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2024-03-28T22:28:18Z
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https://www.slicer.org/w/index.php?title=Slicer3:3.6_Final_Issues&diff=17586
Slicer3:3.6 Final Issues
2010-08-24T17:05:26Z
<p>Hayes: </p>
<hr />
<div>==Issues to include in 3.6.2 patch release==<br />
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927], [http://na-mic.org/Mantis/view.php?id=929 929], [http://na-mic.org/Mantis/view.php?id=936 936]<br />
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928]<br />
* Cannot change the window/level on color-by-orientation dti volumes (Alexy - may not be included in 3.6.1 Not a trivial fix the pipeline of DTIVolumeDisplay node needs to be modified to deal both with scalars and vectors. I suggest leaving out of the patch. Alex).<br />
* Diffusion Tensor Glyphs not showing (Demian)<br />
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)<br />
* VTK GPU Ray Cast flashing (Julien)<br />
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840<br />
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)<br />
* Ron's requested changes to the volume rendering transfer function (email from 8/20): 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. <br />
<br />
<br />
Fixed for 3.6.2<br />
<br />
==Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==<br />
<br />
* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)<br />
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925<br />
* 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). <br />
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)<br />
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)<br />
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)<br />
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)<br />
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]<br />
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)<br />
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]<br />
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.<br />
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)<br />
* 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.<br />
* "Change island" effect of Editor is not functioning when the Scope is set to "all"<br />
* 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]<br />
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851<br />
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch<br />
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch<br />
* 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)<br />
* 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)<br />
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]<br />
* EMSegment command line works now with BRAINS (Kilian)<br />
* Removed KWWidgets that do not work under Windows (Kilian)<br />
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)<br />
* 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])<br />
<br />
<br />
==3.6 Release issues==<br />
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:<br />
<br />
'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]''' <br />
<br />
*VTK GPU ray-cast clipping issue<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]<br />
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]<br />
**90% of the flickering when the camera is inside the volume is removed<br />
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)<br />
<br />
*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).<br />
<br />
Done:<br />
* Remove unused color and glyph options from fiber bundle display (Alex)<br />
* fiducial behavior<br />
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)<br />
** 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)<br />
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch<br />
** 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)<br />
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])<br />
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!<br />
** done for 2d, Andras has tested it and says it's fine<br />
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)<br />
*getting BRAINS tests to pass (Hans is working on it)<br />
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).<br />
* 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''<br />
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''<br />
** 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''<br />
* 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)<br />
* 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! <br />
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:<br />
**for Output DTI volume: DTI Volume<br />
**for Output Baseline Volume: Baseline DTI Volume<br />
**for Otsu Threshold Mask: Otsu Threshold Label Volume<br />
*new default color table (Nicole and Mike)<br />
** 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<br />
** Steve and Nicole to meet June 9 to integrate default editor color table<br />
** 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.<br />
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)<br />
<br />
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]].</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:Builds&diff=17305
Slicer3:Builds
2010-07-27T19:09:41Z
<p>Hayes: </p>
<hr />
<div>Our nightly builds are compiled in Release mode using the following compilers and platforms. <br />
<br />
The --upload flag sends the binary by scp to the server "namic1" into the /clients/Slicer3/WWW/Downloads/Nightly directory. The extend.tcl script is called from getbuildtest.tcl when the --extend or --extend-upload flag is used, and the extensions are uploaded to the machine ext.slicer.org. You can view the extensions by going to http://ext.slicer.org/ext.<br />
<br />
Builds are manually moved from the /clients/Slicer3/WWW/Downloads/Nightly directory to the <br />
/clients/Slicer3/WWW/Downloads/Snapshots/platform or the /clients/Slicer3/WWW/Downloads/Release/platform directory as needed.<br />
<br />
* Windows:<br />
<br />
Windows XP Professional Version 5.1.2600 Service Pack 2 Build 2600<br />
<br />
Microsoft Visual Studio .NET 2003<br />
<br />
The machine we are using is "wintest", and the path to the nightly build directory is C:\Slicer3<br />
<br />
<br />
* Mac (Intel):<br />
<br />
Darwin 8.11.1 Darwin Kernel Version 8.11.1 root:xnu-792.25.20~1/RELEASE_I386 i386 i386<br />
<br />
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5341)<br />
<br />
The machine we are using is "lefty", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
<br />
<br />
* Mac (PPC):<br />
<br />
Darwin 8.7.0 Darwin Kernel Version 8.7.0 root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc<br />
<br />
powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5367)<br />
<br />
The machine we are using is "slicerm", and the path to the nightly build directory is ~slicer/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
We are no longer supporting PPC Mac, but will make custom builds for people as necessary.<br />
<br />
<br />
* Linux (32-bit):<br />
<br />
Ubuntu 8.10<br />
<br />
Linux 2.6.27-7-generic #1 SMP i686 GNU/Linux<br />
<br />
gcc (GCC) 4.3.2<br />
<br />
The machine we are using is the "ubuntu-8.10" virtual machine on spl-t74-4. The virtual machine manager can be run on this host using the command "virt-manager"<br />
<br />
The server ext.slicer.org hangs when 32-bit Linux machines try to submit to it, so we are not uploading extensions until we have a new extension server.<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload<br />
<br />
<br />
* Linux (64-bit):<br />
<br />
Red Hat Enterprise Linux WS release 4 (Nahant)<br />
<br />
Linux 2.6.9-5.ELsmp #1 SMP x86_64 x86_64 x86_64 GNU/Linux<br />
<br />
gcc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)<br />
<br />
The machine we are using is "slicerl", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:Builds&diff=17273
Slicer3:Builds
2010-07-23T17:56:51Z
<p>Hayes: </p>
<hr />
<div>Our nightly builds are compiled in Release mode using the following compilers and platforms. The --upload flag sends the binary by scp to the server "namic1" into the /clients/Slicer3/WWW/Downloads/Nightly directory. The extend.tcl script is called from getbuildtest.tcl when the --extend or --extend-upload flag is used, and the extensions are uploaded to the machine ext.slicer.org. You can view the extensions by going to http://ext.slicer.org/ext.<br />
<br />
<br />
* Windows:<br />
<br />
Windows XP Professional Version 5.1.2600 Service Pack 2 Build 2600<br />
<br />
Microsoft Visual Studio .NET 2003<br />
<br />
The machine we are using is "wintest", and the path to the nightly build directory is C:\Slicer3<br />
<br />
<br />
* Mac (Intel):<br />
<br />
Darwin 8.11.1 Darwin Kernel Version 8.11.1 root:xnu-792.25.20~1/RELEASE_I386 i386 i386<br />
<br />
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5341)<br />
<br />
The machine we are using is "lefty", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
<br />
<br />
* Mac (PPC):<br />
<br />
Darwin 8.7.0 Darwin Kernel Version 8.7.0 root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc<br />
<br />
powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5367)<br />
<br />
The machine we are using is "slicerm", and the path to the nightly build directory is ~slicer/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
We are no longer supporting PPC Mac, but will make custom builds for people as necessary.<br />
<br />
<br />
* Linux (32-bit):<br />
<br />
Ubuntu 8.10<br />
<br />
Linux 2.6.27-7-generic #1 SMP i686 GNU/Linux<br />
<br />
gcc (GCC) 4.3.2<br />
<br />
The machine we are using is the "ubuntu-8.10" virtual machine on spl-t74-4. The virtual machine manager can be run on this host using the command "virt-manager"<br />
<br />
The server ext.slicer.org hangs when 32-bit Linux machines try to submit to it, so we are not uploading extensions until we have a new extension server.<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload<br />
<br />
<br />
* Linux (64-bit):<br />
<br />
Red Hat Enterprise Linux WS release 4 (Nahant)<br />
<br />
Linux 2.6.9-5.ELsmp #1 SMP x86_64 x86_64 x86_64 GNU/Linux<br />
<br />
gcc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)<br />
<br />
The machine we are using is "slicerl", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:Builds&diff=17272
Slicer3:Builds
2010-07-23T15:05:22Z
<p>Hayes: </p>
<hr />
<div>Our nightly builds are compiled in Release mode using the following compilers and platforms. The extend.tcl script is called from getbuildtest.tcl when the --extend or --extend-upload flag is used, and the extensions are uploaded to the machine ext.slicer.org. You can view the extensions by going to http://ext.slicer.org/ext.<br />
<br />
<br />
* Windows:<br />
<br />
Windows XP Professional Version 5.1.2600 Service Pack 2 Build 2600<br />
<br />
Microsoft Visual Studio .NET 2003<br />
<br />
The machine we are using is "wintest", and the path to the nightly build directory is C:\Slicer3<br />
<br />
<br />
* Mac (Intel):<br />
<br />
Darwin 8.11.1 Darwin Kernel Version 8.11.1 root:xnu-792.25.20~1/RELEASE_I386 i386 i386<br />
<br />
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5341)<br />
<br />
The machine we are using is "lefty", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
<br />
<br />
* Mac (PPC):<br />
<br />
Darwin 8.7.0 Darwin Kernel Version 8.7.0 root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc<br />
<br />
powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5367)<br />
<br />
The machine we are using is "slicerm", and the path to the nightly build directory is ~slicer/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
We are no longer supporting PPC Mac, but will make custom builds for people as necessary.<br />
<br />
<br />
* Linux (32-bit):<br />
<br />
Ubuntu 8.10<br />
<br />
Linux 2.6.27-7-generic #1 SMP i686 GNU/Linux<br />
<br />
gcc (GCC) 4.3.2<br />
<br />
The machine we are using is the "ubuntu-8.10" virtual machine on spl-t74-4. The virtual machine manager can be run on this host using the command "virt-manager"<br />
<br />
The server ext.slicer.org hangs when 32-bit Linux machines try to submit to it, so we are not uploading extensions until we have a new extension server.<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload<br />
<br />
<br />
* Linux (64-bit):<br />
<br />
Red Hat Enterprise Linux WS release 4 (Nahant)<br />
<br />
Linux 2.6.9-5.ELsmp #1 SMP x86_64 x86_64 x86_64 GNU/Linux<br />
<br />
gcc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)<br />
<br />
The machine we are using is "slicerl", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:Builds&diff=17271
Slicer3:Builds
2010-07-23T15:05:02Z
<p>Hayes: </p>
<hr />
<div>Our nightly builds are compiled in Release mode using the following compilers and platforms. The extend.tcl script is called from getbuildtest.tcl when the --extend or --extend-upload flag is used, and the extensions are uploaded to the machine ext.slicer.org. You can view the extensions by going to http://ext.slicer.org/ext.<br />
<br />
<br />
* Windows:<br />
<br />
Windows XP Professional Version 5.1.2600 Service Pack 2 Build 2600<br />
<br />
Microsoft Visual Studio .NET 2003<br />
<br />
The machine we are using is "wintest", and the path to the nightly build directory is C:\Slicer3<br />
<br />
<br />
* Mac (Intel):<br />
<br />
Darwin 8.11.1 Darwin Kernel Version 8.11.1 root:xnu-792.25.20~1/RELEASE_I386 i386 i386<br />
<br />
i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5341)<br />
<br />
The machine we are using is "lefty", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
<br />
* Mac (PPC):<br />
<br />
Darwin 8.7.0 Darwin Kernel Version 8.7.0 root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc<br />
<br />
powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc. build 5367)<br />
<br />
The machine we are using is "slicerm", and the path to the nightly build directory is ~slicer/Slicer3-release-gbt/Slicer3<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload<br />
We are no longer supporting PPC Mac, but will make custom builds for people as necessary.<br />
<br />
* Linux (32-bit):<br />
<br />
Ubuntu 8.10<br />
<br />
Linux 2.6.27-7-generic #1 SMP i686 GNU/Linux<br />
<br />
gcc (GCC) 4.3.2<br />
<br />
The machine we are using is the "ubuntu-8.10" virtual machine on spl-t74-4. The virtual machine manager can be run on this host using the command "virt-manager"<br />
<br />
The server ext.slicer.org hangs when 32-bit Linux machines try to submit to it, so we are not uploading extensions until we have a new extension server.<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload<br />
<br />
* Linux (64-bit):<br />
<br />
Red Hat Enterprise Linux WS release 4 (Nahant)<br />
<br />
Linux 2.6.9-5.ELsmp #1 SMP x86_64 x86_64 x86_64 GNU/Linux<br />
<br />
gcc (GCC) 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)<br />
<br />
The machine we are using is "slicerl", and the path to the nightly build directory is ~hayes/Slicer3-release-gbt<br />
<br />
The command for building the nightly is Slicer3/Scripts/getbuildtest.tcl -t "" --update --release --pack --upload --extend-upload</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=17153
Documentation-3.6:ExtensionStatus
2010-07-09T17:53:04Z
<p>Hayes: </p>
<hr />
<div> [[Documentation-3.6#Slicer_Extensions|Back to Documentation for Slicer 3.6]]<br />
<br />
Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
!style="background:silver" align="left" | ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Segmentation: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
|OK <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
| OK<br />
| OK<br />
| OK<br />
|-<br />
!style="background:silver" align="left"| ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=17071
Documentation-3.6:ExtensionStatus
2010-06-24T17:25:03Z
<p>Hayes: </p>
<hr />
<div> [[Documentation-3.6#Slicer_Extensions|Back to Documentation for Slicer 3.6]]<br />
<br />
Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
!style="background:silver" align="left" | ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Segmentation: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=17070
Documentation-3.6:ExtensionStatus
2010-06-24T17:19:08Z
<p>Hayes: </p>
<hr />
<div> [[Documentation-3.6#Slicer_Extensions|Back to Documentation for Slicer 3.6]]<br />
<br />
Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
!style="background:silver" align="left" | ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Segmentation: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|OK <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=17068
Documentation-3.6:ExtensionStatus
2010-06-24T17:12:24Z
<p>Hayes: </p>
<hr />
<div> [[Documentation-3.6#Slicer_Extensions|Back to Documentation for Slicer 3.6]]<br />
<br />
Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
!style="background:silver" align="left" | ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Segmentation: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
!style="background:silver" align="left"| ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
!style="background:silver" align="left"| ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:ChangingVersionsCheckList&diff=16483
Slicer3:ChangingVersionsCheckList
2010-06-04T15:07:26Z
<p>Hayes: </p>
<hr />
<div>When preparing a new release of Slicer3:<br />
<br />
* Create a new branch in the svn repository with the name Slicer-3-x, where x is the next even number<br />
** See [http://www.na-mic.org/Wiki/index.php/Engineering:Subversion_Repository these svn instructions].<br />
** Use a command line:<br />
svn copy http://svn.slicer.org/Slicer3/trunk/ http://svn.slicer.org/Slicer3/branches/Slicer-3-6 -m "ENH: new branch"<br />
* Tag the svn repository for each release candidate build that will be distributed (so we can recreate the source for that binary if needed). Use a command like:<br />
svn copy http://svn.slicer.org/Slicer3/branches/Slicer-3-6 http://svn.slicer.org/Slicer3/tags/Slicer-3-6-RC2 -m "ENH: tag of version of the code used to make the builds on May 15, 2010"<br />
** don't tag it when you branch it<br />
** tag when making release candidates<br />
* check out the new branch using<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-x Slicer3<br />
* Update Slicer3/slicer_variables.tcl to reflect the svn branch <br />
set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/branches/Slicer-3-x"<br />
* Update title bar via the SetName command in<br />
Base/GUI/vtkSlicerApplication.cxx<br />
* Update version in binary name in getbuildtest.tcl<br />
* Update Slicer3_VERSION_MINOR in Slicer3/CMakeLists.txt<br />
* CPack packaging<br />
** installer file name<br />
** installed program name on windows<br />
* Logos<br />
** Welcome module<br />
* On the svn head<br />
** update the title bar to the next odd number, using the SetName command in Base/GUI/vtkSlicerApplication.cxx<br />
** update CPack packaging<br />
*** installer file name<br />
*** installed program name on windows<br />
** optionally update logos</div>
Hayes
https://www.slicer.org/w/index.php?title=Slicer3:ChangingVersionsCheckList&diff=16482
Slicer3:ChangingVersionsCheckList
2010-06-04T15:03:01Z
<p>Hayes: </p>
<hr />
<div>When preparing a new release of Slicer3:<br />
<br />
* Create a new branch in the svn repository with the name Slicer-3-x, where x is the next even number<br />
** See [http://www.na-mic.org/Wiki/index.php/Engineering:Subversion_Repository these svn instructions].<br />
** Use a command line:<br />
svn copy http://svn.slicer.org/Slicer3/trunk/ http://svn.slicer.org/Slicer3/branches/Slicer-3-6 -m "ENH: new branch"<br />
* Tag the svn repository for each release candidate build that will be distributed (so we can recreate the source for that binary if needed). Use a command like:<br />
svn copy http://svn.slicer.org/Slicer3/branches/Slicer-3-6 http://svn.slicer.org/Slicer3/tags/Slicer-3-6-RC2 -m "ENH: tag of version of the code used to make the builds on May 15, 2010"<br />
** don't tag it when you branch it<br />
** tag when making release candidates<br />
* check out the new branch using<br />
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-x Slicer3<br />
* Update Slicer3/slicer_variables.tcl to reflect the svn branch <br />
set ::Slicer3_TAG "http://svn.slicer.org/Slicer3/branches/Slicer-3-x"<br />
* Update title bar via the SetName command in<br />
Base/GUI/vtkSlicerApplication.cxx<br />
* Update version in binary name in getbuildtest.tcl<br />
* CPack packaging<br />
** installer file name<br />
** installed program name on windows<br />
* Logos<br />
** Welcome module<br />
* On the svn head<br />
** update the title bar to the next odd number, using the SetName command in Base/GUI/vtkSlicerApplication.cxx<br />
** update CPack packaging<br />
*** installer file name<br />
*** installed program name on windows<br />
** optionally update logos</div>
Hayes
https://www.slicer.org/w/index.php?title=Developers&diff=16323
Developers
2010-06-01T15:40:49Z
<p>Hayes: </p>
<hr />
<div>{|border="1" cellpadding="5"<br />
|+ '''This page is a portal for information about writing software for 3D Slicer.'''<br />
| style="width:40%" ;align="left"|<br />
*[[Slicer4:Developers|Slicer 4]] (in development)<br />
*[[Slicer3:Developers|Slicer 3.x]]<br />
**See [[Build_instructions|Build instructions]] to learn how to build your own Slicer3.<br />
*Slicer 2<br />
**See [[Slicer:Slicer_2.6_Building|Build instructions]] to learn how to build your own Slicer2.<br />
| style="width:60%" ;align="center"|[[image:ExecutionModelPlugins.png| 350px|center|Slicer3 execution model]]<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Developers&diff=16322
Developers
2010-06-01T15:40:16Z
<p>Hayes: </p>
<hr />
<div>{|border="1" cellpadding="5"<br />
|+ '''This page is a portal for information about writing software for 3D Slicer.'''<br />
| style="width:40%" ;align="left"|<br />
*[[Slicer4:Developers|Slicer 4]] (in development)<br />
*[[Slicer3:Developers|Slicer 3.x]]<br />
**See [[Build_instructions|Build instructions]] to learn how to build your own Slicer3.<br />
*Slicer 2<br />
**See [[Slicer:Slicer_2.6_Building|Slicer_2.6_Building]] to learn how to build your own Slicer2.<br />
| style="width:60%" ;align="center"|[[image:ExecutionModelPlugins.png| 350px|center|Slicer3 execution model]]<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16298
Documentation-3.6:ExtensionStatus
2010-05-28T20:37:36Z
<p>Hayes: </p>
<hr />
<div>Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16297
Documentation-3.6:ExtensionStatus
2010-05-28T20:30:13Z
<p>Hayes: </p>
<hr />
<div>Binaries tested:<br />
<br />
darwin-x86: Slicer3-3.6-RC2-2010-05-25-darwin-x86.tar.gz<br />
<br />
linux-x86_64: Slicer3-3.6-RC2-2010-05-25-linux-x86_64.tar.gz<br />
<br />
win32: Slicer3-3.6-RC2-2010-05-25-win32.exe<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC2'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16287
Documentation-3.6:ExtensionStatus
2010-05-27T15:29:38Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|OK <br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16027
Documentation-3.6:ExtensionStatus
2010-05-18T21:52:42Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=16026
Documentation/3.6
2010-05-18T21:52:13Z
<p>Hayes: /* Slicer Extensions */</p>
<hr />
<div>=Documentation Draft notes=<br />
Key for flagged modules below:<br />
<br />
[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation<br />
<br />
[[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:<br />
* 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.<br />
* for interactive modules, see other modules in Base/GUI for an example.<br />
<br />
[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation<br />
<br />
=Introduction=<br />
<br />
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. <br />
<br />
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.<br />
<br />
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 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)<br />
<br />
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]]. <br />
<br />
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.<br />
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].<br />
*For sample data see [[SampleData|here]]<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak) <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak) <br />
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br />
<br />
=Modules=<br />
<br />
==Core==<br />
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br />
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br />
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)<br />
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller) <br />
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br />
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) <br />
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br />
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br />
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br />
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)<br />
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich) <br />
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)<br />
<br />
==Wizards==<br />
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br />
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)<br />
<br />
==Informatics Modules==<br />
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) <br />
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)<br />
<br />
==Registration==<br />
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.<br />
*Fast Registration<br />
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)<br />
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller) <br />
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller) <br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) <br />
*Robust Registration<br />
**[[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)<br />
**[[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)<br />
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).<br />
*Brain Only Registration<br />
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)<br />
*Non-Raster-Image Data Registration<br />
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)<br />
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)<br />
<br />
==Segmentation==<br />
*[[Modules:SegmentationOverview3.6|Overview]]<br />
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl) <br />
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br />
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)<br />
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).<br />
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).<br />
<br />
==Quantification==<br />
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)<br />
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)<br />
<br />
==Diffusion MRI==<br />
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]<br />
* DWI filtering<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin) <br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
* Diffusion tensor utilities<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) <br />
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br />
* Tractography<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) <br />
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich) <br />
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo) <br />
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)<br />
<br />
==IGT==<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)<br />
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)<br />
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)<br />
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)<br />
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)<br />
<br />
==Time Series==<br />
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)<br />
<br />
==Filtering==<br />
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)<br />
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK<br />
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)<br />
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)<br />
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)<br />
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br />
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)<br />
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br />
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)<br />
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)<br />
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen) <br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan) <br />
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan) <br />
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br />
** [[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<br />
**[[Image:WeakDoc.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan) <br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)<br />
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)<br />
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao) <br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller) <br />
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)<br />
<br />
==Surface Models==<br />
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br />
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) <br />
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br />
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br />
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)<br />
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) <br />
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)<br />
<br />
==Converters==<br />
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br />
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao) <br />
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)<br />
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)<br />
<br />
==Endoscopy==<br />
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)<br />
<br />
==Slicer Extensions==<br />
<br />
[[Documentation-3.6:ExtensionStatus|Extension Status]]<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.<br />
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension<br />
<br />
'''Available Extensions'''<br />
<br />
* Segmentation<br />
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. <br />
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .<br />
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). <br />
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com). <br />
* Registration<br />
**Robust<br />
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com). <br />
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu). <br />
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).<br />
* Wizards<br />
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) . <br />
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
* Tractography<br />
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).<br />
* DWI<br />
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .<br />
* Time Series<br />
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
* Quantification<br />
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)<br />
<br />
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins<br />
<br />
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models<br />
<br />
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br />
<br />
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution<br />
<br />
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures<br />
<br />
'''Installation Instructions'''<br />
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)<br />
[[image:Slicertoolbar.png|Extensions Wizard]]<br />
<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
<br />
'''Info for Developers'''<br />
<br />
*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.<br />
*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.<br />
<br />
*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]]<br />
<br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper<br />
<br />
=Other information=<br />
<br />
'''Developer Tools'''<br />
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)<br />
*Note: most developer tools are not documented for end users, but contain comments in the source code<br />
<br />
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br />
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br />
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''<br />
<br />
<br />
'''QA Table'''<br />
<br />
[[Slicer-3.6-QA|Slicer 3.6 QA table]]<br />
<br />
'''Modules'''<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
'''Requirements for Modules'''<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* 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.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16025
Documentation-3.6:ExtensionStatus
2010-05-18T21:40:02Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSFit<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
| <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16024
Documentation-3.6:ExtensionStatus
2010-05-18T20:42:57Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSFit<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu<br />
|OK<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=16023
Documentation-3.6:ExtensionStatus
2010-05-18T19:56:29Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSFit<br />
| Hans Johnson<br />
|hans-johnson@uiowa.edu|<br />
|OK<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15970
Documentation-3.6:ExtensionStatus
2010-05-17T19:51:39Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSFit<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|OK<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|OK<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15969
Documentation-3.6:ExtensionStatus
2010-05-17T19:48:51Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15968
Documentation-3.6:ExtensionStatus
2010-05-17T19:47:52Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
win32: Slicer3-3.6-RC1-2010-05-17-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|OK<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15938
Documentation-3.6:ExtensionStatus
2010-05-17T17:22:38Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|OK<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|OK<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|OK<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15937
Documentation-3.6:ExtensionStatus
2010-05-17T17:06:08Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
|OK <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|OK<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15936
Documentation-3.6:ExtensionStatus
2010-05-17T16:50:11Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15935
Documentation-3.6:ExtensionStatus
2010-05-17T16:49:53Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
darwin-x86: Slicer3-3.6-RC1-2010-05-12-darwin-x86.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15934
Documentation-3.6:ExtensionStatus
2010-05-17T16:12:51Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|NS<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
|NS <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15933
Documentation-3.6:ExtensionStatus
2010-05-17T16:06:34Z
<p>Hayes: </p>
<hr />
<div>linux-x86_64: Slicer3-3.6-RC1-2010-05-12-linux-x86_64.tar.gz<br />
<br />
{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|<br />
|OK<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|OK<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15790
Documentation-3.6:ExtensionStatus
2010-05-12T17:31:54Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|<br />
|<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| millerjv@research.ge.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15789
Documentation-3.6:ExtensionStatus
2010-05-12T17:25:49Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ '''Available Extensions for Slicer 3.6 RC1'''<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Registration: Robust''<br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu|<br />
|<br />
| <br />
|<br />
|<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Registration: Wizards''<br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Tractography''<br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''DWI''<br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Time Series''<br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Quantification''<br />
|-<br />
! LabelDiameterEstimation<br />
| Andriy Fedorov<br />
| fedorov@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''The Vascular Modeling Toolkit''<br />
|-<br />
! VmtkSlicerModule<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKCenterlines<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKEasyLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKLevelSetSegmentation<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! VMTKVesselEnhancement<br />
| Daniel Haehn<br />
| haehn@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ''Example Modules''<br />
|-<br />
! ExampleCommandLine<br />
| Jim Miller<br />
| <br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ExampleLoadableGuiLessModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! ExampleLoadableModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! PythonSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
! TclSampleScriptedModule<br />
| Steve Pieper<br />
| pieper@bwh.harvard.edu<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
|}</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15788
Documentation-3.6:ExtensionStatus
2010-05-12T17:09:54Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ Available Extensions for Slicer 3.6 RC1<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
| || || || || || <br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu <br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|-<br />
! ''Registration: Robust''<br />
| || || || || || <br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|-<br />
! ''Registration: Wizards''<br />
| || || || || || <br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|-<br />
! SkullStripperModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|-<br />
! ''Tractography''<br />
| || || || || || <br />
|-<br />
! EMFiberClusteringModule<br />
| Mahnaz Maddah<br />
| mmaddah@alum.mit.edu<br />
|-<br />
! ''DWI''<br />
| || || || || || <br />
|-<br />
! RicianNoiseFilter<br />
| Ross Whitaker<br />
| whitaker@cs.utah.edu<br />
|-<br />
! ''Time Series''<br />
| || || || || || <br />
|-<br />
! 4D Analysis<br />
| Junichi Tokuda<br />
| tokuda@bwh.harvard.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
<br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15787
Documentation-3.6:ExtensionStatus
2010-05-12T17:05:30Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ Available Extensions for Slicer 3.6 RC1<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
| || || || || || <br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu <br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|-<br />
! ''Registration: Robust''<br />
| || || || || || <br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|-<br />
! Plastimatch<br />
| Greg Sharp<br />
| gcsharp@partners.org<br />
|-<br />
! ''Registration: Wizards''<br />
| || || || || || <br />
|-<br />
! ARCTIC<br />
| Cedric Mathieu, Clement Vachet<br />
| cvachet@email.unc.edu<br />
|-<br />
! LesionSegmentationApplications<br />
| Mark Scully<br />
| mscully@mrn.org<br />
|-<br />
|}<br />
<br />
<br />
<br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15786
Documentation-3.6:ExtensionStatus
2010-05-12T17:01:01Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ Available Extensions for Slicer 3.6 RC1<br />
! Extension !! Author(s) !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! ''Segmentation''<br />
| || || || || || <br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu <br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|-<br />
! ''Registration: Robust''<br />
| || || || || || <br />
|-<br />
! BRAINSMush<br />
| Hans Johnson<br />
| hans-johnson@uiowa.edu<br />
|-<br />
! CMTK Computational Morphometry Toolkit<br />
| Torsten Rohlfing<br />
| torsten@synapse.sri.com<br />
|-<br />
! HammerRegistration<br />
| Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen<br />
| dgshen@med.unc.edu<br />
|-<br />
|}<br />
<br />
<br />
* Registration<br />
o Robust<br />
+ Image:MissingOrStaleDoc.pngBRAINSMush Hans Johnson (hans-johnson@uiowa.edu) .<br />
+ Image:MissingOrStaleDoc.pngCMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).<br />
+ HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).<br />
+ Plastimatch Greg Sharp (gcsharp@partners.org). <br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15783
Documentation-3.6:ExtensionStatus
2010-05-12T16:52:29Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ Available Extensions for Slicer 3.6 RC1<br />
! Extension !! Author !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! Segmentation<br />
| || || || || || <br />
|-<br />
! ABC<br />
| Marcel Prastawa<br />
| prastawa@sci.utah.edu <br />
|-<br />
! FuzzySegmentationModule<br />
| Xiaodong Tao<br />
| taox@research.ge.com<br />
|-<br />
! SpineSegmentation<br />
| Sylvain Jaume<br />
| sylvain@csail.mit.edu<br />
|-<br />
! Registration<br />
| || || || || || <br />
|}<br />
<br />
<br />
<br />
* Segmentation<br />
o ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6.<br />
o FuzzySegmentationModule Xiaodong Tao (taox at research.ge.com) .<br />
o Image:MissingOrStaleDoc.pngSpineSegmentation Sylvain Jaume (sylvain@csail.mit.edu). <br />
* Registration<br />
o Robust<br />
+ Image:MissingOrStaleDoc.pngBRAINSMush Hans Johnson (hans-johnson@uiowa.edu) .<br />
+ Image:MissingOrStaleDoc.pngCMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).<br />
+ HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).<br />
+ Plastimatch Greg Sharp (gcsharp@partners.org). <br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15782
Documentation-3.6:ExtensionStatus
2010-05-12T16:42:44Z
<p>Hayes: </p>
<hr />
<div>{| border="1"<br />
|+ Available Extensions for Slicer 3.6 RC1<br />
! Extension !! Author !! Contact !! win32 !! darwin-x86 !! linux-x86 !! linux-x86_64<br />
|-<br />
! Row heading 1<br />
| Cell 2 || Cell 3<br />
|-<br />
! Row heading A<br />
| Cell B<br />
| Cell C<br />
|}<br />
<br />
<br />
<br />
* Segmentation<br />
o ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6.<br />
o FuzzySegmentationModule Xiaodong Tao (taox at research.ge.com) .<br />
o Image:MissingOrStaleDoc.pngSpineSegmentation Sylvain Jaume (sylvain@csail.mit.edu). <br />
* Registration<br />
o Robust<br />
+ Image:MissingOrStaleDoc.pngBRAINSMush Hans Johnson (hans-johnson@uiowa.edu) .<br />
+ Image:MissingOrStaleDoc.pngCMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).<br />
+ HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).<br />
+ Plastimatch Greg Sharp (gcsharp@partners.org). <br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15781
Documentation-3.6:ExtensionStatus
2010-05-12T16:40:52Z
<p>Hayes: </p>
<hr />
<div>Available Extensions<br />
<br />
{| border="1"<br />
|+ The table's caption<br />
! Column heading 1 !! Column heading 2 !! Column heading 3<br />
|-<br />
! Row heading 1<br />
| Cell 2 || Cell 3<br />
|-<br />
! Row heading A<br />
| Cell B<br />
| Cell C<br />
|}<br />
<br />
<br />
<br />
* Segmentation<br />
o ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6.<br />
o FuzzySegmentationModule Xiaodong Tao (taox at research.ge.com) .<br />
o Image:MissingOrStaleDoc.pngSpineSegmentation Sylvain Jaume (sylvain@csail.mit.edu). <br />
* Registration<br />
o Robust<br />
+ Image:MissingOrStaleDoc.pngBRAINSMush Hans Johnson (hans-johnson@uiowa.edu) .<br />
+ Image:MissingOrStaleDoc.pngCMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).<br />
+ HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).<br />
+ Plastimatch Greg Sharp (gcsharp@partners.org). <br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6:ExtensionStatus&diff=15780
Documentation-3.6:ExtensionStatus
2010-05-12T16:34:00Z
<p>Hayes: Created page with ' Available Extensions * Segmentation o ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6. o FuzzySegmentationM…'</p>
<hr />
<div><br />
<br />
Available Extensions<br />
<br />
* Segmentation<br />
o ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6.<br />
o FuzzySegmentationModule Xiaodong Tao (taox at research.ge.com) .<br />
o Image:MissingOrStaleDoc.pngSpineSegmentation Sylvain Jaume (sylvain@csail.mit.edu). <br />
* Registration<br />
o Robust<br />
+ Image:MissingOrStaleDoc.pngBRAINSMush Hans Johnson (hans-johnson@uiowa.edu) .<br />
+ Image:MissingOrStaleDoc.pngCMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).<br />
+ HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).<br />
+ Plastimatch Greg Sharp (gcsharp@partners.org). <br />
* Wizards<br />
o ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .<br />
o LesionSegmentationApplications Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
o Image:MissingOrStaleDoc.pngSkullStripperModule Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
o EMFiberClusteringModule Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools). <br />
* DWI<br />
o Image:MissingOrStaleDoc.pngRicianNoiseFilter Ross Whitaker (whitaker@cs.utah.edu) . <br />
* Time Series<br />
o 4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI) Junichi Tokuda (tokuda@bwh.harvard.edu) <br />
* Quantification<br />
o LabelDiameterEstimation Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
*<br />
The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* VmtkSlicerModule prerequisite install for all VMTK plug-ins <br />
<br />
* VMTKCenterlines providing centerline computation of surface models <br />
<br />
* VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution <br />
<br />
* VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures <br />
* Example Modules<br />
<br />
<br />
<br />
<br />
* ExampleCommandLine Jim Miller <br />
<br />
* ExampleLoadableGuiLessModule Steve Pieper <br />
<br />
* ExampleLoadableModule Steve Pieper <br />
<br />
* PythonSampleScriptedModule Steve Pieper <br />
<br />
* TclSampleScriptedModule Steve Pieper</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6/ExtensionStatus&diff=15779
Documentation-3.6/ExtensionStatus
2010-05-12T16:23:41Z
<p>Hayes: Blanked the page</p>
<hr />
<div></div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=15778
Documentation/3.6
2010-05-12T16:23:12Z
<p>Hayes: /* Slicer Extensions */</p>
<hr />
<div>=Documentation Draft notes=<br />
Key for flagged modules below:<br />
<br />
[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation<br />
<br />
[[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:<br />
* 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.<br />
* for interactive modules, see other modules in Base/GUI for an example.<br />
<br />
[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation<br />
<br />
=Introduction=<br />
<br />
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. <br />
<br />
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.<br />
<br />
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 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)<br />
<br />
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]]. <br />
<br />
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.<br />
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].<br />
*For sample data see [[SampleData|here]]<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak) <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak) <br />
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br />
<br />
=Modules=<br />
<br />
==Core==<br />
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br />
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br />
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)<br />
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller) <br />
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br />
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) <br />
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br />
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br />
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br />
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)<br />
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich) <br />
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)<br />
<br />
==Wizards==<br />
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br />
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)<br />
<br />
==Informatics Modules==<br />
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) <br />
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)<br />
<br />
==Registration==<br />
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.<br />
*Fast Registration<br />
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)<br />
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]: automated fast affine registration , (Jim Miller) <br />
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Jim Miller) <br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) <br />
*Robust Registration<br />
**[[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)<br />
**[[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)<br />
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).<br />
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).<br />
*Brain Only Registration<br />
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)<br />
*Non-Raster-Image Data Registration<br />
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)<br />
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)<br />
<br />
==Segmentation==<br />
*[[Modules:SegmentationOverview3.6|Overview]]<br />
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl) <br />
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl) <br />
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br />
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)<br />
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).<br />
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).<br />
<br />
==Quantification==<br />
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)<br />
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)<br />
<br />
==Diffusion MRI==<br />
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]<br />
* DWI filtering<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br />
* Diffusion tensor utilities<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) <br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) <br />
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br />
* Tractography<br />
**[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) <br />
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper) <br />
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich) <br />
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo) <br />
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)<br />
<br />
==IGT==<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)<br />
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)<br />
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)<br />
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)<br />
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)<br />
<br />
==Time Series==<br />
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)<br />
<br />
==Filtering==<br />
*[[Registration:Resampling|'''Overview of Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)<br />
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK<br />
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)<br />
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)<br />
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)<br />
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br />
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)<br />
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br />
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)<br />
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)<br />
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen) <br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan) <br />
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan) <br />
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br />
** [[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<br />
**[[Image:WeakDoc.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan) <br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]] (Bill Lorensen)<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)<br />
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)<br />
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao) <br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller) <br />
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)<br />
<br />
==Surface Models==<br />
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br />
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)<br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) <br />
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br />
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br />
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)<br />
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) <br />
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)<br />
<br />
==Converters==<br />
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br />
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] (Xiaodong Tao) <br />
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)<br />
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao) <br />
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)<br />
<br />
==Endoscopy==<br />
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)<br />
<br />
==Slicer Extensions==<br />
<br />
[[Documentation-3.6:ExtensionStatus|Extension Status]]<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension<br />
<br />
'''Available Extensions'''<br />
<br />
* Segmentation<br />
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. <br />
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .<br />
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). <br />
* Registration<br />
**Robust<br />
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) . <br />
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com). <br />
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu). <br />
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).<br />
* Wizards<br />
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) . <br />
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .<br />
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com). <br />
* Tractography<br />
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).<br />
* DWI<br />
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .<br />
* Time Series<br />
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
* Quantification<br />
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) . <br />
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)<br />
<br />
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins<br />
<br />
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models<br />
<br />
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br />
<br />
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution<br />
<br />
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures<br />
<br />
'''Installation Instructions'''<br />
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)<br />
[[image:Slicertoolbar.png|Extensions Wizard]]<br />
<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
<br />
'''Info for Developers'''<br />
<br />
*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.<br />
*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.<br />
<br />
*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]]<br />
<br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper <br />
<br />
* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper<br />
<br />
=Other information=<br />
<br />
'''Developer Tools'''<br />
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)<br />
*Note: most developer tools are not documented for end users, but contain comments in the source code<br />
<br />
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br />
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br />
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''<br />
<br />
<br />
'''QA Table'''<br />
<br />
[[Slicer-3.6-QA|Slicer 3.6 QA table]]<br />
<br />
'''Modules'''<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
'''Requirements for Modules'''<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* 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.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation-3.6/ExtensionStatus&diff=15777
Documentation-3.6/ExtensionStatus
2010-05-12T16:20:42Z
<p>Hayes: Created page with 'foo'</p>
<hr />
<div>foo</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12615
Documentation/3.6
2010-03-23T17:18:12Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com) '''Not yet 3.6'''<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]] '''Not yet 3.6'''<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]] '''Not yet 3.6'''<br />
<br />
* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]] '''Not yet 3.6'''<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] '''Not yet 3.6'''<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] '''Not yet 3.6'''<br />
<br />
* [[Modules:Examples|Examples]] '''Not yet 3.6'''<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] '''Not yet 3.6'''<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12577
Documentation/3.6
2010-03-19T19:24:20Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) <br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu)<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu)<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]]<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) <br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) <br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org)<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu)<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu)<br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface <br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms <br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. <br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures <br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)<br />
<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12576
Documentation/3.6
2010-03-19T19:23:31Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu)<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu)<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]]<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6''' (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org)<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu)<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu)<br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)<br />
<br />
<br />
<br />
'''Non-SPL Supported Compatibility Packages'''<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12574
Documentation/3.6
2010-03-19T19:09:28Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]]<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]]<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]]<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]]<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6''' (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]]<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]]<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]]<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] <br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12573
Documentation/3.6
2010-03-19T18:49:04Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]]<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]]<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]]<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]]<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6''' (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]]<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]]<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]]<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] <br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12572
Documentation/3.6
2010-03-19T18:48:08Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BioImageSuite|BioImageSuite]]<br />
<br />
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]]<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSMush|BRAINSMush]]<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit<br />
<br />
* [[Modules:DiffusionWarp|DiffusionWarp]]<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6''' (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]]<br />
<br />
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]]<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]]<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] <br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12571
Documentation/3.6
2010-03-19T18:44:31Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
<br />
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
<br />
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6''' (a.k.a. Quantitative Diffusion Tools)<br />
<br />
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
<br />
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
<br />
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6''<br />
<br />
* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule)<br />
<br />
* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
<br />
* [[Modules:Plastimatch|Plastimatch]]<br />
<br />
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
<br />
* [[Modules:SkullStripperModule|SkullStripperModule]]<br />
<br />
* [[Modules:SpineSegmentation|SpineSegmentation]] <br />
<br />
* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
<br />
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
<br />
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
<br />
<br />
<br />
'''Example Extensions'''<br />
<br />
* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
<br />
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
<br />
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
<br />
* [[Modules:Examples|Examples]]<br />
<br />
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
<br />
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
<br />
<br />
<br />
'''Deprecated Extensions'''<br />
<br />
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)</div>
Hayes
https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=12570
Documentation/3.6
2010-03-19T18:33:28Z
<p>Hayes: /* Listing of plug-ins */</p>
<hr />
<div>This is work in progress<br />
<br />
=Main GUI=<br />
<br />
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] <br />
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] <br />
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]] <br />
*[[Modules:Loading-Data-3.6| Data Loading Details]] <br />
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]] <br />
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] <br />
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]<br />
<br />
=Modules=<br />
*Please copy the template linked below, paste it into your page and customize it with your module's information.<br />
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]] '''Not yet 3.6'''<br />
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br />
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
=Requirements for Modules=<br />
{| border="00" cellpadding="5" cellspacing="0"<br />
|-<br />
| rowspan="2"| <br />
* The module is '''feature complete''', it does everything that it advertises it can do<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br />
*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.<br />
* 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.]]<br />
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br />
** '''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. <br />
** '''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.)<br />
* 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.<br />
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]<br />
| style="background: #e5e5e5" align="center"| Examples for the Help and <br />
Acknowledgment Panels<br />
|-<br />
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br />
|}<br />
<br />
=List of Modules added since the 3.4 release=<br />
<br />
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume) '''Not yet 3.6'''<br />
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br />
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev) '''Not yet 3.6'''<br />
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov) '''Not yet 3.6'''<br />
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br />
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) '''Not yet 3.6'''<br />
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett) '''Not yet 3.6'''<br />
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br />
<br />
=List of pre-existing Modules=<br />
==Core==<br />
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br />
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br />
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''<br />
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br />
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br />
<br />
==Specialized Modules==<br />
<br />
Please adhere to the naming scheme for the module documentation:<br />
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br />
<br />
===Wizards===<br />
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''<br />
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''<br />
===Informatics Modules===<br />
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br />
===Registration===<br />
*[[Slicer3:Registration|Overview of all Registration Modules ]] <br />
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''<br />
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br />
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''<br />
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Segmentation===<br />
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''<br />
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br />
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Statistics===<br />
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
===Diffusion===<br />
====DWI====<br />
*Estimation<br />
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*Filter<br />
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br />
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br />
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
<br />
====DTI====<br />
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*Analysis<br />
<br />
===Tractography===<br />
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br />
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''<br />
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''<br />
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br />
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br />
<br />
===IGT===<br />
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br />
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br />
===Filtering===<br />
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''<br />
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Arithmetic<br />
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''<br />
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br />
*Denoising<br />
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br />
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br />
*Morphology<br />
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br />
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
===Surface Models===<br />
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''<br />
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br />
<br />
*Freesurfer Surface Section Extraction (Katharina Quintus)<br />
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich) '''Not yet 3.6'''<br />
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin) '''Not yet 3.6'''<br />
<br />
===Batch processing===<br />
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis) '''Not yet 3.6'''<br />
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward) '''Not yet 3.6'''<br />
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet) '''Not yet 3.6'''<br />
<br />
===Converters===<br />
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br />
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br />
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br />
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper) '''Not yet 3.6'''<br />
<br />
=Slicer Extensions=<br />
<br />
==Extensions for Downloading==<br />
===Introduction===<br />
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br />
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br />
* Some of the extensions do not use the Slicer license. Please review carefully.<br />
* 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.<br />
* The version that is available through the extension manager is chosen by the developer of that extension <br />
<br />
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.<br />
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.<br />
<br />
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br />
To add extension modules to an installed binary of slicer:<br />
* Use the View->Extension Manager menu option<br />
* The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br />
** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br />
** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br />
* Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br />
* To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.<br />
<br />
<br />
*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]]<br />
<br />
'''Installation'''<br />
*Click on the icon to start the extensions wizard<br />
[[image:ExtensionsWizard.png|Extensions Wizard]]<br />
<br />
===Listing of plug-ins===<br />
<br />
'''Available Extensions'''<br />
<br />
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) '''Not yet 3.6'''<br />
<br />
* [[Modules:ARCTIC|ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)<br />
<br />
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)<br />
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* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)<br />
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* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) '''Not yet 3.6'''<br />
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* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br />
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* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com)<br />
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* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br />
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* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6''<br />
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* [[Modules:LesionSegmentationApplications|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org)<br />
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* [[Modules:LocalRegionSeg|LocalRegionSeg]]<br />
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* [[Modules:Plastimatch|Plastimatch]]<br />
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* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu)<br />
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* [[Modules:SkullStripperModule|SkullStripperModule]]<br />
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* [[Modules:SpineSegmentation|SpineSegmentation]] <br />
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* [[Modules:VMTKCenterlines|VTMKCenterlines]] Daniel Haehn (haehn@bwh.harvard.edu) <br />
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* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br />
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* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms '''Not yet 3.6'''<br />
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* [[Modules:VMTKSlicerModule|VMTKkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins. '''Not yet 3.6'''<br />
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* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures '''Not yet 3.6'''<br />
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'''Example Extensions'''<br />
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* [[Modules:ExampleCommandLine|ExampleCommandLine]]<br />
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* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]]<br />
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* [[Modules:ExampleLoadableModule|ExampleLoadableModule]]<br />
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* [[Modules:Examples|Examples]]<br />
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* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]]<br />
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* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]]<br />
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'''Deprecated Extensions'''<br />
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* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com)</div>
Hayes