From f8f2aad1fe02693be184d4cca79bdf4facd19aad Mon Sep 17 00:00:00 2001
From: Jean-Christophe Fillion-Robin
The goal of this NSF funded project is to extend Auto3dgm to open source software platform and make it more user-friendly to a larger scientific community. Towards this goal, we developed the Auto3dgm module in 3D Slicer, an open source software platform for medical image informatics, image processing, and three-dimensional visualization. The module enables scientists to perform Auto3dgm on a collection of shapes effectively within 3D Slicer. The package also alllows users to visualize and save the aligned results to local machines for downstream analysis.
This project is supported by a NSF Advances in Biological Informatics Collaborative grant to Murat Maga (ABI-1759883), Adam Summers (ABI-1759637) and Doug Boyer (ABI-1759839).
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/ToothAndClaw/SlicerAuto3dgm/master/Auto3dgmScreenshot.png
diff --git a/AutomatedDentalTools.s4ext b/AutomatedDentalTools.s4ext
index d800bf3e1..c13dfa6f3 100644
--- a/AutomatedDentalTools.s4ext
+++ b/AutomatedDentalTools.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/DCBIA-OrthoLab/SlicerAutomatedDentalTools#readme
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Maxime Gillot (University of Michigan), Baptiste Baquero (UoM), Juan Carlos Prieto (University of North Carolina)
+contributors Maxime Gillot (University of Michigan), Baptiste Baquero (UoM), Juan Carlos Prieto (University of North Carolina), Nathan Hutin (UoM), Luc Anchling (UoM), Jeanne Claret (UoM)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
@@ -37,7 +37,7 @@ iconurl https://raw.githubusercontent.com/DCBIA-OrthoLab/SlicerAutomatedDentalTo
status
# One line stating what the module does
-description This extension will allow clinicians to perform automatic CBCT scan segmentation as well as automatic lamndmark identification in CBCT and IOS using machine learning tools
+description This extension will allow clinicians to perform automatic CBCT scan segmentation as well as automatic lamndmark identification in CBCT and IOS using machine learning tools.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/DCBIA-OrthoLab/SlicerAutomatedDentalTools/main/ADT-exemple.png
diff --git a/BigImage.s4ext b/BigImage.s4ext
index 2a6a68ba1..8c1fca65e 100644
--- a/BigImage.s4ext
+++ b/BigImage.s4ext
@@ -22,7 +22,7 @@ homepage https://slicerscope.github.io
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Yi Gao (Shenzhen University)
+contributors Yi Gao (Shenzhen University), Andras Lasso (PerkLab, Queen's University)
# Match category in the xml description of the module (where it shows up in Modules menu)
category BigImage
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/gaoyi/SlicerBigImage/main/SlicerBigIma
status
# One line stating what the module does
-description BigImage is the extension hosting 3D Slicer based GB-level microscopic image viewing and computing.
+description BigImage is the extension for viewing and analyzing big (>1GB) microscopy and other images.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/gaoyi/SlicerBigImage/main/Screenshots/1.png
diff --git a/BoneThicknessMapping.s4ext b/BoneThicknessMapping.s4ext
index 572f16c4e..2ca19b511 100644
--- a/BoneThicknessMapping.s4ext
+++ b/BoneThicknessMapping.s4ext
@@ -15,7 +15,7 @@ build_subdirectory .
homepage https://github.com/Auditory-Biophysics-Lab/SlicerBoneThicknessMappingExtension
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
-contributors Evan Simpson (Western University)
+contributors Evan Simpson (HML & SKA Lab, Western University)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Shape Analysis
@@ -27,10 +27,10 @@ iconurl https://raw.githubusercontent.com/Auditory-Biophysics-Lab/SlicerBoneThic
status beta
# One line stating what the module does
-description This module calculates and visualizes bone thickness of a volume using VTK ray-casting
+description 3D Slicer extension that calculates the bone thickness of a volume using VTK ray-casting.
# Space separated list of urls
-screenshoturls https://raw.githubusercontent.com/Auditory-Biophysics-Lab/SlicerBoneThicknessMappingExtension/master/Images/general_screenshot.png
+screenshoturls https://raw.githubusercontent.com/Auditory-Biophysics-Lab/SlicerBoneThicknessMappingExtension/master/Images/general_screenshot.png https://raw.githubusercontent.com/Auditory-Biophysics-Lab/Slicer-BoneThicknessMapping/master/Images/complete.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/BrainVolumeRefinement.s4ext b/BrainVolumeRefinement.s4ext
index bb76b36b2..8814a5e9d 100644
--- a/BrainVolumeRefinement.s4ext
+++ b/BrainVolumeRefinement.s4ext
@@ -28,7 +28,7 @@ contributors Antonio Carlos da S. Senra Filho, Fabricio H. Simozo, Luiz Otavio M
category Segmentation
# url to icon (png, size 128x128 pixels)
-iconurl https://www.slicer.org/slicerWiki/images/2/2c/BVeR-logo.png
+iconurl https://raw.githubusercontent.com/CSIM-Toolkits/SlicerBrainVolumeRefinement/master/BrainVolumeRefinement.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
diff --git a/Breast_DCEMRI_FTV.s4ext b/Breast_DCEMRI_FTV.s4ext
index 83529fde9..2da0e9890 100644
--- a/Breast_DCEMRI_FTV.s4ext
+++ b/Breast_DCEMRI_FTV.s4ext
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/rnadkarni2/SlicerBreast_DCEMRI_FTV/mas
status
# One line stating what the module does
-description This extension contains both of the modules needed to compute functional tumor volume (FTV) from a dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) exam of a breast cancer patient. The current version of this extension is intended for use on bilateral breast MR exams with axial slices.
+description This extension contains both of the modules needed to compute functional tumor volume (FTV) from a dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) exam of a breast cancer patient. The current version of this extension is intended for use on bilateral breast MR exams with axial slices.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/rnadkarni2/SlicerBreast_DCEMRI_FTV/master/Module1Screenshot.png https://raw.githubusercontent.com/rnadkarni2/SlicerBreast_DCEMRI_FTV/master/Module2Screenshot.png
diff --git a/CleverSeg.s4ext b/CleverSeg.s4ext
index 1dbaf0c25..aefc433b3 100644
--- a/CleverSeg.s4ext
+++ b/CleverSeg.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/lassoan/SlicerCleverSegmentation#cleversegmentation
# Jonathan Ramos ([University of São Paulo - USP, ] ICMC)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Jonathan Ramos (University of São Paulo - USP), ICMC
+contributors Jonathan Ramos (ICMC, University of São Paulo - USP)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/lassoan/SlicerCleverSegmentation/maste
status Beta
# One line stating what the module does
-description his is the implementation of the CleverSeg method that supports multi-label segmentations
+description This is the implementation of the CleverSeg method that supports multi-label segmentations
# Space separated list of urls
screenshoturls https://user-images.githubusercontent.com/3834596/66679138-d7dc1700-ec43-11e9-8c36-51976a1121d3.png https://user-images.githubusercontent.com/3834596/66679174-f215f500-ec43-11e9-84f1-85f8b5c4d568.png
diff --git a/DatabaseInteractor.s4ext b/DatabaseInteractor.s4ext
index 845bd5039..22f33db04 100644
--- a/DatabaseInteractor.s4ext
+++ b/DatabaseInteractor.s4ext
@@ -28,7 +28,7 @@ contributors Clement Mirabel (University of Michigan), Juan Carlos Prieto (UNC)
category Web System Tools
# url to icon (png, size 128x128 pixels)
-iconurl https://www.slicer.org/slicerWiki/images/7/7f/DatabaseInteractor_Logo.png
+iconurl https://raw.githubusercontent.com/DCBIA-OrthoLab/DatabaseInteractorExtension/master/DatabaseInteractor.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
@@ -38,7 +38,7 @@ status
description This extension can interact with online data in a database and local folders.
# Space separated list of urls
-screenshoturls https://www.slicer.org/slicerWiki/images/1/1f/FullView_DatabaseInteractor.png
+screenshoturls https://raw.githubusercontent.com/DCBIA-OrthoLab/DatabaseInteractorExtension/master/FullView_DatabaseInteractor.png https://raw.githubusercontent.com/DCBIA-OrthoLab/DatabaseInteractorExtension/master/DatabaseInteractor_Interface.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/DeveloperToolsForExtensions.s4ext b/DeveloperToolsForExtensions.s4ext
index 1c2799336..e8eff154e 100644
--- a/DeveloperToolsForExtensions.s4ext
+++ b/DeveloperToolsForExtensions.s4ext
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/Slicer/SlicerDeveloperToolsForExte
status
# One line stating what the module does
-description This extension offers different tools to help developers when they create Slicer extension.
+description This extension offers different tools to help developers when they create and maintain Slicer extension.
# Space separated list of urls
screenshoturls https://www.slicer.org/slicerWiki/images/5/54/SlicerExtension-SlicerDeveloperToolsForExtensions-Screenshot.png https://www.slicer.org/slicerWiki/images/d/db/SlicerExtensions-SlicerDeveloperToolsForExtensions-Screenshot-panels.png
diff --git a/DiffusionQC.s4ext b/DiffusionQC.s4ext
index 7e17cdf2b..bef780eb1 100644
--- a/DiffusionQC.s4ext
+++ b/DiffusionQC.s4ext
@@ -8,7 +8,7 @@ build_subdirectory .
homepage https://github.com/pnlbwh/SlicerDiffusionQC
-contributors Tashrif Billah, Isaiah Norton, Yogesh Rathi, Sylvain Bouix (Brigham & Women's Hospital).
+contributors Tashrif Billah (Brigham & Women's Hospital), Isaiah Norton (Brigham & Women's Hospital), Yogesh Rathi (Brigham & Women's Hospital), Sylvain Bouix (Brigham & Women's Hospital)
category Diffusion
diff --git a/ExtraMarkups.s4ext b/ExtraMarkups.s4ext
index 07f0517c0..bc2fef1e6 100644
--- a/ExtraMarkups.s4ext
+++ b/ExtraMarkups.s4ext
@@ -38,7 +38,7 @@ status
description This extension adds a Label markups node that draws an arrow with a text label, and a Shape markups node that can draw defined primitive shapes (circle, cone...). The result is controlled by placing usual control points in slice views and 3D views. Each object can be saved in scene and reloaded.
# Space separated list of urls
-screenshoturls https://github.com/chir-set/SlicerExtraMarkups/raw/main/Label/Label_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Cone_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Cylinder_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Disk_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Ring_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Sphere_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Tube_0.png
+screenshoturls https://github.com/chir-set/SlicerExtraMarkups/raw/main/Label/Label_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Cone_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Cylinder_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Disk_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Ring_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Sphere_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Tube_0.png https://github.com/chir-set/SlicerExtraMarkups/raw/main/Shape/Arc_0.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/IDCBrowser.s4ext b/IDCBrowser.s4ext
index 0655aa2a4..f397a7e07 100644
--- a/IDCBrowser.s4ext
+++ b/IDCBrowser.s4ext
@@ -22,7 +22,7 @@ contributors Andrey Fedorov (SPL and BWH)
category Informatics
# url to icon (png, size 128x128 pixels)
-iconurl https://github.com/ImagingDataCommons/SlicerIDCBrowser/blob/main/IDCBrowser/Resources/Icons/IDCBrowser_alpha.png
+iconurl https://raw.githubusercontent.com/ImagingDataCommons/SlicerIDCBrowser/main/IDCBrowser/Resources/Icons/IDCBrowser.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand beind?
diff --git a/ImageCompare.s4ext b/ImageCompare.s4ext
index 7752c2486..e4d604f61 100644
--- a/ImageCompare.s4ext
+++ b/ImageCompare.s4ext
@@ -20,7 +20,7 @@ build_subdirectory .
# homepage
homepage https://www.slicer.org/wiki/Documentation/Nightly/Extensions/ImageCompare
-contributors Paolo Zaffino(Magna Graecia Univeristy of Catanzaro, Italy), Maria Francesca Spadea(Magna Graecia Univeristy of Catanzaro, Italy)
+contributors Paolo Zaffino (Magna Graecia University of Catanzaro, Italy), Maria Francesca Spadea (Magna Graecia University of Catanzaro, Italy)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Quantification
diff --git a/KidneyStoneCalculator.s4ext b/KidneyStoneCalculator.s4ext
index a29c9fb9c..69a6adff1 100644
--- a/KidneyStoneCalculator.s4ext
+++ b/KidneyStoneCalculator.s4ext
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/fredericpanthier/SlicerKidneyStoneCalc
status
# One line stating what the module does
-description volumetric evaluation of kidney stones and estimatation of lithotripsy time (surgical duration)
+description Extension for volumetric evaluation of kidney stones and estimatation of lithotripsy time (surgical duration).
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/fredericpanthier/SlicerKidneyStoneCalculator/master/screenshot.jpg
diff --git a/LungCTAnalyzer.s4ext b/LungCTAnalyzer.s4ext
index 35b4e495b..5f170a494 100644
--- a/LungCTAnalyzer.s4ext
+++ b/LungCTAnalyzer.s4ext
@@ -12,7 +12,7 @@ scmrevision master
# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
-depends NA
+depends PyTorch SegmentEditorExtraEffects SurfaceWrapSolidify
# Inner build directory (default is ".")
build_subdirectory .
diff --git a/MONAILabel.s4ext b/MONAILabel.s4ext
index 771d1559f..751858770 100644
--- a/MONAILabel.s4ext
+++ b/MONAILabel.s4ext
@@ -38,7 +38,7 @@ status
description This extension offers Active Learning solution developed under project MONAILabel (Powered by the NVIDIA, KCL).
# Space separated list of urls
-screenshoturls https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/1.png
+screenshoturls https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/1.png https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/2.png https://github.com/Project-MONAI/MONAILabel/raw/main/plugins/slicer/MONAILabel/Screenshots/3.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/MONAIViz.s4ext b/MONAIViz.s4ext
index 3d727ef5f..25ac588f4 100644
--- a/MONAIViz.s4ext
+++ b/MONAIViz.s4ext
@@ -12,7 +12,7 @@ scmrevision main
# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
-depends NA
+depends PyTorch
# Inner build directory (default is ".")
build_subdirectory .
diff --git a/MUST-segmenter.s4ext b/MUST-segmenter.s4ext
index 72aa1b261..49ca26f6d 100644
--- a/MUST-segmenter.s4ext
+++ b/MUST-segmenter.s4ext
@@ -38,8 +38,7 @@ status
description Multiple SUV Thresholding (MUST)-segmenter is a semi-automated PET image segmentation tool that enables delineation of multiple lesions at once, and extracts the lesions' features.
# Space separated list of urls
-screenshoturls https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/Slicer-MUST-segmenter_screenshot.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/9.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/12.png
-https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/10.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/25.png
+screenshoturls https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/Slicer-MUST-segmenter_screenshot.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/9.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/12.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/10.png https://raw.githubusercontent.com/kyliekeijzer/Slicer-PET-MUST-segmenter/master/screenshots/25.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/MatlabBridge.s4ext b/MatlabBridge.s4ext
index 98e86f205..f475f4eea 100644
--- a/MatlabBridge.s4ext
+++ b/MatlabBridge.s4ext
@@ -35,7 +35,7 @@ iconurl https://www.slicer.org/slicerWiki/images/e/e8/MatlabBridgeLogo.png
status
# One line stating what the module does
-description The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer. The only prerequisites for running Matlab scripts are having this extension and Matlab installed on the 3D Slicer computer (building of 3D Slicer, MEX files, etc. is not needed).
+description The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer. The only prerequisites for running Matlab scripts are having this extension and Matlab installed on the 3D Slicer computer (building of 3D Slicer, MEX files, etc. is not needed). Extension version: 0.14.0.
# Space separated list of urls
screenshoturls https://www.slicer.org/slicerWiki/images/2/2f/MatlabBridgeScreenshot1.png https://www.slicer.org/slicerWiki/images/1/16/MatlabBridgeScreenshot2.png https://www.slicer.org/slicerWiki/images/b/b9/MatlabBridgeScreenshot3.png
diff --git a/ModelClip.s4ext b/ModelClip.s4ext
index 0187ad7f4..c608a4f55 100644
--- a/ModelClip.s4ext
+++ b/ModelClip.s4ext
@@ -28,7 +28,7 @@ contributors Jun LIN, Xiaojun CHEN, Ph.D (SJTU)
category Surface Models
# url to icon (png, size 128x128 pixels)
-iconurl https://www.slicer.org/slicerWiki/images/b/bd/ModelClipIcon.png
+iconurl https://raw.githubusercontent.com/jamesobutler/ModelClip/main/Resources/Icons/ModelClip.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
@@ -38,7 +38,7 @@ status
description This is an extension module to set the osteotomy trajectory with multiple planes and clip with just one click.
# Space separated list of urls
-screenshoturls https://www.slicer.org/slicerWiki/index.php/File:ModelClipScreenShot.png
+screenshoturls https://raw.githubusercontent.com/jamesobutler/ModelClip/main/ModelClipScreenShot.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/NNUNet.s4ext b/NNUNet.s4ext
index 624866df7..29594fde7 100644
--- a/NNUNet.s4ext
+++ b/NNUNet.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/KitwareMedical/SlicerNNUnet
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Thibault Pelletier (KITWARE SAS)
+contributors Thibault Pelletier (Kitware SAS)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
@@ -35,7 +35,7 @@ iconurl https://github.com/KitwareMedical/SlicerNNUnet/raw/main/SlicerNNUnet/Res
status stable
# One line stating what the module does
-description 3D Slicer nnUNet integration to streamline usage for nnUNet based AI extensions.
+description 3D Slicer nnUNet integration to streamline usage for nnUNet based AI extensions.
It allows for quick and relable nnUNet dependency installation in 3D Slicer environment and provides simple logic to launch nnUNet prediction on given directories.
The installation steps are based on the work done in the SlicerTotalSegmentator exension (https://github.com/lassoan/SlicerTotalSegmentator)
# Space separated list of urls
screenshoturls https://github.com/KitwareMedical/SlicerNNUnet/raw/main/Screenshots/1.png
diff --git a/NvidiaAIAssistedAnnotation.s4ext b/NvidiaAIAssistedAnnotation.s4ext
index 7599c074e..ee8cca03b 100644
--- a/NvidiaAIAssistedAnnotation.s4ext
+++ b/NvidiaAIAssistedAnnotation.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/NVIDIA/ai-assisted-annotation-client/tree/master/sli
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Sachidanand Alle (NVIDIA)
+contributors Sachidanand Alle (NVIDIA), Andras Lasso (PerkLab)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
diff --git a/OrthodonticAnalysis.s4ext b/OrthodonticAnalysis.s4ext
index 2d7e9c6b5..f24c188b3 100644
--- a/OrthodonticAnalysis.s4ext
+++ b/OrthodonticAnalysis.s4ext
@@ -35,12 +35,7 @@ iconurl https://raw.githubusercontent.com/OrthodonticAnalysis/SlicerOrthodonticA
status
# One line stating what the module does
-description The extension was developed to perform the most common dental analysis: model space discrepancies, Bolton and Peck and Peck. All point instructions for performing the analysis are available in Python interactor after study method points are selected. The Analysis button shows the result.
-The model discrepancy calculates the difference between the required space and the present space. If the difference is positive, there is an excess of space available, if the difference is negative, it means that there is a space deficit.
-The required upper and lower spaces are obtained from measurements of the mesiodistal diameters of the incisors, canines, and premolars. The present spaces are obtained in six straight line segments: from the mesial face of the first molar to the distal face of the canine, from the distal face of the canine to the mesial face of the canine and from the mesial face of the canine to the midline.
-Bolton's analysis takes into account two proportional size ratios between the upper and lower arches. The first is based on the sums of mesiodistal diameters of the teeth from the first molars, including the same, totaling 12 teeth per arch. The second is based on the sums of mesiodistal diameters of the teeth from the canines, including the canines, totaling 6 teeth per arch.
-The teeth evaluated in Peck and Peck analysis are the lower incisors. The measurements taken are the mesiodistal and buccolingual diameters. The value of the mesiodistal diameter is divided by the buccolingual diameter to obtain the proportion and make the evaluation.
-
+description The extension was developed to perform the most common dental analysis: model space discrepancies, Bolton and Peck and Peck. All point instructions for performing the analysis are available in Python interactor after study method points are selected. The Analysis button shows the result.
The model discrepancy calculates the difference between the required space and the present space. If the difference is positive, there is an excess of space available, if the difference is negative, it means that there is a space deficit.
The required upper and lower spaces are obtained from measurements of the mesiodistal diameters of the incisors, canines, and premolars. The present spaces are obtained in six straight line segments: from the mesial face of the first molar to the distal face of the canine, from the distal face of the canine to the mesial face of the canine and from the mesial face of the canine to the midline.
Bolton's analysis takes into account two proportional size ratios between the upper and lower arches. The first is based on the sums of mesiodistal diameters of the teeth from the first molars, including the same, totaling 12 teeth per arch. The second is based on the sums of mesiodistal diameters of the teeth from the canines, including the canines, totaling 6 teeth per arch.
The teeth evaluated in Peck and Peck analysis are the lower incisors. The measurements taken are the mesiodistal and buccolingual diameters. The value of the mesiodistal diameter is divided by the buccolingual diameter to obtain the proportion and make the evaluation.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/OrthodonticAnalysis/SlicerOrthodonticAnalysis/master/OrthodonticAnalysisScreenshot.png
diff --git a/OsteotomyPlanner.s4ext b/OsteotomyPlanner.s4ext
index d453eae41..ed2bc5e5c 100644
--- a/OsteotomyPlanner.s4ext
+++ b/OsteotomyPlanner.s4ext
@@ -28,7 +28,7 @@ contributors Sam Horvath (Kitware Inc.), Johan Andruejol (Kitware Inc.)
category Osteotomy Planning
# url to icon (png, size 128x128 pixels)
-iconurl https://github.com/KitwareMedical/OsteotomyPlanner/blob/master/ReplayPlan/Resources/Icons/ReplayPlan.png
+iconurl https://raw.githubusercontent.com/KitwareMedical/OsteotomyPlanner/master/ReplayPlan/Resources/Icons/ReplayPlan.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
diff --git a/PETCPhantom.s4ext b/PETCPhantom.s4ext
index 197b6dec8..8c6b28f5e 100644
--- a/PETCPhantom.s4ext
+++ b/PETCPhantom.s4ext
@@ -35,10 +35,10 @@ iconurl https://raw.githubusercontent.com/QIICR/SlicerPETPhantomAnalysis/mas
status
# One line stating what the module does
-description The PETCPhantom Extension allows measurement of calibration and uniformity in a cylinder phantom PET scan.
+description The PET Phantom Analysis Extension allows measurement of calibration and uniformity in a cylinder phantom PET scan.
# Space separated list of urls
-screenshoturls
+screenshoturls https://www.slicer.org/w/img_auth.php/0/01/PETCylinderPhantomAnalysisModule.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/PathReconstruction.s4ext b/PathReconstruction.s4ext
index ea52b16ab..63963442d 100644
--- a/PathReconstruction.s4ext
+++ b/PathReconstruction.s4ext
@@ -35,10 +35,10 @@ iconurl https://raw.githubusercontent.com/SlicerIGT/SlicerPathReconstruction
status experimental
# One line stating what the module does
-description The module allows creation of catheter models from electromagnetic spatial tracking.
+description This extension contains a module for reconstructing catheter paths from spatial tracking information. Intended users should have real-time tracking hardware (e.g. electromagnetic field generator and sensors) connected to 3D Slicer through OpenIGTLink network.
# Space separated list of urls
-screenshoturls
+screenshoturls https://www.slicer.org/w/img_auth.php/7/78/SlicerIGTScreenshot.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/PercutaneousApproachAnalysis.s4ext b/PercutaneousApproachAnalysis.s4ext
index 05945e672..f251d67b7 100644
--- a/PercutaneousApproachAnalysis.s4ext
+++ b/PercutaneousApproachAnalysis.s4ext
@@ -1,6 +1,6 @@
build_subdirectory .
category IGT
-contributors Koichiro Murakami (Shiga University of Medical Science, Japan, SPL), Laurent Chauvin (SPL), Junichi Tokuda (SPL)
+contributors Koichiro Murakami (Shiga University of Medical Science, Japan, SPL), Atsushi Yamada (Shiga University of Medical Science, Japan), Laurent Chauvin (SPL), Junichi Tokuda (SPL)
depends NA
description The Percutaneous Approach Analysis is used to calculate and visualize the accessibility of liver tumor with a percutaneous approach.
enabled 1
diff --git a/PickAndPaintExtension.s4ext b/PickAndPaintExtension.s4ext
index 6a2676b0b..945eed357 100644
--- a/PickAndPaintExtension.s4ext
+++ b/PickAndPaintExtension.s4ext
@@ -22,7 +22,7 @@ homepage https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Exten
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Lucie Macron (University of Michigan), Jean-Baptiste Vimort (University of Michigan)
+contributors Lucie Macron (University of Michigan), Jean-Baptiste Vimort (University of Michigan), James Hoctor (Kitware Inc.)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Shape Analysis
diff --git a/Pipelines.s4ext b/Pipelines.s4ext
index 32b53ef52..d0891522a 100644
--- a/Pipelines.s4ext
+++ b/Pipelines.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/KitwareMedical/SlicerPipelines/blob/main/README.md
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Connor Bowley (Kitware, Inc.), Sam Horvath (Kitware, Inc.)
+contributors Connor Bowley (Kitware, Inc.), Sam Horvath (Kitware, Inc.), Harald Scheirich (Kitware Inc.), David Allemang (Kitware Inc.)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Pipelines
@@ -35,10 +35,10 @@ iconurl https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Pi
status
# One line stating what the module does
-description SlicerPipelines is an extension for 3DSlicer that offers the ability to create simple modules (aka pipelines) via a GUI interface with no coding knowledge needed
+description SlicerPipelines is an extension for 3D Slicer that offers the ability to create simple modules (aka pipelines) via a GUI interface with no coding knowledge needed
# Space separated list of urls
-screenshoturls https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Screenshots/1.png https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Screenshots/2.png
+screenshoturls https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Screenshots/1.png https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Screenshots/2.png https://raw.githubusercontent.com/KitwareMedical/SlicerPipelines/main/Screenshots/3.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/PyTorch.s4ext b/PyTorch.s4ext
index 551371115..45b422f45 100644
--- a/PyTorch.s4ext
+++ b/PyTorch.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/fepegar/SlicerPyTorch
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Fernando Pérez-García (University College London and King's College London)
+contributors Fernando Pérez-García (University College London and King's College London), Andras Lasso (PerkLab Queen's University)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Utilities
diff --git a/Q3DC.s4ext b/Q3DC.s4ext
index 67510acff..2169fa305 100644
--- a/Q3DC.s4ext
+++ b/Q3DC.s4ext
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/DCBIA-OrthoLab/Q3DCExtension/master/Q3
status
# One line stating what the module does
-description This extension contains one module of the same name. Using placed fiducials, it allows users to compute 2D angles: Yaw, Pitch and Roll; and decompose the 3D distance into the three different components: R-L , A-P and S-I. It is possible to compute the middle point between two fiducials and export the values.
+description This extension contains one module of the same name. Using placed fiducials, it allows users to compute 2D angles: Yaw, Pitch and Roll; and decompose the 3D distance into the three different components: R-L, A-P and S-I. It is possible to compute the middle point between two fiducials and export the values.
# Space separated list of urls
screenshoturls https://www.slicer.org/slicerWiki/index.php/File:Q3DC_Interface.png
diff --git a/RVXLiverSegmentation.s4ext b/RVXLiverSegmentation.s4ext
index 3a7327f7f..24d2d0a5a 100644
--- a/RVXLiverSegmentation.s4ext
+++ b/RVXLiverSegmentation.s4ext
@@ -12,7 +12,7 @@ scmrevision main
# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
-depends MarkupsToModel SlicerVMTK SegmentEditorExtraEffects PyTorch
+depends SlicerVMTK MarkupsToModel SegmentEditorExtraEffects PyTorch
# Inner build directory (default is ".")
build_subdirectory .
@@ -22,7 +22,7 @@ homepage https://github.com/R-Vessel-X/SlicerRVXLiverSegmentation
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Lucie Macron (Kitware SAS), Thibault Pelletier (Kitware SAS), Camille Huet (Kitware SAS)
+contributors Lucie Macron (Kitware SAS), Thibault Pelletier (Kitware SAS), Camille Huet (Kitware SAS), Leo Sanchez (Kitware SAS)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
diff --git a/ResectionPlanner.s4ext b/ResectionPlanner.s4ext
index f75a8a9ee..bc92b4e3c 100644
--- a/ResectionPlanner.s4ext
+++ b/ResectionPlanner.s4ext
@@ -1,7 +1,7 @@
build_subdirectory .
category IGT
contributors Matt Lougheed (Queen's University)
-depends NA
+depends SlicerRT
description Modules for surgical resection planning.
enabled 1
homepage https://www.slicer.org/wiki/Documentation/Nightly/Extensions/ResectionPlanner
@@ -9,5 +9,5 @@ iconurl https://wiki.slicer.org/slicerWiki/images/d/d6/ResectionPlannerLogo.png
scm git
scmrevision master
scmurl https://github.com/SlicerIGT/ResectionPlanner.git
-screenshoturls https://www.slicer.org/slicerWiki/index.php/File:ResectionVolume_Screenshot.png
+screenshoturls https://www.slicer.org/w/img_auth.php/8/82/ResectionVolume_Screenshot.png
status
diff --git a/Sandbox.s4ext b/Sandbox.s4ext
index 7c9325e16..b98119703 100644
--- a/Sandbox.s4ext
+++ b/Sandbox.s4ext
@@ -38,7 +38,7 @@ status
description Collection of utilities that are not polished implementations but can be useful to users
# Space separated list of urls
-screenshoturls
+screenshoturls https://raw.githubusercontent.com/PerkLab/SlicerSandbox/master/RemovePatientTable.jpg https://raw.githubusercontent.com/PerkLab/SlicerSandbox/master/Lights.jpg
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/Scoliosis.s4ext b/Scoliosis.s4ext
index 20269cf87..1f090f3cd 100644
--- a/Scoliosis.s4ext
+++ b/Scoliosis.s4ext
@@ -25,7 +25,7 @@ homepage https://www.assembla.com/spaces/Scoliosis/wiki
contributors Franklin King (PerkLab, Queen's University), Tamas Ungi (PerkLab, Queen's University)
# Match category in the xml description of the module (where it shows up in Modules menu)
-category Scoliosis
+category Quantification
# url to icon (png, size 128x128 pixels)
iconurl https://www.slicer.org/slicerWiki/images/2/2b/ScoliosisLogo.png
diff --git a/SegmentEditorExtraEffects.s4ext b/SegmentEditorExtraEffects.s4ext
index 57415d69f..55cc41452 100644
--- a/SegmentEditorExtraEffects.s4ext
+++ b/SegmentEditorExtraEffects.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/lassoan/SlicerSegmentEditorExtraEffects
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Andras Lasso (PerkLab, Queen's), Kyle MacNeil
+contributors Andras Lasso (PerkLab, Queen's), Kyle MacNeil (Med-i Lab, Queen's; SPL, BWH), Andrey Fedorov (SPL, BWH)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Segmentation
diff --git a/SequenceRegistration.s4ext b/SequenceRegistration.s4ext
index 6e4bb3897..380c38cb3 100644
--- a/SequenceRegistration.s4ext
+++ b/SequenceRegistration.s4ext
@@ -22,7 +22,7 @@ homepage https://github.com/moselhy/SlicerSequenceRegistration
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Mohamed Moselhy (Western University), Andras Lasso (PerkLab, Queen's University)
+contributors Mohamed Moselhy (Western University), Andras Lasso (PerkLab, Queen's University), Feng Su (Western University)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Sequences
diff --git a/ShapeVariationAnalyzer.s4ext b/ShapeVariationAnalyzer.s4ext
index 5d3250707..8077ab0a7 100644
--- a/ShapeVariationAnalyzer.s4ext
+++ b/ShapeVariationAnalyzer.s4ext
@@ -22,13 +22,13 @@ homepage https://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extension
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Priscille de Dumast (University of Michigan), Laura Pascal (University of Michigan)
+contributors Priscille de Dumast (University of Michigan), Laura Pascal (University of Michigan), Nina Tubau (University of Michigan), Juan Carlos Prieto (University of North Carolina)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Quantification
# url to icon (png, size 128x128 pixels)
-iconurl https://www.slicer.org/slicerWiki/images/3/30/ShapeVariationAnalyzer-Logo.png
+iconurl https://raw.githubusercontent.com/DCBIA-OrthoLab/ShapeVariationAnalyzer/master/ShapeVariationAnalyzer.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
@@ -38,7 +38,7 @@ status
description ShapeVariationAnalyzer allows the classification of 3D models, according to their morphological variations. This tool is based on a deep learning neural network.
# Space separated list of urls
-screenshoturls https://www.slicer.org/slicerWiki/images/f/f0/FullView_ShapeVariationAnalyzer.png https://www.slicer.org/slicerWiki/images/5/57/ShapeVariationAnalyzer-GUI.png https://www.slicer.org/slicerWiki/images/3/30/ShapeVariationAnalyzer-Logo.png
+screenshoturls https://raw.githubusercontent.com/DCBIA-OrthoLab/ShapeVariationAnalyzer/master/doc/images/FullView_ShapeVariationAnalyzer.png https://raw.githubusercontent.com/DCBIA-OrthoLab/ShapeVariationAnalyzer/master/doc/images/ShapeVariationAnalyzer-GUI.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/SkeletalRepresentation.s4ext b/SkeletalRepresentation.s4ext
index c80b22621..f5096086c 100644
--- a/SkeletalRepresentation.s4ext
+++ b/SkeletalRepresentation.s4ext
@@ -22,10 +22,10 @@ homepage https://github.com/KitwareMedical/SlicerSkeletalRepresentation/blob/mas
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Zhiyuan Liu (University of North Carolina at Chapel Hill), Junpyo Hong (University of North Carolina at Chapel Hill), Stephen M. Pizer (University of North Carolina at Chapel Hill), Jared Vicory (Kitware, Inc.), Pablo Hernandez-Cerdan (Kitware, Inc.), Beatriz Paniagua (Kitware, Inc.), Jean-Christophe Fillion-Robin (Kitware, Inc.)
+contributors Zhiyuan Liu (University of North Carolina at Chapel Hill), Junpyo Hong (University of North Carolina at Chapel Hill), Stephen M. Pizer (University of North Carolina at Chapel Hill), Jared Vicory (Kitware, Inc.), Pablo Hernandez-Cerdan (Kitware, Inc.), Beatriz Paniagua (Kitware, Inc.), Jean-Christophe Fillion-Robin (Kitware, Inc.), Connor Bowley (Kitware, Inc.)
# Match category in the xml description of the module (where it shows up in Modules menu)
-category Topology, Skeletonization
+category Shape Analysis
# url to icon (png, size 128x128 pixels)
iconurl https://raw.githubusercontent.com/KitwareMedical/SlicerSkeletalRepresentation/master/img/SRep.png
@@ -35,10 +35,10 @@ iconurl https://raw.githubusercontent.com/KitwareMedical/SlicerSkeletalRepresent
status
# One line stating what the module does
-description Toolkit that provides users to establish, refine, and visualize skeletal representation of an object.
+description This extension allows for the creation, refinement, and viewing of Skeletal representations (s-reps).
# Space separated list of urls
-screenshoturls https://cdn.rawgit.com/KitwareMedical/SlicerSkeletalRepresentation/529b95bc/VisualizationScreenshot.png
+screenshoturls https://raw.githubusercontent.com/KitwareMedical/SlicerSkeletalRepresentation/529b95bc6d5275297c68b7666772242abd65b897/VisualizationScreenshot.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/SlicerBatchAnonymize.s4ext b/SlicerBatchAnonymize.s4ext
index 252a923cc..029e10ca0 100644
--- a/SlicerBatchAnonymize.s4ext
+++ b/SlicerBatchAnonymize.s4ext
@@ -28,7 +28,7 @@ contributors Hina Shah (UNC Chapel Hill), Juan Carlos Prieto (UNC, Chapel Hill)
category DSCI
# url to icon (png, size 128x128 pixels)
-iconurl https://github.com/hina-shah/SlicerBatchAnonymize/blob/main/SlicerBatchAnonymize.png
+iconurl https://raw.githubusercontent.com/hina-shah/SlicerBatchAnonymize/main/SlicerBatchAnonymize.png
# Give people an idea what to expect from this code
# - Is it just a test or something you stand behind?
@@ -38,7 +38,7 @@ status
description SlicerBatchAnonymize is a Slicer extension that provides a user friendly interface to anonymize a 'batch' of DICOM images.
# Space separated list of urls
-screenshoturls https://github.com/hina-shah/SlicerBatchAnonymize/blob/main/Documentation/GUIPreview.png
+screenshoturls https://raw.githubusercontent.com/hina-shah/SlicerBatchAnonymize/main/Documentation/GUIPreview.png
# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
diff --git a/SlicerCBCTToothSegmentation.s4ext b/SlicerCBCTToothSegmentation.s4ext
index 6dcd694ef..759dd93b3 100644
--- a/SlicerCBCTToothSegmentation.s4ext
+++ b/SlicerCBCTToothSegmentation.s4ext
@@ -22,10 +22,10 @@ homepage https://github.com/KitwareMedical/SlicerCBCTToothSegmentation
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Sadhana Ravikumar (Kitware Inc.)
+contributors Sadhana Ravikumar (Kitware Inc.), Jared Vicory (Kitware Inc.), James Fishbaugh (Kitware Inc.), Beatriz Paniagua (Kitware Inc.)
# Match category in the xml description of the module (where it shows up in Modules menu)
-category DentalCBCTToolkit
+category Segmentation
# url to icon (png, size 128x128 pixels)
iconurl https://raw.githubusercontent.com/KitwareMedical/SlicerCBCTToothSegmentation/master/CBCTToothSegmentation/Resources/Icons/CBCTToothSegmentation.png
diff --git a/SlicerCaseIterator.s4ext b/SlicerCaseIterator.s4ext
index 1ff858277..d0565039d 100644
--- a/SlicerCaseIterator.s4ext
+++ b/SlicerCaseIterator.s4ext
@@ -22,7 +22,7 @@ homepage https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SlicerCase
# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
-contributors Joost van Griethuysen (NKI)
+contributors Joost van Griethuysen (AVL-NKI), Christian Herz (CHOP)
# Match category in the xml description of the module (where it shows up in Modules menu)
category Utilities
@@ -35,7 +35,7 @@ iconurl https://raw.githubusercontent.com/JoostJM/SlicerCaseIterator/master/Slic
status beta
# One line stating what the module does
-description Simple scripted module that allows you to iterate through a set of cases defined in a csv-file.
+description Scripted module for iterating over a set of cases listed in a CSV file for segmentation or review.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/JoostJM/SlicerCaseIterator/master/SlicerCaseIterator-Screenshot.png
diff --git a/SlicerCervicalSpine.s4ext b/SlicerCervicalSpine.s4ext
index 1a37f49bf..96211d845 100644
--- a/SlicerCervicalSpine.s4ext
+++ b/SlicerCervicalSpine.s4ext
@@ -36,9 +36,7 @@ iconurl https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCe
status
# One line stating what the module does
-description Cervical Spine is the upper part of the spine that supports the head and the neck. It contains certebrae C1-C7. This extension provides tools for cervical spine segmentation in addition to ligaments insertion and origin points detetction. There are two modules in this extension. The first provide tools for a single cervical spine, the second provide the same tools for the whole cervical spine. This extension require few seconds to complete the task. It uses a cusomised set of parameters for elastix toolbox. The extension depends on SlicerElastix extension. It downloads a few necessary files so it will take some minutes when use first time. For testing, cervical spine sample datasets can be downloaded using Slicer Data Store module. This extension can be extended easily to cover registration and segmentation of the whole spine in addition to extract more spine points and features(future works). You are welcome to contribute by optimising the code or sharing your cervical spine dataset. For questions or problems using this extension please post in the gitHub issue or in Slicer forum. For more details please read the related publications:
-Ibraheem AL-Dhamari, Sabine Bauer, Eva Keller and Dietrich Paulus, (2019), Automatic Detection Of Cervical Spine Ligaments Origin And Insertion Points, EEE International Symposium on Biomedical Imaging (ISBI), Venice, Italy.
-Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, (2018), Automatic Multi-modal Cervical Spine Image Atlas Segmentation Using Adaptive Stochastic Gradient Descent, Bildverarbeitung für die Medizin 2018 pp 303-308.
+description The Cervical spine is the upper part of the spine that supports the head and its movements. It containes seven vertebrae C1 to C7. There are two modules in this extension (more are coming). Both modules do the same tasks but the first one for a single vertebra and the second module for the complete cervical spine.
Features:
1. Work on multi-modal images (so far it is tested against CT and MRI).
2. fast (around 5 seconds). 2. Automatic segmentation.
3. Automatic ligaments points detection.
4. Can be generalized to other parts of the spine or body. Cervical spien sample datasets are available in Slicer Data Store module.
You are welcome to contribute by correcting, enhancing, optimising the code or sharing your cervical spine dataset. For questions or problems using this extension please use gitHub issue or post in 3D Slicer forum. For more details please cite the related publications:
1. Ibraheem AL-Dhamari, Sabine Bauer, Eva Keller and Dietrich Paulus, Automatic Detection of Cervical Spine Ligaments Origin and Insertion Points. Accepted in The IEEE International Symposium on Biomedical Imaging (ISBI) 2019, Venice, Italy.
2. Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, (2018), Automatic Multi-modal Cervical Spine Image Atlas Segmentation Using Adaptive Stochastic Gradient Descent, Bildverarbeitung für die Medizin 2018 pp 303-308.
# Space separated list of urls
screenshoturls https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CS00.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CVT01.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CVT02.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CVT03.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CVT04.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CVT05.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CST01.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CST02.png https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCervicalSpine/master/Screenshots/CST03.png
diff --git a/SlicerCochlea.s4ext b/SlicerCochlea.s4ext
index 6f7dff013..684b52ce0 100644
--- a/SlicerCochlea.s4ext
+++ b/SlicerCochlea.s4ext
@@ -33,11 +33,7 @@ iconurl https://raw.githubusercontent.com/MedicalImageAnalysisTutorials/SlicerCo
status
# One line stating what the module does
-description The cochlea is a very important part of the inner ear. It is responsible for the transfer of audio signals to the brain. There are two modules in this extension. The first module, Cochlea Registration, registers and fuses cochlea images from different modalities. The second plugin, Cochlea Segmenttaion, segment out the cochlea structure, scala tympani and other scalae (media and vestibuli) in addition to measure the length and the size of the scala tympani. Both modules required a few seconds to complete the tasks. They use a cusomised set of parameters for elastix toolbox. The extension will download elastix binaries and other necessary files so it will take some minutes when use first time. For testing, cochlea sample datasets can be downloaded using Slicer Data Store module. You are welcome to contribute by optimising the code or sharing your cochlea dataset. For questions or problems using this extension please post in the gitHub issue or in Slicer forum. For more details please read the related publications:
-Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Rania Helal, Friedrich Lisseck and Roland Jacob, (2018), Automatic Cochlear Length and Volume Size Estimation, Accepted in: First International Workshop on Context-Aware Operating Theater OR 2, MICCAI 2018, Granada Spain.
-Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Roland Jacob, (2018), Automatic Cochlea Multi-modal Images Segmentation Using Adaptive Stochastic Gradient Descent. In: CI2018 DC Emerging Issues in Cochlear Implantation, Washington DC, USA. (link).
-Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus and Roland Jacob, (2017): Automatic Cochlea Segmentation Using Diffusion Snakes. In: 15th Symposium on Cochlear Implants in Children, CI 2017, San Francisco, USA (link).
-Ibraheem Al-Dhamari, Sabine Bauer, Dietrich Paulus, Friedrich Lisseck and Roland Jacob, (2017): ACIR: automatic cochlea image registration. In: Proceedings SPIE Medical Imaging 2017: Image Processing
+description The cochlea is a very important part of the inner ear. It is responsible for the transfer of audio signals to the brain.
There are two modules in this extension:
Both modules required a few seconds to complete the tasks. They use a customized set of parameters from elastix toolbox (itself using Insight Toolkit (ITK)). The extension will download elastix binaries and other necessary files so it will take some minutes when use first time. For testing, cochlea sample datasets can be downloaded using Slicer Data Store module.