of
Iowa.
</pre>

==More Information==

===Acknowledgement===

Acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.

===References===

More information on Dicom format for diffusion weighted images on [http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI NA-MIC Wiki.]

Documentation/3.6

2010-05-25T15:05:12Z

Taox: /* Slicer Extensions */

=Introduction=

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)

The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is and the following [[Announcments-3.6-Team|acknowledged here]].

*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
*For sample data see [[SampleData|here]]

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=

==Core==
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*Fast Registration
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust Registration
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
*Brain Only Registration
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data Registration
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
* DWI Denoising
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion Tensor Utilities
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Slicer Extensions==

[[Documentation-3.6:ExtensionStatus|Extension Status]]

'''Introduction'''

* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Import/Export
** [[Image:MissingOrStaleDoc.png]][[Modules:PlastimatchDICOMRT|Plastimatch > DICOM RT Import]] Greg Sharp (gcsharp@partners.org).
* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).
* Registration
**Robust
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit)
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Quantification
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=Other information=

'''Developer Tools'''
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

'''Non-SPL Supported Compatibility Packages'''
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

'''QA Table'''

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

Modules:SkullStripperModule

2010-05-25T15:04:25Z

Taox: /* Usability issues */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|340px|Input T1 Image]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
|}
|[[Image:SkullStripperSurface-3-6.png|thumb|375px|Brain surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. Some limited test has been done on T2 weighted images. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary. This can be used for most of visualization tasks and applications where accuracy in cortex is not critical.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

Modules:SkullStripperModule

2010-05-25T15:03:33Z

Taox: /* Usability issues */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|340px|Input T1 Image]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
|}
|[[Image:SkullStripperSurface-3-6.png|thumb|375px|Brain surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. Some limited test has been done on T2 weighted images. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

Modules:SkullStripperModule

2010-05-25T15:02:27Z

Taox: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|340px|Input T1 Image]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|340px|Brain mask as contour]]
|}
|[[Image:SkullStripperSurface-3-6.png|thumb|375px|Brain surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

Modules:SkullStripperModule

2010-05-25T15:00:36Z

Taox: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|280px|Input T1 Image]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|280px|Brain mask as contour]]
|}
|[[Image:SkullStripperSurface-3-6.png|thumb|280px|Brain surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

File:SkullStripperSurface-3-6.png

2010-05-25T14:59:17Z

Taox:

File:SkullStripperOutput-3-6.png

2010-05-25T14:59:01Z

Taox:

File:SkullStripperInput-3-6.png

2010-05-25T14:58:45Z

Taox:

File:SkullStripper-3-6.png

2010-05-25T14:54:06Z

Taox:

Modules:SkullStripperModule

2010-05-25T14:52:26Z

Taox: /* References */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|280px|Input Image with Mask]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|280px|Segmentation Results]]
|-
|[[Image:SkullStripperSurface-3-6.png|thumb|280px|Segmentation Results]]
|}
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.
* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

Modules:SkullStripperModule

2010-05-25T14:51:16Z

Taox: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== Skull Stripper {| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:Fuzzy…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Skull Stripper

{| border="0"http://wiki.slicer.org/slicerWiki/index.php?title=Modules:FuzzySegmentationModule&action=edit
|[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:SkullStripperInput-3-6.png|thumb|280px|Input Image with Mask]]
|-
|[[Image:SkullStripperOutput-3-6.png|thumb|280px|Segmentation Results]]
|-
|[[Image:SkullStripperSurface-3-6.png|thumb|280px|Segmentation Results]]
|}
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

== Usage ==

===Examples, Use Cases & Tutorials===

===Quick Tour of Features and Use===

== Development ==

===Dependencies===

No other modules are required for this module.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images from OASIS database. In some cases, when partial volume artifact is severe, the algorithm does not find the accurate brain boundary.

===Source code & documentation===

Source Code:

XML Description:

Usage:

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

Documentation/3.6

2010-05-25T14:14:00Z

Taox:

=Introduction=

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)

The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is and the following [[Announcments-3.6-Team|acknowledged here]].

*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
*For sample data see [[SampleData|here]]

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)

=Modules=

==Core==
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*Fast Registration
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust Registration
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]: automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
*Brain Only Registration
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data Registration
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
* DWI Denoising
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
* Diffusion Tensor Utilities
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
* Tractography
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Slicer Extensions==

[[Documentation-3.6:ExtensionStatus|Extension Status]]

'''Introduction'''

* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Import/Export
** [[Image:MissingOrStaleDoc.png]][[Modules:PlastimatchDICOMRT|Plastimatch > DICOM RT Import]] Greg Sharp (gcsharp@partners.org).
* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox AT research.ge.com).
* Registration
**Robust
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit)
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Quantification
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

=Other information=

'''Developer Tools'''
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

'''Non-SPL Supported Compatibility Packages'''
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

'''QA Table'''

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

'''Modules'''
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

'''Requirements for Modules'''
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Documentation Draft notes=
Key for flagged modules below:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:
* for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
* for interactive modules, see other modules in Base/GUI for an example.

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

Modules:PolyDataToLabelmap-Documentation-3.6

2010-04-30T17:12:37Z

Taox: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resamples the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels (in mm) in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

Documentation/3.6

2010-04-30T17:00:28Z

Taox: /* Slicer Extensions */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Documentation/3.6

2010-04-30T16:59:54Z

Taox: /* Converters */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Documentation/3.6

2010-04-30T16:58:50Z

Taox: /* Filtering */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Documentation/3.6

2010-04-30T16:56:03Z

Taox: /* Filtering */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Image:MissingOrStaleDocLink.png]][[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Image:MissingOrStaleDocLink.png]][[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Documentation/3.6

2010-04-30T16:55:46Z

Taox: /* Filtering */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Image:MissingOrStaleDocLink.png]][[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Image:MissingOrStaleDocLink.png]][[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Documentation/3.6

2010-04-30T16:55:11Z

Taox: /* Converters */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Image:MissingOrStaleDocLink.png]][[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Image:MissingOrStaleDocLink.png]][[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Modules:PolyDataToLabelmap-Documentation-3.6

2010-04-30T16:50:16Z

Taox: moved Modules:PolyDatToLabelmap-Documentation-3.6 to Modules:PolyDataToLabelmap-Documentation-3.6: typo

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

Modules:PolyDatToLabelmap-Documentation-3.6

2010-04-30T16:50:16Z

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#REDIRECT [[Modules:PolyDataToLabelmap-Documentation-3.6]]

Documentation/3.6

2010-04-30T16:28:23Z

Taox: /* Surface Models */

This is work in progress

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:LabelMapEditor-Documentation-3.6| Label Map Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Image:MissingOrStaleDocLink.png]][[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Image:MissingOrStaleDocLink.png]][[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Image:MissingOrStaleDocLink.png]][[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

Modules:PolyDataToLabelmap-Documentation-3.6

2010-04-30T16:27:17Z

Taox: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== PolyData to LabelMap {| |GUI panel |[[Im…'

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

Documentation/3.6

2010-04-30T16:23:35Z

Taox: /* Surface Models */

This is work in progress

=Main GUI=

*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)
* Robust Statistical Segmentation (Yi Gao)
* Model Transform (Alex Yarmarkovich)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Image:MissingOrStaleDoc.png]][[Modules:LabelMapEditor-Documentation-3.6| Label Map Editor]] (Steve Pieper)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Image:MissingOrStaleDocLink.png]][[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Image:MissingOrStaleDocLink.png]][[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Image:MissingOrStaleDocLink.png]][[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Image:MissingOrStaleDocLink.png]][[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Image:MissingOrStaleDocLink.png]][[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelMap-Documentation-3.6| PolyDataToLabelMap]] (Xiaodong Tao, Nicole Aucoin)

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented for end users, but contain comments in the source code

=Slicer Extensions=

'''Introduction'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

'''Installation Instructions'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

'''Info for Developers'''

*We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
*Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper

* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=

Key for flagged modules above:

[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation

[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module

[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation

[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Modules:OrientImages-Documentation-3.6

2010-04-30T15:18:15Z

Taox:

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
Orient Images

{|
|[[Image:OrientImage-3-6.png|thumb|280px|Orient Images UI]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Converters

===Authors, Collaborators & Contact===
* Author: Bill Lorensen
* Contact: bill.lorensen at gmail.com

===Module Description===
Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module is useful for transforming volume from its original orientation to a given orientation. Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image. It does not change the spatial position and orientation of the volume in the physical space.

When combined with "Create a Dicom Series" module, one can synthesize a sagittal acquisition from an axially acquired volume.

* A command line example of the module is

OrientImage
--orientation Axial
${MRML_DATA}/fixed.nrrd
${TEMP}/OrientImageTestAxial.nrrd

===Quick Tour of Features and Use===
List all the panels in your interface, their features, what they mean, and how to use them. For instance:

* '''Input/output panel:'''
[[Image:OrientImage-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
User specifies the input volume and creates an output volume.

* '''Parameters panel:'''
[[Image:OrientImage-OrientationPanels-3-6.png|thumb|right|280px|Orientation panels]]
User selects the desired orientation.

* '''Viewing panel:'''

Since Slicer3 takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume.

Note, that the module does not align the voxel space axes with the physical space axes. If your input image is not axis-aligned, the output will preserve the direction cosines of the input image.

== Development ==

===Dependencies===

Depends only on Slicer3's core IO and display functionalities.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OrientImage.cxx?view=annotate OrientImage.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/OrientImage.xml?view=co Orient orientImage.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/OrientImageTest.cxx?rev=11535&view=log OrientImageTest.cxx]

Usage:
<pre>
./OrientImage [--processinformationaddress <std::string>] [--xml]
[--echo] [-o <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP|RIA
|LIA|RSA|LSA|IRP|ILP|SRP|SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI
|LAI|RPS|LPS|RAS|LAS|PRI|PLI|ARI|ALI|PRS|PLS|ARS|ALS|IPR
|SPR|IAR|SAR|IPL|SPL|IAL|SAL|PIR|PSR|AIR|ASR|PIL|PSL|AIL
|ASL>] [--] [--version] [-h] <std::string> <std::string>

Where:

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

-o <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP|RIA|LIA|RSA|LSA|IRP|ILP|SRP
|SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI|LAI|RPS|LPS|RAS|LAS|PRI|PLI|ARI|ALI
|PRS|PLS|ARS|ALS|IPR|SPR|IAR|SAR|IPL|SPL|IAL|SAL|PIR|PSR|AIR|ASR|PIL
|PSL|AIL|ASL>, --orientation <Axial|Coronal|Sagittal|RIP|LIP|RSP|LSP
|RIA|LIA|RSA|LSA|IRP|ILP|SRP|SLP|IRA|ILA|SRA|SLA|RPI|LPI|RAI|LAI|RPS
|LPS|RAS|LAS|PRI|PLI|ARI|ALI|PRS|PLS|ARS|ALS|IPR|SPR|IAR|SAR|IPL|SPL
|IAL|SAL|PIR|PSR|AIR|ASR|PIL|PSL|AIL|ASL>
Orientation choices (default: LPS)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume 1

<std::string>
(required) The oriented volume

Description: Orients an output volume. Rearranges the slices in a volume
accoording to the selected orientation. The resulting volume will cover
the original volume.

Author(s): Bill Lorensen

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Internally, the module uses itk::OrientImageFilter. More details on algorithm can be found [http://public.kitware.com/Insight/Doxygen/html/classitk_1_1OrientImageFilter.html here].

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T15:11:17Z

Taox: /* Acknowledgment */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

File:FCMResultLabels-3-6.png

2010-04-30T15:08:58Z

Taox:

Modules:FuzzySegmentationModule

2010-04-30T15:08:48Z

Taox: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===Module Name===
Fuzzy Tissue Classification

{| border="0"
|[[Image:FCMUI-3-6.png|thumb|280px|Module UI]]
| style="text-align: center;" |
{| border="0"
|[[Image:FCMInput-3-6.png|thumb|280px|Input Image with Mask]]
|-
|[[Image:FCMResultLabels-3-6.png|thumb|280px|Segmentation Results]]
|-
|[[Image:FCMResult-3-6.png|thumb|280px|Segmentation Results]]
|}
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Segmentation

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao
* Contact: taox at research.ge.com

===Module Description===

This module computes voxel by voxel tissue classification of an MR brain image using a fuzzy c-means algortihm. Bias field is modeled as a lower order polynomial. Bias field and tissue classification are estimated iteratively in an EM fashion. Internally, each voxel is assigned tissue membership function values, which range from 0 to 1. At any voxel, the sum of membership function of all classes is either 0 (outside of brain), or 1. The membership functions are converted in tissue labels to generate hard segmentation.

== Usage ==

===Examples, Use Cases & Tutorials===

This module is typically used to assign tissue labels to an image. For example, in MR brain image analysis, many applications need to know which voxels belong to gray matter, white matter, and CSF.

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:FCM-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes two input volumes and generate two output volumes. '''Input Volume''' is the MR image to be segmented. '''Input Mask''' gives the mask within which segmentation is applied. '''Hard Segmentation''' is an output label map. And '''Bias Field''' is the estimated bias field.

* '''Parameters panel:'''
[[Image:FCM-ParametersPanels-3-6.png|thumb|right|280px|Parameters panels]]

User can specify two parameters: '''NumberOfClasses''' tells the algorithm how many different tissues there are in the given mask. For brain, we use 3 -- gray matter, white matter, and CSF; '''BiasOption''' specifies how bias field is modeled -- 0: no bias correction; 1: global linear; 2: global quadratic; 3: region based linear; 4: region based quadratic. From 0 to 4, computation time increases as the accuracy increases.

== Development ==

===Dependencies===

No other modules are required for this module. The mask can be generated using any skull stripping algorithm.

===Known bugs===

None.

===Usability issues===

Developed and tested on T1 weighted images. Performance on images from other modality or with other MR contrasts may be limited.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/BrainTissueClassification/TissueClassification.cxx?rev=6314&root=NAMICSandBox&view=log TissueClassification.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/BrainTissueClassification/TissueClassification.xml?rev=6314&root=NAMICSandBox&view=log TissueClassification.xml]

Test: [http://viewvc.slicer.org/viewcvs.cgi/trunk/BrainTissueClassification/Testing/TissueClassificationTest.cxx?rev=6314&root=NAMICSandBox&sortby=author&view=log TissueClassificationTest.cxx]

Usage:
<pre>
USAGE:

../Slicer3-ext/BrainTissueClassification-build/lib/Slicer3/Plugins/Tissu
eClassification
[--returnparameterfile
<std::string>]
[--processinformationaddress
<std::string>] [--xml] [--echo] [-b
<int>] [-c <int>] [--] [--version]
[-h] <std::string> <std::string>
<std::string> <std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

-b <int>, --biasoption <int>
Option for bias correction (0: no bias correction; 1: global linear;
2: global quadratic; 3: region based linear; 4: region based
quadratic) (default: 0)

-c <int>, --class <int>
Number of classes (default: 3)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input T1 Image.

<std::string>
(required) Only voxels inside the mask are classified

<std::string>
(required) Output brain mask map.

<std::string>
(required) Estimated bias field

Description: This module computes voxel by voxel tissue classification
of an MR brain image using a fuzzy c-means algortihm. Bias field is
modeled as a lower order polynomial. Bias field and tissue
classification are estimated iteratively in an EM fashion. Internally,
each voxel is assigned tissue membership function values, which range
from 0 to 1. At any voxel, the sum of membership function of all classes
is either 0 (outside of brain), or 1. The membership functions are
converted in tissue labels to generate hard segmentation.

Author(s): Xiaodong Tao, taox @ research . ge . com

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Implementation of the Fuzzy Classification was contributed by Dr.
Ming-Ching Chang from GE Research.

</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Implementation of the Fuzzy Classification was contributed by Dr. Ming-Ching Chang from GE Research.

[http://www.oasis-brains.org/ OASIS datasets] were used to generate images on this page.

===References===

* Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.

File:FCMUI-3-6.png

2010-04-30T15:08:03Z

Taox: uploaded a new version of "File:FCMUI-3-6.png"

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T14:10:56Z

Taox: /* Usability issues */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

When the object has a geometry such that the centroid of all vertices lie outside of the object, the module will fail to generate the correct label for the object.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Slicer-3.6-QA

2010-04-30T01:50:28Z

Taox: /* Application CLI Modules */

[[Documentation-3.6|Return to Slicer 3.6 documentation]]

*This page contains our assessment of the Slicer 3.6 modules

*See also the [http://wiki.na-mic.org/Wiki/index.php/2010_Slicer36_Module_Cull module culling event] at the end of April 2010

= Testing Status =

== Core Modules ==

{|class="wikitable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Current Owner
|-
|style="background:white"|??||style="width:33%"| Camera ||complete||yes, no link||no|| Sebastien Barre
|-
|style="background:white"|??||style="width:33%"| Welcome ||complete||yes and yes||yes and yes ||Wendy Plesniak
|-
|style="background:white"|??||style="width:33%"| Volumes ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Diffusion Editor ||complete||yes and yes||no|| CF Westin
|-
|style="background:white"|??||style="width:33%"| Models ||complete||yes and yes||yes and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Measurements ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Fiducials||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Data ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Slices ||complete||yes and yes||yes and yes|| Jim Miller
|-
|style="background:white"|??||style="width:33%"| Colors ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Interactive Editor ||complete||no and yes ||yes and no || Steve Pieper
|-
|style="background:white"|??||style="width:33%"| ROI Module ||complete||no and yes||no and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Volume Rendering ||complete||yes and yes||no and yes|| Yanling Liu
|-
|style="background:white"|??||style="width:33%"| PET/CT Fusion ||complete||yes and yes||yes and yes|| Wendy Plesniak
|-
|}
<references/>

== Application CLI Modules ==

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Test coverage <ref>in % for non-interactive part</ref>!!valgrind errors!!Current Owner!!Comments <ref>Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files</ref>!!3.6 Documentation Name <ref>http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6</ref>
|-
|style="background:gold"|1Gold||style="width:33%"|my module||complete||yes and yes||yes, yes, yes||80%||0|| ||||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionWeightedTest ||no||no||yes and yes|| 69.8% || 0||CF Westin||||n/a||
|-
|style="background:silver"|2Silver||style="width:33%"| DiffusionTensorEstimation || complete ||yes and no||yes and yes|| 79.7% || 9 ||CF Westin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorMathematics ||no||yes and no||yes and yes|| 56.2% || 5||CF Westin||||Diffusion Tensor Scalar Measurements||
|-
|style="background:gold"|1Gold||style="width:33%"| OrientImage ||complete||yes and yes||yes and yes|| 85.7% || 0 ||Bill Lorensen||||OrientImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| LinearRegistration ||complete||yes and no||yes and yes|| 66.7% || 4 ||Daniel Blezek||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| RigidRegistration ||complete||yes and yes||yes and yes||style="background:red"| 1.0% || 92 ||Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| RegisterImages (RegisterImagesMultiRes) ||complete||yes and yes||yes and yes|| 83.5% || Unknown || Casey Goodlett, Stephen Aylward||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Fast Affine Registration ||complete||yes and no||yes and yes||style="background:red" |1.4% || 82 || Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| BSplineDeformableRegistration ||complete||yes and yes||yes and yes|| 82.3% || 6 || Bill Lorensen||||Fast Nonrigid BSpline Registration||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| TestGridTransformRegistration ||no||no||yes and yes || 90.7% || 0 ||Yinglin Lee||||n/a||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CheckerBoard ||complete||yes and yes||yes and yes|| 67.4% || 0 ||Bill Lorensen||||CheckerBoard Filter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ResampleVolume ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| PolyDataToLabelmap ||complete||yes and yes||yes and yes|| 87.9% || 0 ||Nicole Aucoin, Xiaodong Tao||||same||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GaussianBlurImageFilter ||complete||yes and no||yes and yes|| 55.9% || 0 ||Julien Jomier, Stephen Aylward||||Gaussian Blur||
|-
|style="background:gold"|1Gold||style="width:33%"| ConfidenceConnected||complete||yes and no||yes and yes|| 87.5% || 0 ||Jim Miller||||Simple region growing||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ExecutionModelTour ||no||yes and yes||yes and yes|| 87.2% || 0 ||Daniel Blezek, Bill Lorensen||||n/a||
|-
|style="background:gold"|1Gold||style="width:33%"| ImageReadDicomWrite ||complete||yes and yes||yes and yes|| 86.1% || 0 ||Bill Lorensen||||Create a Dicom Series||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CurvatureAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 64.3% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GradientAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 63.4% || 0 ||Bill Lorensen||||GradientAnisotropicFilter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| MedianImageFilter ||complete||yes and yes||yes and yes|| 51.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| HistogramMatching ||complete||yes and yes||yes and yes|| 65.0% || 0 ||Bill Lorensen||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| OtsuThresholdImageFilter ||no||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||OtsuThreshold||
|-
|style="background:gold"|1Gold||style="width:33%"| OtsuThresholdSegmentation ||complete||yes and no||yes and yes|| 90.9% || 0 ||Bill Lorensen||||same||
|-
|style="background:silver"|2Silver||style="width:33%"| Subtract ||complete||yes and yes||yes and yes|| 71.7% || 0 ||Bill Lorensen||||SubtractImages||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Multiply ||yes||yes and yes||yes and yes|| 77.6% || 0 ||Bill Lorensen||||MultiplyImages||
|-
|style="background:gold"|1Gold||style="width:33%"| Add ||complete||yes and yes||yes and yes|| 84.9% || 0 ||Bill Lorensen||||AddImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| Threshold ||complete||yes and yes||yes and yes|| 55.8% || 0 ||Nicole Aucoin||||ThresholdImage||
|-
|style="background:gold"|1Gold||style="width:33%"| Mask ||complete||yes and yes||yes and yes|| 80.0% || 0 ||Nicole Aucoin||||Mask Image||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Cast ||complete||yes and yes||yes and yes||style="background:red"| 14.6% || 0 ||Nicole Aucoin||||Cast Image||
|-
|style="background:gold"|1Gold||style="width:33%"| VotingBinaryHoleFillingImageFilter ||complete||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||Voting Binary Hole Filling||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ModelMaker ||complete||yes and yes||yes and yes|| 57.4% || 1 ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MultipleModelsExample ||no||yes and no||yes and yes||style="background:red"| 1.9%|| 50 ||Bill Lorensen||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| GrayscaleModelMaker ||no||yes and no||yes and yes|| 82.1% || 1 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| MergeModels ||yes||yes and yes||yes and yes|| 62.7% || 0 ||Nicole Aucoin, Daniel Haehn||||same||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GrayscaleFillHoleImageFilter ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||Grayscale Fill Hole||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GrayscaleGrindPeakImageFilter ||complete||yes and yes||yes and yes|| 64.5% || 0 ||Bill Lorensen||||Grayscale Grind Peak||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| LabelMapSmoothing ||no||yes and no||yes and yes|| 87.9% || 0 ||Dirk Padfield, Josh Cates, Ross Whitaker||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ImageLabelCombine ||complete||yes and no||yes and no||style="background:red"| 7.5% || 50 ||Alex Yarmarkovich||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleVolume2 ||no||yes and yes||yes and yes||style="background:red"| 46.8% || 0 ||Francois Budin||||Resample Scalar/Vector/DWI Volume||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ZeroCrossingBasedEdgeDetectionImageFilter ||no||yes and no||yes and yes|| 62.5%|| 0 || Elliot Uvero||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| FreesurferSurfaceSectionExtraction ||no||yes and no||yes and yes|| 60.0% || 62 || Sylvain Bouix||||n/a/||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSDemonWarp ||complete||yes and no||yes and no|| style="background:red"| 0.0% || Unknown ||Hans Johnson, Greg Harris ||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSFit ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unkown || Eun Young Kim||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSMush ||complete||no||no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSResample ||no||yes and yes||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSROIAuto ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorEstimation BatchMake ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Lauren O'Donnell||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| EMSegment BatchMake||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Brad Davis||||EM Segmenter batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Gaussian Blur BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Julien Finet||||Gaussian Blur batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| RegisterImages BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Stephen Aylward, Julien Finet||||Register Images batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleScalarVolume BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Julien Finet||||Resample Volume batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Diffeomorphic Demons Algorithm ||no||no||yes and yes|| style="background:red"| 0.0% || Unknown ||Tom Vercauteren, Ender Konukoglu, Kilian Pohl||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ResampleDTIVolume ||complete||yes and yes||yes and yes|| style="background:red"| 37.0% || 0 ||Francois Budin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristan Vega, Santiago Aja Fernandez, Marc Niethammer||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Unbiased Non Local Means filter for DWI ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja-Fernandez||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Joint Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja Fernández||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Extract Skeleton ||no||yes and no||no and yes|| style="background:red"| 0.0% || Unknown ||Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MRI Bias Field Correction ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Sylvain Jaume||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| N4ITK MRI Bias Correction ||yes||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nick Tustison, Andriy Fedorov||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ACPC Transform ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Mesh Contour Segmentation ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% ||Unknown||Peter Karasev, Karol Chudy, Allen Tannenbaum||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Utah BSpline Deformable registration ||no||yes and no||yes and yes|| style="background:red"| 0.0% ||Unknown||Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Calculate Volume Statistics ||no||no||no|| style="background:red"| 0.0% ||0||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Generate Connectivity Map ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ROI Tract Filter ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Stochastic Tractography Filter ||no||no||no||style="background:red"| 0.0% || Unknown||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MIDAS Data and Slicer Tutorials ||no||yes and no||yes and no|| style="background:red"| 0.0% ||Unknown||Patrick Reynolds, Stephen Aylward||||n/a||
|-
|}

<references/>

= Testing Partition =

Most Slicer modules have a '''GUI component''' and a '''Data Processing''' component.

Testing GUI components is still a challenge, so we will focus here on testing the '''Data Processing''' components. This can be done in most cases by partitioning the module into a GUI section and a Data Processing section, where the second one usually takes the form of a C++ class (although that is not a requirement).

The '''data processing''' section can be tested by using standard CTest/CMake mechanisms. Basically by adding ADD_TEST() entries to the CMakeLists.txt file of the module.

=Luis Ibanez' scoring system=

The following scoring will be applied to the '''data processing''' sections of all modules:

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance Scoring</big>
|-
!Score!!Code Coverage!!Valgrind Errors!!Documentation!!Tutorial
|-
|style="background:gold"| '''1Gold''' || > 80% || 0 ||yes || yes
|-
|style="background:silver"| '''2Silver''' || > 70% || < 10 ||yes || yes
|-
|style="background:darkgoldenrod"| '''3Bronze''' || > 60% || < 50 ||yes || yes
|-
|style="background:darkorange"| '''4Clay''' || > 50% || < 100 ||yes || yes
|-
|style="color:white; background:black"| '''5Coal''' ||style="background:red"|< 50% || > 100 || yes || yes
|-
|style="color:white; background:hotpink"| '''6Hazard''' || unknown || unknown || no || no
|}

The code coverage and Valgrind error must be the ones reported on the Nightly Slicer Dashboard. Anecdotal data is not acceptable.

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:49:02Z

Taox: /* Examples, Use Cases & Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:48:35Z

Taox: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]
This module takes three input: '''Input Volume''' is the reference volume. '''Model''' is the surface model from whose interior is to be labeled as foreground, and '''Output Volume''' is the output label map. Output Volume has the same image parameters (size, resolution, orientation, etc) as Input Volume.

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]
Since surface can be very sparsely triangulated, this module first resample the input surface model in an appropriate resolution. The parameter '''Sample Distance''' controls how fine the surface is sampled. The ballpark value for this parameter is the smallest size of voxels in Input Volume.

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:42:31Z

Taox: /* Examples, Use Cases & Tutorials */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:
<pre>
./PolyDataToLabelmap --distance 1.0
InputReferenceVolume.nrrd
InputSurfaceModel.vtp
OutputLabelMap.nrrd
</pre>

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

File:PolyDataToLabelMap-ParametersPanels-3-6.png

2010-04-30T01:40:30Z

Taox:

File:PolyDatToLabelMap-IOPanels-3-6.png

2010-04-30T01:40:14Z

Taox:

File:PolyDataToLabelMap-ViewingPanelResult-3-6.png

2010-04-30T01:39:46Z

Taox:

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:37:37Z

Taox: /* Module Name */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model overlaid on ref image]]
|[[Image:PolyDataToLabelMap-ViewingPanelResult-3-6.png|thumb|280px|Label map generated from surface]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

File:PolyDataToLabelMap-ViewingPanel-3-6.png

2010-04-30T01:36:25Z

Taox:

File:PolyDataToLabelMap-UI-3-6.png

2010-04-30T01:36:04Z

Taox:

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:27:48Z

Taox: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model and label map]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.cxx?rev=12452&view=log PolyDataToLabelmap.cxx]

XML Description: [http://viewvc.slicer.org/viewcvs.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?rev=9268&view=log PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:25:43Z

Taox: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
__NOTOC__
===Module Name===
PolyData to LabelMap

{|
|[[Image:PolyDataToLabelMap-UI-3-6.png|thumb|280px|GUI panel]]
|[[Image:PolyDataToLabelMap-ViewingPanel-3-6.png|thumb|280px|Surface model and label map]]
|}

== General Information ==
===Module Type & Category===

Type: CLI

Category: Surface Models

===Authors, Collaborators & Contact===
* Author: Xiaodong Tao and Nicole Aucoin
* Contact: taox at research.ge.com

===Module Description===

This module creates a label map of the interior of an input model within a reference volume. The module first label voxels that intersects the surface as foreground, then use a flood fill to label all interior.

== Usage ==

===Examples, Use Cases & Tutorials===

* This module may be thought of as the inverse of Marching Cubes.

* A command line example:

===Quick Tour of Features and Use===
* '''Input/Output panels:'''

[[Image:PolyDatToLabelMap-IOPanels-3-6.png|thumb|right|280px|Input/Output panels]]

* '''Parameters panel:'''
[[Image:PolyDataToLabelMap-ParametersPanels-3-6.png|thumb|right|280px|Parameters Parameters]]

== Development ==

===Dependencies===

This module depends only on the core "Volumes" module of slice for data IO.

===Known bugs===

None.

===Usability issues===

None.

===Source code & documentation===

Source Code: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/PolyDataToLabelMap.cxx?view=annotate PolyDataToLabelmap.cxx]

XML Description: [http://www.na-mic.org/ViewVC/index.cgi/trunk/Applications/CLI/PolyDataToLabelmap.xml?view=co PolyDataToLabelmap.xml]

Test: [http://viewvc.na-mic.org/viewcvs.cgi/trunk/Applications/CLI/Testing/PolyDataToLabelmapTest.cxx?rev=11537&view=log PolyDataToLabelmapTest.cxx]

Usage:
<pre>
./PolyDataToLabelmap --help

USAGE:

./PolyDataToLabelmap [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--distance <float>] [--]
[--version] [-h] <std::string> <std::string>
<std::string>

Where:

--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).

--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (default: 0)

--xml
Produce xml description of command line arguments (default: 0)

--echo
Echo the command line arguments (default: 0)

--distance <float>
Sample distance (default: 1)

--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.

--version
Displays version information and exits.

-h, --help
Displays usage information and exits.

<std::string>
(required) Input volume

<std::string>
(required) Model

<std::string>
(required) The label volume

Description: Intersects an input model with an reference volume and
produces an output label map.

Author(s): Nicole Aucoin BWH, Xiaodong Tao, GE

Acknowledgements: This work is part of the National Alliance for Medical
Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
</pre>

== More Information ==

===Acknowledgment===
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149.
Information on the National Centers for Biomedical Computing
can be obtained from [http://www.ncbcs.org/ National Centers for Biomedical Computing].

===References===

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T01:00:55Z

Taox: /* Quick Tour of Features and Use */

Modules:PolyDatToLabelMap-Documentation-3.6

2010-04-30T00:59:57Z

Taox: Created page with 'Return to Slicer 3.6 Documentation __NOTOC__ ===Module Name=== PolyData to LabelMap {| |GUI panel |[[Im…'

Documentation/3.6

2010-04-30T00:43:29Z

Taox: /* Surface Models */

This is work in progress

=Main GUI=

*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

=Requirements for Modules=
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules added or significantly revised since the 3.4 release=
* Interactive Editor
* Volume Rendering
* Colors (Nicole Aucoin)
* MRI Bias Field Correction (Sylvain Jaume)
* 4D Image (Viewer) (Junichi Tokuda)
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
* Fast Marching segmentation (Andriy Fedorov)
* Mesh Contour Segmentation (Peter Karasev)
* Crop Volume (Subvolume extraction with ROI widget) (Andriy Fedorov)
* Measurements (rulers and angles) (Nicole Aucoin)
* Affine registration (Casey Goodlett)
* Collect Patient Fiducials (Andrew Wiles)
* IGT Tool Selector (Andrew Wiles)
* Fiducials (Nicole Aucoin)
* PETCTFusion (Wendy Plesniak)
* N4 Bias Field Correction (Andriy Fedorov)

=List of Modules=

Please adhere to the naming scheme for the module documentation:
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

==Core==
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:LabelMapEditor-Documentation-3.6| Label Map Editor]] (Steve Pieper) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)

==Wizards==
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)

==Informatics Modules==
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)

==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller)
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu). Belongs to registration, robust
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu) . Belongs to registration robust

*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)

==Segmentation==
*[[Modules:SegmentationOverview3.6|Overview]]
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl)
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).

==Quantification==
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)

==Diffusion MRI==
*Diffusion MRI
** DWI filtering
***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)
***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)
** Diffusion tensor utilities
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
** Resampling
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
** Tractography
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)

==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)

==Time Series==
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)

==Filtering==
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

==Surface Models==
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
*[[Modules:PolyDatToLabelMap-Documentation-3.6| PolyDataToLabelMap]] (Xiaodong Tao, Nicole Aucoin) ('''in progress''')

==Batch processing==
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)

==Converters==
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)

==Endoscopy==
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)

==Developer Tools==
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
*Note: most developer tools are not documented

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search here] to see a listing of Slicer 3 extensions on NITRC.

[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
To add extension modules to an installed binary of slicer:
* Use the View->Extension Manager menu option
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.

*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]

'''Installation'''
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
[[image:Slicertoolbar.png|Extensions Wizard]]

===Listing of plug-ins===

'''Available Extensions'''

* Segmentation
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
* Registration
**Robust
*** [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''.
*** [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''.
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''.
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''.
* Wizards
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''.
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''.
** [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''.
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
* Tractography
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
* DWI
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''.
* Time Series
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
* Statistics
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''.
* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins

:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models

:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

'''Non-SPL Supported Compatibility Packages'''

* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''

=QA=
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

Slicer-3.6-QA

2010-04-29T19:43:36Z

Taox: /* Application CLI Modules */

[[Documentation-3.6|Return to Slicer 3.6 documentation]]

*This page contains our assessment of the Slicer 3.6 modules

*See also the [http://wiki.na-mic.org/Wiki/index.php/2010_Slicer36_Module_Cull module culling event] at the end of April 2010

= Testing Status =

== Core Modules ==

{|class="wikitable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Current Owner
|-
|style="background:white"|??||style="width:33%"| Camera ||complete||yes, no link||no|| Sebastien Barre
|-
|style="background:white"|??||style="width:33%"| Welcome ||complete||yes and yes||yes and yes ||Wendy Plesniak
|-
|style="background:white"|??||style="width:33%"| Volumes ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Diffusion Editor ||complete||yes and yes||no|| CF Westin
|-
|style="background:white"|??||style="width:33%"| Models ||complete||yes and yes||yes and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Measurements ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Fiducials||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Data ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Slices ||complete||yes and yes||yes and yes|| Jim Miller
|-
|style="background:white"|??||style="width:33%"| Colors ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Interactive Editor ||complete||no and yes ||yes and no || Steve Pieper
|-
|style="background:white"|??||style="width:33%"| ROI Module ||complete||no and yes||no and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Volume Rendering ||complete||yes and yes||no and yes|| Yanling Liu
|-
|style="background:white"|??||style="width:33%"| PET/CT Fusion ||complete||yes and yes||yes and yes|| Wendy Plesniak
|-
|}
<references/>

== Application CLI Modules ==

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Test coverage <ref>in % for non-interactive part</ref>!!valgrind errors!!Current Owner!!Comments <ref>Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files</ref>!!3.6 Documentation Name <ref>http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6</ref>
|-
|style="background:gold"|1Gold||style="width:33%"|my module||complete||yes and yes||yes, yes, yes||80%||0|| ||||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionWeightedTest ||no||no||yes and yes|| 69.8% || 0||CF Westin||||n/a||
|-
|style="background:silver"|2Silver||style="width:33%"| DiffusionTensorEstimation || complete ||yes and no||yes and yes|| 79.7% || 9 ||CF Westin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorMathematics ||no||yes and no||yes and yes|| 56.2% || 5||CF Westin||||Diffusion Tensor Scalar Measurements||
|-
|style="background:gold"|1Gold||style="width:33%"| OrientImage ||complete||yes and yes||yes and yes|| 85.7% || 0 ||Bill Lorensen||||OrientImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| LinearRegistration ||complete||yes and no||yes and yes|| 66.7% || 4 ||Daniel Blezek||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| RigidRegistration ||complete||yes and yes||yes and yes||style="background:red"| 1.0% || 92 ||Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| RegisterImages (RegisterImagesMultiRes) ||complete||yes and yes||yes and yes|| 83.5% || Unknown || Casey Goodlett, Stephen Aylward||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Fast Affine Registration ||complete||yes and no||yes and yes||style="background:red" |1.4% || 82 || Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| BSplineDeformableRegistration ||complete||yes and yes||yes and yes|| 82.3% || 6 || Bill Lorensen||||Fast Nonrigid BSpline Registration||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| TestGridTransformRegistration ||no||no||yes and yes || 90.7% || 0 ||Yinglin Lee||||n/a||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CheckerBoard ||complete||yes and yes||yes and yes|| 67.4% || 0 ||Bill Lorensen||||CheckerBoard Filter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ResampleVolume ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| PolyDataToLabelmap ||no||yes and yes||yes and yes|| 87.9% || 0 ||Nicole Aucoin, Xiaodong Tao||||n/a||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GaussianBlurImageFilter ||complete||yes and no||yes and yes|| 55.9% || 0 ||Julien Jomier, Stephen Aylward||||Gaussian Blur||
|-
|style="background:gold"|1Gold||style="width:33%"| ConfidenceConnected||complete||yes and no||yes and yes|| 87.5% || 0 ||Jim Miller||||Simple region growing||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ExecutionModelTour ||no||yes and yes||yes and yes|| 87.2% || 0 ||Daniel Blezek, Bill Lorensen||||n/a||
|-
|style="background:gold"|1Gold||style="width:33%"| ImageReadDicomWrite ||complete||yes and yes||yes and yes|| 86.1% || 0 ||Bill Lorensen||||Create a Dicom Series||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CurvatureAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 64.3% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GradientAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 63.4% || 0 ||Bill Lorensen||||GradientAnisotropicFilter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| MedianImageFilter ||complete||yes and yes||yes and yes|| 51.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| HistogramMatching ||complete||yes and yes||yes and yes|| 65.0% || 0 ||Bill Lorensen||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| OtsuThresholdImageFilter ||no||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||OtsuThreshold||
|-
|style="background:gold"|1Gold||style="width:33%"| OtsuThresholdSegmentation ||complete||yes and no||yes and yes|| 90.9% || 0 ||Bill Lorensen||||same||
|-
|style="background:silver"|2Silver||style="width:33%"| Subtract ||complete||yes and yes||yes and yes|| 71.7% || 0 ||Bill Lorensen||||SubtractImages||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Multiply ||yes||yes and yes||yes and yes|| 77.6% || 0 ||Bill Lorensen||||MultiplyImages||
|-
|style="background:gold"|1Gold||style="width:33%"| Add ||complete||yes and yes||yes and yes|| 84.9% || 0 ||Bill Lorensen||||AddImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| Threshold ||complete||yes and yes||yes and yes|| 55.8% || 0 ||Nicole Aucoin||||ThresholdImage||
|-
|style="background:gold"|1Gold||style="width:33%"| Mask ||complete||yes and yes||yes and yes|| 80.0% || 0 ||Nicole Aucoin||||Mask Image||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Cast ||complete||yes and yes||yes and yes||style="background:red"| 14.6% || 0 ||Nicole Aucoin||||Cast Image||
|-
|style="background:gold"|1Gold||style="width:33%"| VotingBinaryHoleFillingImageFilter ||complete||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||Voting Binary Hole Filling||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ModelMaker ||complete||yes and yes||yes and yes|| 57.4% || 1 ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MultipleModelsExample ||no||yes and no||yes and yes||style="background:red"| 1.9%|| 50 ||Bill Lorensen||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| GrayscaleModelMaker ||no||yes and no||yes and yes|| 82.1% || 1 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| MergeModels ||yes||yes and yes||yes and yes|| 62.7% || 0 ||Nicole Aucoin, Daniel Haehn||||same||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GrayscaleFillHoleImageFilter ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||Grayscale Fill Hole||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GrayscaleGrindPeakImageFilter ||complete||yes and yes||yes and yes|| 64.5% || 0 ||Bill Lorensen||||Grayscale Grind Peak||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| LabelMapSmoothing ||no||yes and no||yes and yes|| 87.9% || 0 ||Dirk Padfield, Josh Cates, Ross Whitaker||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ImageLabelCombine ||complete||yes and no||yes and no||style="background:red"| 7.5% || 50 ||Alex Yarmarkovich||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleVolume2 ||no||yes and yes||yes and yes||style="background:red"| 46.8% || 0 ||Francois Budin||||Resample Scalar/Vector/DWI Volume||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ZeroCrossingBasedEdgeDetectionImageFilter ||no||yes and no||yes and yes|| 62.5%|| 0 || Elliot Uvero||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| FreesurferSurfaceSectionExtraction ||no||yes and no||yes and yes|| 60.0% || 62 || Sylvain Bouix||||n/a/||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSDemonWarp ||complete||yes and no||yes and no|| style="background:red"| 0.0% || Unknown ||Hans Johnson, Greg Harris ||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSFit ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unkown || Eun Young Kim||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSMush ||complete||no||no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSResample ||no||yes and yes||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSROIAuto ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorEstimation BatchMake ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Lauren O'Donnell||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| EMSegment BatchMake||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Brad Davis||||EM Segmenter batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Gaussian Blur BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Julien Finet||||Gaussian Blur batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| RegisterImages BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Stephen Aylward, Julien Finet||||Register Images batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleScalarVolume BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Julien Finet||||Resample Volume batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Diffeomorphic Demons Algorithm ||no||no||yes and yes|| style="background:red"| 0.0% || Unknown ||Tom Vercauteren, Ender Konukoglu, Kilian Pohl||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ResampleDTIVolume ||complete||yes and yes||yes and yes|| style="background:red"| 37.0% || 0 ||Francois Budin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristan Vega, Santiago Aja Fernandez, Marc Niethammer||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Unbiased Non Local Means filter for DWI ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja-Fernandez||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Joint Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja Fernández||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Extract Skeleton ||no||yes and no||no and yes|| style="background:red"| 0.0% || Unknown ||Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MRI Bias Field Correction ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Sylvain Jaume||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| N4ITK MRI Bias Correction ||yes||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nick Tustison, Andriy Fedorov||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ACPC Transform ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Mesh Contour Segmentation ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% ||Unknown||Peter Karasev, Karol Chudy, Allen Tannenbaum||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Utah BSpline Deformable registration ||no||yes and no||yes and yes|| style="background:red"| 0.0% ||Unknown||Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Calculate Volume Statistics ||no||no||no|| style="background:red"| 0.0% ||0||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Generate Connectivity Map ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ROI Tract Filter ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Stochastic Tractography Filter ||no||no||no||style="background:red"| 0.0% || Unknown||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MIDAS Data and Slicer Tutorials ||no||yes and no||yes and no|| style="background:red"| 0.0% ||Unknown||Patrick Reynolds, Stephen Aylward||||n/a||
|-
|}

<references/>

= Testing Partition =

Most Slicer modules have a '''GUI component''' and a '''Data Processing''' component.

Testing GUI components is still a challenge, so we will focus here on testing the '''Data Processing''' components. This can be done in most cases by partitioning the module into a GUI section and a Data Processing section, where the second one usually takes the form of a C++ class (although that is not a requirement).

The '''data processing''' section can be tested by using standard CTest/CMake mechanisms. Basically by adding ADD_TEST() entries to the CMakeLists.txt file of the module.

=Luis Ibanez' scoring system=

The following scoring will be applied to the '''data processing''' sections of all modules:

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance Scoring</big>
|-
!Score!!Code Coverage!!Valgrind Errors!!Documentation!!Tutorial
|-
|style="background:gold"| '''1Gold''' || > 80% || 0 ||yes || yes
|-
|style="background:silver"| '''2Silver''' || > 70% || < 10 ||yes || yes
|-
|style="background:darkgoldenrod"| '''3Bronze''' || > 60% || < 50 ||yes || yes
|-
|style="background:darkorange"| '''4Clay''' || > 50% || < 100 ||yes || yes
|-
|style="color:white; background:black"| '''5Coal''' ||style="background:red"|< 50% || > 100 || yes || yes
|-
|style="color:white; background:hotpink"| '''6Hazard''' || unknown || unknown || no || no
|}

The code coverage and Valgrind error must be the ones reported on the Nightly Slicer Dashboard. Anecdotal data is not acceptable.

Slicer-3.6-QA

2010-04-29T19:41:53Z

Taox: /* Application CLI Modules */

[[Documentation-3.6|Return to Slicer 3.6 documentation]]

*This page contains our assessment of the Slicer 3.6 modules

*See also the [http://wiki.na-mic.org/Wiki/index.php/2010_Slicer36_Module_Cull module culling event] at the end of April 2010

= Testing Status =

== Core Modules ==

{|class="wikitable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Current Owner
|-
|style="background:white"|??||style="width:33%"| Camera ||complete||yes, no link||no|| Sebastien Barre
|-
|style="background:white"|??||style="width:33%"| Welcome ||complete||yes and yes||yes and yes ||Wendy Plesniak
|-
|style="background:white"|??||style="width:33%"| Volumes ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Diffusion Editor ||complete||yes and yes||no|| CF Westin
|-
|style="background:white"|??||style="width:33%"| Models ||complete||yes and yes||yes and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Measurements ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Fiducials||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Data ||complete||yes and yes||yes and yes ||Steve Pieper
|-
|style="background:white"|??||style="width:33%"| Slices ||complete||yes and yes||yes and yes|| Jim Miller
|-
|style="background:white"|??||style="width:33%"| Colors ||complete||yes and yes||yes and yes|| Nicole Aucoin
|-
|style="background:white"|??||style="width:33%"| Interactive Editor ||complete||no and yes ||yes and no || Steve Pieper
|-
|style="background:white"|??||style="width:33%"| ROI Module ||complete||no and yes||no and yes|| Alex Yarmarkovich
|-
|style="background:white"|??||style="width:33%"| Volume Rendering ||complete||yes and yes||no and yes|| Yanling Liu
|-
|style="background:white"|??||style="width:33%"| PET/CT Fusion ||complete||yes and yes||yes and yes|| Wendy Plesniak
|-
|}
<references/>

== Application CLI Modules ==

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance</big>
|-
!Score!!Name!!Documentation!!Help <ref>including link to website documentation</ref>!!Acknowledgment <ref>including name of author and of supervisor</ref> !!Test coverage <ref>in % for non-interactive part</ref>!!valgrind errors!!Current Owner!!Comments <ref>Test coverage percentage determined by: [# lines code covered / total # lines of code (covered and non-covered) *100] of relevant .cxx and .h files</ref>!!3.6 Documentation Name <ref>http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.6</ref>
|-
|style="background:gold"|1Gold||style="width:33%"|my module||complete||yes and yes||yes, yes, yes||80%||0|| ||||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionWeightedTest ||no||no||yes and yes|| 69.8% || 0||CF Westin||||n/a||
|-
|style="background:silver"|2Silver||style="width:33%"| DiffusionTensorEstimation || complete ||yes and no||yes and yes|| 79.7% || 9 ||CF Westin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorMathematics ||no||yes and no||yes and yes|| 56.2% || 5||CF Westin||||Diffusion Tensor Scalar Measurements||
|-
|style="background:gold"|1Gold||style="width:33%"| OrientImage ||complete||yes and yes||yes and yes|| 85.7% || 0 ||Bill Lorensen||||OrientImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| LinearRegistration ||complete||yes and no||yes and yes|| 66.7% || 4 ||Daniel Blezek||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| RigidRegistration ||complete||yes and yes||yes and yes||style="background:red"| 1.0% || 92 ||Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| RegisterImages (RegisterImagesMultiRes) ||complete||yes and yes||yes and yes|| 83.5% || Unknown || Casey Goodlett, Stephen Aylward||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Fast Affine Registration ||complete||yes and no||yes and yes||style="background:red" |1.4% || 82 || Daniel Blezek||||same||
|-
|style="background:gold"|1Gold||style="width:33%"| BSplineDeformableRegistration ||complete||yes and yes||yes and yes|| 82.3% || 6 || Bill Lorensen||||Fast Nonrigid BSpline Registration||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| TestGridTransformRegistration ||no||no||yes and yes || 90.7% || 0 ||Yinglin Lee||||n/a||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CheckerBoard ||complete||yes and yes||yes and yes|| 67.4% || 0 ||Bill Lorensen||||CheckerBoard Filter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ResampleVolume ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| PolyDataToLabelmap ||no||yes and yes||yes and yes|| 87.9% || 0 ||Nicole Aucoin, Xiaodong Tao||||n/a||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GaussianBlurImageFilter ||complete||yes and no||yes and yes|| 55.9% || 0 ||Julien Jomier, Stephen Aylward||||Gaussian Blur||
|-
|style="background:gold"|1Gold||style="width:33%"| ConfidenceConnected||complete||yes and no||yes and yes|| 87.5% || 0 ||Jim Miller||||Simple region growing||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ExecutionModelTour ||no||yes and yes||yes and yes|| 87.2% || 0 ||Daniel Blezek, Bill Lorensen||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ImageReadDicomWrite ||yes||yes and yes||yes and yes|| 86.1% || 0 ||Bill Lorensen||||Create a Dicom Series||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| CurvatureAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 64.3% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GradientAnisotropicDiffusion ||complete||yes and yes||yes and yes|| 63.4% || 0 ||Bill Lorensen||||GradientAnisotropicFilter||
|-
|style="background:darkorange"|4Clay||style="width:33%"| MedianImageFilter ||complete||yes and yes||yes and yes|| 51.1% || 0 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| HistogramMatching ||complete||yes and yes||yes and yes|| 65.0% || 0 ||Bill Lorensen||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| OtsuThresholdImageFilter ||no||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||OtsuThreshold||
|-
|style="background:gold"|1Gold||style="width:33%"| OtsuThresholdSegmentation ||complete||yes and no||yes and yes|| 90.9% || 0 ||Bill Lorensen||||same||
|-
|style="background:silver"|2Silver||style="width:33%"| Subtract ||complete||yes and yes||yes and yes|| 71.7% || 0 ||Bill Lorensen||||SubtractImages||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Multiply ||yes||yes and yes||yes and yes|| 77.6% || 0 ||Bill Lorensen||||MultiplyImages||
|-
|style="background:gold"|1Gold||style="width:33%"| Add ||complete||yes and yes||yes and yes|| 84.9% || 0 ||Bill Lorensen||||AddImages||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| Threshold ||complete||yes and yes||yes and yes|| 55.8% || 0 ||Nicole Aucoin||||ThresholdImage||
|-
|style="background:gold"|1Gold||style="width:33%"| Mask ||complete||yes and yes||yes and yes|| 80.0% || 0 ||Nicole Aucoin||||Mask Image||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| Cast ||complete||yes and yes||yes and yes||style="background:red"| 14.6% || 0 ||Nicole Aucoin||||Cast Image||
|-
|style="background:gold"|1Gold||style="width:33%"| VotingBinaryHoleFillingImageFilter ||complete||yes and yes||yes and yes|| 100% || 0 ||Bill Lorensen||||Voting Binary Hole Filling||
|-
|style="background:darkorange"|4Clay||style="width:33%"| ModelMaker ||complete||yes and yes||yes and yes|| 57.4% || 1 ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MultipleModelsExample ||no||yes and no||yes and yes||style="background:red"| 1.9%|| 50 ||Bill Lorensen||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| GrayscaleModelMaker ||no||yes and no||yes and yes|| 82.1% || 1 ||Bill Lorensen||||same||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| MergeModels ||yes||yes and yes||yes and yes|| 62.7% || 0 ||Nicole Aucoin, Daniel Haehn||||same||
|-
|style="background:darkorange"|4Clay||style="width:33%"| GrayscaleFillHoleImageFilter ||complete||yes and yes||yes and yes|| 57.1% || 0 ||Bill Lorensen||||Grayscale Fill Hole||
|-
|style="background:darkgoldenrod"|3Bronze||style="width:33%"| GrayscaleGrindPeakImageFilter ||complete||yes and yes||yes and yes|| 64.5% || 0 ||Bill Lorensen||||Grayscale Grind Peak||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| LabelMapSmoothing ||no||yes and no||yes and yes|| 87.9% || 0 ||Dirk Padfield, Josh Cates, Ross Whitaker||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ImageLabelCombine ||complete||yes and no||yes and no||style="background:red"| 7.5% || 50 ||Alex Yarmarkovich||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleVolume2 ||no||yes and yes||yes and yes||style="background:red"| 46.8% || 0 ||Francois Budin||||Resample Scalar/Vector/DWI Volume||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ZeroCrossingBasedEdgeDetectionImageFilter ||no||yes and no||yes and yes|| 62.5%|| 0 || Elliot Uvero||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| FreesurferSurfaceSectionExtraction ||no||yes and no||yes and yes|| 60.0% || 62 || Sylvain Bouix||||n/a/||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSDemonWarp ||complete||yes and no||yes and no|| style="background:red"| 0.0% || Unknown ||Hans Johnson, Greg Harris ||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSFit ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unkown || Eun Young Kim||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSMush ||complete||no||no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSResample ||no||yes and yes||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| BRAINSROIAuto ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Hans Johnson||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| DiffusionTensorEstimation BatchMake ||no||yes and no||yes and no|| style="background:red"| 0.0% || Unknown || Lauren O'Donnell||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| EMSegment BatchMake||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Brad Davis||||EM Segmenter batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Gaussian Blur BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown || Julien Jomier, Stephen Aylward, Julien Finet||||Gaussian Blur batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| RegisterImages BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Stephen Aylward, Julien Finet||||Register Images batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ResampleScalarVolume BatchMake ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Julien Finet||||Resample Volume batch||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Diffeomorphic Demons Algorithm ||no||no||yes and yes|| style="background:red"| 0.0% || Unknown ||Tom Vercauteren, Ender Konukoglu, Kilian Pohl||||n/a||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| ResampleDTIVolume ||complete||yes and yes||yes and yes|| style="background:red"| 37.0% || 0 ||Francois Budin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristan Vega, Santiago Aja Fernandez, Marc Niethammer||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Unbiased Non Local Means filter for DWI ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja-Fernandez||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Joint Rician LMMSE Image Filter ||complete||yes and no||yes and yes|| style="background:red"| 0.0% || Unknown ||Antonio Tristán Vega, Santiago Aja Fernández||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Extract Skeleton ||no||yes and no||no and yes|| style="background:red"| 0.0% || Unknown ||Pierre Seroul, Martin Styner, Guido Gerig, Stephen Aylward||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MRI Bias Field Correction ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Sylvain Jaume||||same||
|-
|style="color:white; background:black"|5Coal||style="width:33%"| N4ITK MRI Bias Correction ||yes||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nick Tustison, Andriy Fedorov||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ACPC Transform ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% || Unknown ||Nicole Aucoin||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Mesh Contour Segmentation ||complete||yes and yes||yes and yes|| style="background:red"| 0.0% ||Unknown||Peter Karasev, Karol Chudy, Allen Tannenbaum||||same||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Utah BSpline Deformable registration ||no||yes and no||yes and yes|| style="background:red"| 0.0% ||Unknown||Sam Gerber, Jim Miller, Steve Pieper, Ross Whitaker||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Calculate Volume Statistics ||no||no||no|| style="background:red"| 0.0% ||0||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Generate Connectivity Map ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| ROI Tract Filter ||no||no||no||style="background:red"| 0.0% || Unknown ||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| Stochastic Tractography Filter ||no||no||no||style="background:red"| 0.0% || Unknown||Tri Ngo||||n/a||
|-
|style="background:hotpink"|6Hazard||style="width:33%"| MIDAS Data and Slicer Tutorials ||no||yes and no||yes and no|| style="background:red"| 0.0% ||Unknown||Patrick Reynolds, Stephen Aylward||||n/a||
|-
|}

<references/>

= Testing Partition =

Most Slicer modules have a '''GUI component''' and a '''Data Processing''' component.

Testing GUI components is still a challenge, so we will focus here on testing the '''Data Processing''' components. This can be done in most cases by partitioning the module into a GUI section and a Data Processing section, where the second one usually takes the form of a C++ class (although that is not a requirement).

The '''data processing''' section can be tested by using standard CTest/CMake mechanisms. Basically by adding ADD_TEST() entries to the CMakeLists.txt file of the module.

=Luis Ibanez' scoring system=

The following scoring will be applied to the '''data processing''' sections of all modules:

{|class="wikitable sortable labelpage labelpagetable" border="1" style="text-align:center"
|+ <big>Slicer 3.6 Quality Assurance Scoring</big>
|-
!Score!!Code Coverage!!Valgrind Errors!!Documentation!!Tutorial
|-
|style="background:gold"| '''1Gold''' || > 80% || 0 ||yes || yes
|-
|style="background:silver"| '''2Silver''' || > 70% || < 10 ||yes || yes
|-
|style="background:darkgoldenrod"| '''3Bronze''' || > 60% || < 50 ||yes || yes
|-
|style="background:darkorange"| '''4Clay''' || > 50% || < 100 ||yes || yes
|-
|style="color:white; background:black"| '''5Coal''' ||style="background:red"|< 50% || > 100 || yes || yes
|-
|style="color:white; background:hotpink"| '''6Hazard''' || unknown || unknown || no || no
|}

The code coverage and Valgrind error must be the ones reported on the Nightly Slicer Dashboard. Anecdotal data is not acceptable.