Slicer Wiki - User contributions [en]

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T19:16:20Z

Elhawary: /* Use Cases, Examples */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and deformedlabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

No known bugs currently reported.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Slicer3:VisualBlog

2010-04-27T19:09:28Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
Image:IntraOpDTI.jpg| Intra-operative querying of white matter tracts is now possible by interfacing Slicer 3.6 to the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:BetaProbe.jpg| Intra-operative navigation of a positron probe can help detect regions of high [18F]-FDG uptake, potentially improving tumor removal at resection borders. The first two image shows a PET/CT scan of the phantom showing where radiation is located, and the third image shows results as indicated by the positron probe.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T19:09:07Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
Image:IntraOpDTI.jpg| Intra-operative querying of white matter tracts is now possible by interfacing Slicer 3.6 to the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:BetaProbe.jpg| Intra-operative navigation of a positron probe can help detect regions of high [18F]-FDG uptake as shown in this phantom, potentially improving tumor removal at resection borders. The first two image shows a PET/CT scan of the phantom showing where radiation is located, and the third image shows results as indicated by the positron probe.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T19:06:10Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
Image:IntraOpDTI.jpg| Intra-operative querying of white matter tracts is now possible by interfacing Slicer 3.6 to the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T19:04:54Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
Image:IntraOpDTI.jpg| Intra-operative querying of white matter tracts is now possible by interfacing Slicer 3.6 to the Brainlab navigation system using Yale's BioImage Suite.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T19:00:52Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
Image:IntraOpDTI.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T18:59:55Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Slicer3:VisualBlog

2010-04-27T18:58:22Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:RegistrationResults2.jpg| B-Spline Registration in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

File:BetaProbe.jpg

2010-04-27T18:55:18Z

Elhawary:

File:RegistrationResults2.jpg

2010-04-27T18:54:56Z

Elhawary:

File:IntraOpDTI.jpg

2010-04-27T18:54:39Z

Elhawary:

Slicer3:VisualBlog

2010-04-27T18:53:43Z

Elhawary:

__NOTOC__
<gallery caption="2010" widths="200px" perrow="4">
Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only). This renderer will be available in Slicer 3.6.
Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer. It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
</gallery>
<gallery caption="2009" widths="200px" perrow="4">
Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules. See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
Image:Dual 3D View.png|Multiple 3D rendering windows
Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology. (See [[Nagy-videos-2009:Notes|Notes]]).
Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other. This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis. Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
</gallery>
<gallery caption="2008" widths="200px" perrow="4">
Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials. Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.''' Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.''' A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools. Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008''' Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008''' Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
Image:Slicer_IGTL_PartialImage.png|'''Partial image update using OpenIGTLink, February 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] allows an external imaging scanner (Ultrasound/CT/MR) to update part of a volume, which has already been loaded on the Slicer. This is helpful if the imaging plane sweeps the subject, and images are transfered to the Slicer on-the-fly.
Image:Slicer_CudaHead.jpg|'''The First MRML node rendering using CUDA February 2008''' [[Slicer3:Volume_Rendering_With_Cuda| Cuda Volume Rendering]] provides a Volume Rendering Method on the new and advanced NVidia Hardware.
Image:Slicer_OpenIGTLINK.png|'''The First Implementation of OpenIGTLink, January 2008''' [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] protocol provides plug-and-play connectivity to tracking devices, imagers (MR, ultrasound ...) and other medical devices. A real-time image transfer to the Slicer in 10 fps is demonstrated in the screenshot.
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
</gallery>
<gallery caption="2007" widths="200px" perrow="4">
Image:ENT.png|'''Image from Jaesung Hong December 2007''' Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007''' Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
Image:VolumeRenderScene.png|'''Image from Steve Pieper, Andy Freudling December 2007''' More volume rendering examples. New Threshold tool makes it easy to visualize surfaces.
Image:Canine-heart1.png|'''Image from Steve Pieper, December 2007''' Display of segmented heart data results using volume rendering inside Slicer3. See [https://caportal.cis.jhu.edu/ JHU Computational Anatomy Portal] for more information.
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007''' Display of Stochastic Tractography results using volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography '''here'''] for more information.
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007''' First results of volume rendering inside Slicer3. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Volume_Rendering '''here'''] for more information.
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007''' QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007''' Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move (subject to change).
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007''' A new label map smoothing tool has been added to help with our [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007''' New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007''' Example of [http://wiki.na-mic.org/Wiki/index.php/Projects/Structural/2007_Project_Week_EMSegmentation_Validation EMSegmenter in Slicer3]
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007''' Slicer3 Module for [http://wiki.na-mic.org/Wiki/index.php/Algorithm:MIT:DTI_StochasticTractography Stochastic Tractography] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007''' UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007''' Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007''' The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007''' EMSegment screenshot---segmentation results and work-flow GUI
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007''' Mimx Logo in Slicer3 for VoxelMeshingModule
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM''' Python incorporated into [[Slicer3:Python| Slicer]]. [[Slicer3:VisualBlog_Extension#Image_from_blezek_on_Tuesday.2C_April.2C_10.2C_2007_at_8:00AM | More ...]]
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM''' New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM''' From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
</gallery>
<gallery caption="2006" widths="200px" perrow="4">
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM''' Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M''' New 3D Slicer logo integrated with slicer GUI.
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M''' FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM''' Clipping with the slice plane is now supported, along with thresholded image display.
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm''' The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am''' The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM''' A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM''' Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM''' Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM''' Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&rev=0&sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM''' Example model read from vtk file and loaded in slicer3
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM''' Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM''' New annotations and key bindings. Middle mouse to pan, right mouse to zoom.
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM''' results of the command line median filter module
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM''' {First command line module to export data, execute, and import data back into Slicer}
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM''' {Command line module with an enumerated parameter as a radio button}
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM''' {Slicer applications settings panel showing the module search path}
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM''' Another command line module example from Jim
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM''' Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM''' Example screen shot showing that there is a basic interface in place.
</gallery>
 

== About the VisualBlog ==

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.

Documentation/3.6

2010-04-27T18:29:21Z

Elhawary: /* Registration */

This is work in progress

=Main GUI=

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

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

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

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

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

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

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

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

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

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Registration]]: automated fast affine registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:AffineRegistration-Documentation-3.4|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.6 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Updated to 3.6 but needs checking
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]]: obsolete: old version of the ''Fast Rigid Registration'' (Daniel Blezek) Not yet 3.6Not yet 3.6

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

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

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

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

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

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) Not yet 3.6Not yet 3.6
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

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

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

==Experimental==
* [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] '''(in progress)''' (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to Statistics.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

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

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

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

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

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

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

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

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

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

Documentation/3.6

2010-04-27T18:28:34Z

Elhawary: /* Registration */

This is work in progress

=Main GUI=

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

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

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

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

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

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

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

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

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

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Registration]]: automated fast affine registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:AffineRegistration-Documentation-3.4|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.6 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Not yet 3.6Updated to 3.6 but needs checking
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]]: obsolete: old version of the ''Fast Rigid Registration'' (Daniel Blezek) Not yet 3.6Not yet 3.6

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

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

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

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

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

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) Not yet 3.6Not yet 3.6
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

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

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

==Experimental==
* [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] '''(in progress)''' (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to Statistics.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

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

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

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

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

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

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

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

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

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

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:21:28Z

Elhawary: /* More Information */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

No known bugs currently reported.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:20:58Z

Elhawary: /* Development */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

No known bugs currently reported.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:20:10Z

Elhawary: /* Development */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

No known bugs currently reported.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:20:02Z

Elhawary: /* Development */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

No known bugs currently reported.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:19:34Z

Elhawary: /* Development */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer. The module is based on the ITK library.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:18:06Z

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

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:17:55Z

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

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
* '''Viewing panel:'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:17:33Z

Elhawary:

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

{|
|
* '''Input Images panel:'''
** '''Image Volume 1 and Image Volume 2 are two label map images which you wish to compare'''
** '''Output DistanceMap Volume presents a graphical representation of the HD at each point of the contour of Image Volume 1'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:12:05Z

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

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:11:56Z

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

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:11:05Z

Elhawary: /* Tutorials */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory with the information in this wiki page.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:10:50Z

Elhawary: /* Tutorials */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

There are no tutorials for this module, since it is quite self-explanatory.

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:10:22Z

Elhawary: /* Use Cases, Examples */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:06:24Z

Elhawary: /* Usage */

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Nobuhiko Hata, hata [at] bwh.harvard.edu or Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:03:31Z

Elhawary: /* Module Description */

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:03:07Z

Elhawary: /* Authors, Collaborators & Contact */

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:02:42Z

Elhawary: /* Authors, Collaborators & Contact */

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:02:09Z

Elhawary:

Modules:RegistrationMetrics-Documentation-3.6

2010-04-27T18:00:57Z

Elhawary: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== MyModule {| |[[Image:screen…'

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

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|[[Image:screenshotBlank.png|thumb|280px|Output]]
|[[Image:screenshotBlank.png|thumb|280px|Caption]]
|}

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

Type: Interactive or CLI

Category: Base or (Filtering, Registration, ''etc.'')

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

===Use Cases, Examples===

This module is especially appropriate for these use cases:

* Use Case 1:
* Use Case 2:

Examples of the module in use:

* Example 1
* Example 2

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

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

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''First input'''
** '''Second input'''
* '''Parameters panel:'''
** '''First parameter'''
** '''Second parameter'''
* '''Output panel:'''
** '''First output'''
** '''Second output'''
* '''Viewing panel:'''
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Documentation/3.6

2010-04-27T18:00:10Z

Elhawary:

This is work in progress

=Main GUI=

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

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

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

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

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

=List of Modules=
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) Not yet 3.6Not yet 3.6
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)

==Specialized Modules==

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

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

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

===Registration===
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
*Fast
**[[Modules:Transforms-Documentation-3.6|Transforms]]: manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Registration]]: automated fast affine registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:AffineRegistration-Documentation-3.4|Fast Rigid Registration]]: automated fast rigid (6 DOF) registration , (Daniel Blezek) Not yet 3.6Not yet 3.6'
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)
*Robust
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]: automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)
*Brain Only
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: align a single brain along AC-PC line , (Nicole Aucoin)
*Non-Raster-Image Data
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*Experimental and auxiliary
**[[Modules:RegistrationMetrics-Documentation-3.6 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) Not yet 3.6Not yet 3.6
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]]: obsolete: old version of the ''Fast Rigid Registration'' (Daniel Blezek) Not yet 3.6Not yet 3.6

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

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)

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

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

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

===Filtering===
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)
*Arithmetic
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) Not yet 3.6Not yet 3.6
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) Not yet 3.6Not yet 3.6
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) Not yet 3.6Not yet 3.6
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller) Not yet 3.6Not yet 3.6
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) Not yet 3.6Not yet 3.6
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)

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

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) Not yet 3.6 (in progress)Not yet 3.6 (in progress)
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)

==Experimental==
* [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] '''(in progress)''' (Andriy Fedorov)

=Slicer Extensions=

==Extensions for Downloading==
===Introduction===
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
* Some of the extensions do not use the Slicer license. Please review carefully.
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
* The version that is available through the extension manager is chosen by the developer of that extension

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

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

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

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

===Listing of plug-ins===

'''Available Extensions'''

* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation

* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust

* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust

* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography

* [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)

* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.

* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to Statistics.

* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.

* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.

* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI

* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards

* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards

* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)

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

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

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

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

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

====Example Extensions====

* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''

* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''

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

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

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

Modules:RegistrationMetrics-Documentation-3.5

2009-06-30T18:19:35Z

Elhawary: /* Registration Metrics */

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Slicer3:Module Documentation-3.5 Template

2009-06-29T22:59:03Z

Elhawary: Undo revision 9943 by Elhawary (Talk)

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
MyModule

{|
|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 2]]
|[[Image:screenshotBlank.png|thumb|280px|Caption 3]]
|}

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

Type: Interactive or CLI

Category: Base or (Filtering, Registration, ''etc.'')

===Authors, Collaborators & Contact===
* Author1: Affiliation & logo, if desired
* Contributor1: Affiliation & logo, if desired
* Contributor2: Affiliation & logo, if desired
* Contact: name, email

===Module Description===
Overview of what the module does goes here.

== Usage ==

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

* Note use cases for which this module is especially appropriate, and/or link to examples.
* Link to examples of the module's use
* Link to any existing tutorials

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

* '''Input panel:'''
* '''Parameters panel:'''
* '''Output panel:'''
* '''Viewing panel:'''

== Development ==

===Dependencies===

Other modules or packages that are required for this module's use.

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.5

2009-06-29T22:57:28Z

Elhawary: New page: Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Registration Metrics=== MyModule {| |[[Image:Registr...

[[Documentation-3.5|Return to Slicer 3.5 Documentation]]

[[Announcements:Slicer3.5#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Documentation/3.5

2009-06-29T22:56:13Z

Elhawary: /* List of Modules new to 3.5 */

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

= Requirements for Modules =
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' 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.
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules new to 3.5=
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Nicolas Rannou, Sylvain Jaume)

* [[Modules:FourDAnalysis-Documentation-3.5|4D Image Analysis]] (Junichi Tokuda)
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]]
* [[Modules:ExractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)

=List of pre-existing Modules=
===Core===
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*Overview:
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies.
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment.
**Linear, affine and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output.
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis

===Tractography===
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)

Documentation/3.5

2009-06-29T22:55:06Z

Elhawary: /* List of Modules new to 3.5 */

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

= Requirements for Modules =
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' 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.
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules new to 3.5=
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Nicolas Rannou, Sylvain Jaume)

* [[Modules:FourDAnalysis-Documentation-3.5|4D Image Analysis]] (Junichi Tokuda)
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]]
* [[Modules:ExractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)
* [[Modules:RegistrationMetrics_Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)

=List of pre-existing Modules=
===Core===
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*Overview:
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies.
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment.
**Linear, affine and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output.
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis

===Tractography===
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)

Documentation/3.5

2009-06-29T22:54:56Z

Elhawary: /* List of Modules new to 3.5 */

=Modules=
*Please copy the template linked below, paste it into your page and customize it with your module's information.
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]
*See [[Documentation-3.5#Requirements for Modules|below]] for info to be put into the Help and Acknowledgment Tabs
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.5|My Module Name With Spaces] ] (First Last Name)

= Requirements for Modules =
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* The module is '''feature complete''', it does everything that it advertises it can do
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page.
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledgment''' 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.
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
| style="background: #e5e5e5" align="center"| Examples for the Help and
Acknowledgment Panels
|-
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
|}

=List of Modules new to 3.5=
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Nicolas Rannou, Sylvain Jaume)

* [[Modules:FourDAnalysis-Documentation-3.5|4D Image Analysis]] (Junichi Tokuda)
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]]
* [[Modules:ExractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)
* [[Modules:RegistrationMetrics_Documentation-3.5 | Registration Metrics (HD and DSC) ] (Haytham Elhawary)

=List of pre-existing Modules=
===Core===
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller)
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.4| Volume Rendering Module]] (Alex Yarmarkovich)

==Specialized Modules==

Please adhere to the naming scheme for the module documentation:
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)

===Wizards===
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)
===Informatics Modules===
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)
===Registration===
*Overview:
**The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies.
**The Transforms Module allows to manually align two volumes. This can be used for initial alignment.
**Linear, affine and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output.
**Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.
*[[Modules:RegisterImages-Documentation-3.4|Register Images]] (Stephen Aylward)
*[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)
*[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)
*[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek)
*[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen)
*[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)

===Segmentation===
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)

===Statistics===
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper)

===Diffusion===
====DWI====
*Estimation
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien von Siebenthal)
*Filter
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez)
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja Fernandez, Marc Niethammer)
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja Fernandez)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien von Siebenthal)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien von Siebenthal)

====DTI====
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)
*Analysis

===Tractography===
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich)
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien von Siebenthal)

===IGT===
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda)
===Filtering===
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin)
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen)
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen)
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen)
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen)
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)

===Surface Models===
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin)
*Grayscale Model Maker (Bill Lorensen)

*Freesurfer Surface Section Extraction (Katharina Quintus)
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)

===Batch processing===
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)

===Converters===
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)

Slicer3:RegistrationMetrics Documentation-3.5

2009-06-29T22:53:35Z

Elhawary: New page: Return to Slicer 3.5 Documentation Gallery of New Features __NOTOC__ ===Registration Metrics=== MyModule {| |[[Image:Registr...

Slicer3:Module Documentation-3.5 Template

2009-06-29T22:52:32Z

Elhawary:

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:51:41Z

Elhawary: /* Module Description */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. The HD is the maximum distance of a set to the nearest point in another set and gives a measure of contour alignment between structures. The DSC gives a measure of the volumetric overlap between the two segmented structures, and indicates twice the number of voxels which are shared by or are common to both structures divided by the total number of non-zero voxels in both structures. The DSC can range from zero to one, where zero is no alignment between images and one is perfect alignment. These two metrics are explained more formally in papers presented in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:49:00Z

Elhawary: /* References */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. These two metrics are explained in detail in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
The first publication refers to an explanation of the 95% Hausdorff distance and the second to the use of the Dice Similarity Coefficient.

*Archip N, Clatz O, Whalen S, et al. Non-rigid alignment of pre-operative MRI, fMRI, and DT-MRI with intra-operative MRI for enhanced visualization and navigation in image-guided neurosurgery. Neuroimage 2007; 35:609-624.
*A. Bharatha, M. Hirose, N. Hata, S. K. Warfield, M. Ferrant, K. H. Zou, E. Suarez-Santana, J. Ruiz-Alzola, A. D'Amico, R. A. Cormack, R. Kikinis, F. A. Jolesz, and C. M. Tempany, "Evaluation of three-dimensional finite element-based deformable registration of pre- and intraoperative prostate imaging," Med Phys, vol. 28(12), pp. 2551-60, 2001.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:46:14Z

Elhawary: /* Module Description */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images. These two metrics are explained in detail in the References section.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:44:59Z

Elhawary: /* Acknowledgment */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
This work was made possible by Grants Number 5U41RR019703, 1R01CA124377 and 5U54EB005149 from NIH, and by Intelligent Surgical Instruments Project of METI (Japan).

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:41:29Z

Elhawary: /* Source code & documentation */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:40:52Z

Elhawary: /* Source code & documentation */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Source code, color map and example data can be found [http://svn.na-mic.org/NAMICSandbox/trunk/IGTLoadableModules/RegistrationMetrics here].

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:39:11Z

Elhawary: /* Source code & documentation */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:RegistrationMetrics-Documentation-3.4

2009-06-29T22:38:57Z

Elhawary: /* Development */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]

[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]

__NOTOC__
===Registration Metrics===
MyModule

{|
|[[Image:RegistrationMetricsScreenshot.png|thumb|280px|Screen shot of Registration Metrics module showing an axial slice with a color map representing alignment error between the two label map images]]
|[[Image:SlicerPanel.PNG|thumb|280px|Screen shot of panel for Registration Metrics Module]]
|}

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

Type: CLI

Category: Registration

===Authors, Collaborators & Contact===
* Haytham Elhawary: Brigham and Women's Hospital, SPL
* Sota Oguro: Brigham and Women's Hospital, SPL
* Nobuhiko Hata: Brigham and Women's Hospital, SPL
* Contact: Haytham Elhawary, elhawary [at] bwh.harvard.edu

===Module Description===
This module is capable of calculating the 95% Hausdorff distance (HD) and the Dice Similarity Coefficient (DSC) between two label map images. If the two label map images represent registered segmented structures then the 95% HD and DSC will provide a measure of contour and volumetric alignment between the images.

== Usage ==

* Image Volume 1 and Image Volume 2 are two label map images which you wish to load and compare
* The module will provide the DSC and 95% HD between the two images, and will also provide an output volume. The output volume represents the contour of one of the images with each pixel value representing the Hausdorff Distance to the contour of the other image. Both the DSC and 95% HD will be printed onto the Log viewer in Slicer (can be accessed by clicking on the "X" icon that is located at the bottom right hand corner of the Slicer window) and on the Terminal for operating systems other than Windows.
* For improved visualization, the output image should be viewed with a color map. The code provides a color map entitled "Matlab_colormap.txt" which should be used for visualization of the output volume. Change the lower bound of the Threshold in the Display panel of the Volume Module to 0.01.

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

* Here are two example label map images, CTlabel.nrrd and Defolabel.nrrd: [[Media: ExampleData.tar.gz | ExampleData]]
* Load them into the RegistrationMetrics Module, which can be found under the Registration category in the Modules menu.
* The DSC should be 0.959906 and the 95% HD is 3.66408mm, which is printed into the Log Viewer in Slicer and the Terminal
* An output volume named "Registration Metrics Volume" should be created, which shows the contour of one of the input images.
* Go to the Module named "Color" and load the text file named "Matlab_colormap.txt", which is provided with the source code of the RegistrationMetrics Module.
* Go to the Volumes tab, choose "Registration Metrics Volume" as the Active Volume and then in the Display panel, choose "Matlab_colormap.txt" in the Color Select menu.
* Change threshold to "manual" and make the lower bound of the interval 0.01. Change the Window/Level to make the output volume take on the range of colors from blue to red.
* The red pixels represent the pixels that have the highest HD with respect to the contour of the other input image. The pixel value shows the HD. This shows which part of the contour is further away (i.e. have highest grade of misalignment) from the contour of the other input image.

== Development ==

===Dependencies===

No dependencies are required, except the Volume module to load images into Slicer.

===Source code & documentation===

Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.

[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

== More Information ==

===Acknowledgment===
Include funding and other support here.

===References===
Publications related to this module go here. Links to pdfs would be useful.