https://public.kitware.com/Wiki/api.php?action=feedcontributions&user=Cates&feedformat=atomKitwarePublic - User contributions [en]2024-03-29T12:14:29ZUser contributionsMediaWiki 1.38.6https://public.kitware.com/Wiki/index.php?title=ITK/Fall_v4_2011_Meeting&diff=43525ITK/Fall v4 2011 Meeting2011-09-26T03:49:18Z<p>Cates: /* Attendance Matrix */</p>
<hr />
<div>ITKv4 Fall Meeting<br />
<br />
*'''Dates: September 27-28, 2011, Work day September 29, 2011'''<br />
** Start Time: 0800 (TBD), September 27<br />
** End Time: 1600 (TBD), September 28<br />
** Hackathon: 0800-1700 (TBD), September 29<br />
*'''City: Bethesda, MD'''<br />
*'''Location: NLM'''<br />
<br />
UPDATE: The hotel rooming block will be available until Wednesday, September 7, 2011.<br />
<br />
== Travel / Hotel Information ==<br />
<br />
NEW - The reservation deadline for the rooming block has been extended until September 7, 2011.<br />
<br />
The code for the block of rooms is '''"ITK"'''<br />
<br />
The Meeting will take place at the NLM in Bethesda, MD<br />
<br />
A block of hotel rooms has been set aside at the nearby DoubleTree Bethesda Hotel, $269/night.<br />
<br />
<br />
Doubletree Hotel Bethesda<br />
8120 Wisconsin Ave., Bethesda, MD<br />
(301) 652-2000<br />
<br />
Please make reservations before *September 7, 2011.* (extended from the original date of 2-Sep-2011).<br />
<br />
Points of interest for your ITK Travelers:<br />
- Guestrooms have Complimentary Wireless Internet<br />
- Location and Transportation to NIH<br />
4 Blocks or Just a 10 Minute Walk to Campus Visitors Entrance<br />
Hotel Provides an Hourly Complimentary Shuttle to Campus<br />
<br />
- Hotel has 4 Dining Options on Property<br />
The Cup- Starbucks Coffee, Pastries, and To- Go Sandwiches and Salads<br />
The OZ Restaurant- 3 Sophisticated Meals a Day: Full American Buffet Breakfast, Buffet and A La Carte Lunch Menu, Elegant yet Comforting Dinner Entrees and Ambiance<br />
The Bar- Beer on Tap, Mixed Drinks, 60 Wines by the Glass, and a Great Bar Menu, Perfect for the Gov. Per Diem Traveler<br />
Room Service- Full Menu Available 6:00am- 11:00pm Daily<br />
- Parking<br />
Valet Parking is $20 Overnight<br />
Public Parking Lot Behind Hotel is $0.75 per Hour<br />
- Other Complimentary Services<br />
24- Hour Gym<br />
24- Hour Free and Unlimited Business Center<br />
Wireless Internet in Lobby<br />
<br />
The hotel website is: <br />
<br />
http://www.doubletreebethesda.com<br />
<br />
<br />
* Additional details will be provided in the near future<br />
<br />
== Registration Information ==<br />
<br />
* Kitware will assist in<br />
** Collecting registration fees and<br />
** Dealing with caterers<br />
<br />
Please fill up the following form and<br />
email it to admin at kitware dot com<br />
<br />
* [[Media:ITKv4_Fall_Registration.pdf|Registration Form PDF]]<br />
<br />
== Meeting Room ==<br />
<br />
The opening session of the 2011 Fall ITKv4 meeting will be held in the NLM Visitor's Center, 9 AM-Noon, Tuesday 27-September-2001.<br />
<br />
The remaining sessions will be held in the NLM Board Room. Networking/WiFi support will be available in the Board Room.<br />
<br />
== Meeting Agenda ==<br />
<br />
=== Must See Topics ===<br />
<br />
Carried-over from June, 2011 meeting<br />
<br />
* [[ITK_Release_4 | ITKv4 Status: Beta Release]]<br />
<br />
* Projects<br />
** [[ITK_Release_4/GPU_Acceleration]]<br />
** [[ITK_Release_4/Modularization]]<br />
** [[ITK_Release_4/SimpleITK]]<br />
** [[ITK_Release_4/Wrapping]]<br />
** [[ITK_Release_4/DICOM]]<br />
** [[ITK_Release_4/Enhancing_Image_Registration_Framework]]<br />
** [[ITK_Release_4/Migration_Plan]]<br />
** [[ITK_Release_4/Refactoring_Level_Set_Framework]]<br />
** [[ITK_Release_4/ITK 3.x Migration Guidelines]]<br />
<br />
=== September 27th - A2D2 Summit ===<br />
<br />
* [[ITK_Release_4/The Team/A2D2 Development Team|A2D2 Development Team]]<br />
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]<br />
<br />
* 8:30 am Welcome: Terry Yoo<br />
<br />
<br />
=== September 28th ===<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
<br />
=== September 29th ===<br />
<br />
* [[Fall_ITKv4_2011_Meeting/Hackathon|Hackaton]]<br />
<br />
== Attendees ==<br />
<br />
Please add your name to the list below if you are planning to attend.<br />
<br />
=== Attendance Matrix ===<br />
<br />
{| border="1"<br />
|- bgcolor="#abcdef"<br />
! Name !! Organization !! Project !! September 27 !! September 28 !! September 29<br />
|-<br />
| Luis Ibanez || Kitware || ITKv4 || X || X || X<br />
|-<br />
| Bill Hoffman || Kitware || ITKv4 || X || X || <br />
|-<br />
| Stephen Aylward || Kitware || ITKv4 || X || X ||<br />
|-<br />
| Matt McCormick || Kitware || ITKv4 || X || X || X<br />
|-<br />
| Xiaoxiao Liu || Kitware || ITKv4 || X || X || X<br />
|-<br />
| Andinet Enquobahrie || Kitware || ITKv4 || X || X || X<br />
|-<br />
| Amitha Perera || Kitware || A2D2-VideoExt || X || X ||<br />
|-<br />
| Patrick Reynolds || Kitware || A2D2-(VideoExt,SCORE,SCORE++) || X || X || X<br />
|-<br />
| Andrew Wasem || CoSMo || ITKv4 || X || X ||<br />
|-<br />
|-<br />
| Raghu Machiraju || OSU || A2D2s || X || ||<br />
|-<br />
| Marc Niethammer || UNC || A2D2-Deconvolution || X || X ||<br />
|-<br />
| Cory Quammen || UNC || A2D2-Deconvolution || X || X ||<br />
|-<br />
| Hans Johnson || UIowa || ITKv4 || X || X || X <br />
|-<br />
| Bill Ryan || Mayo || ITKv4 || X || X || X <br />
|-<br />
| Sean Megason || HMS || ITKv4 || X || X || <br />
|-<br />
| Arnaud Gelas || HMS || ITKv4 || X || X || X<br />
|-<br />
| Bill Lorensen || Noware || ITK... || X || X ||<br />
|-<br />
| Marcel Prastawa || Utah || A2D2-SCORE || X || X || X<br />
|-<br />
| Suyash Awate || Utah || A2D2-Denoising || X || X || <br />
|-<br />
| Kris Zygmunt || Utah || A2D2-Denoising || X || X || <br />
|-<br />
| Josh Cates || Utah || A2D2-LongitudinalShape || X || X || <br />
|-<br />
| Michel Audette || Old Dominion || A2D2-FEM 3D registration || X || || <br />
|-<br />
| Jim Miller || GE Research || ITKv4 || X || X || <br />
|-<br />
| Dan Blezek || Mayo Clinic || ITKv4 || X || X || <br />
|-<br />
| Patrick Cheng || CNMC || A2D2-VideoGrabber || X || || <br />
|-<br />
| Ziv Yaniv || CNMC || A2D2-Registration || X || X || X <br />
|}</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41276Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T19:41:40Z<p>Cates: </p>
<hr />
<div>== Overlap and Similarity ==<br />
* Level of integration questions.<br />
* Bridges to 3rd party libs<br />
* Distribution questions: How to build/package with 3rd party libs. How to distribute data.<br />
<br />
== ITKv4 Features ==<br />
* GPU<br />
* Registration framework<br />
<br />
== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* Sample dataset for testing.<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Procrustes registration<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
* Future: support for mesh representation, GPU<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41275Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T18:02:49Z<p>Cates: /* ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling */</p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery <br />
== Overlap and Similarity ==<br />
* Level of integration questions.<br />
* Bridges to 3rd party libs<br />
* Distribution questions: How to build/package with 3rd party libs. How to distribute data.<br />
<br />
== ITKv4 Features ==<br />
* GPU<br />
* Registration framework<br />
<br />
<br />
== PBMNRRegistration ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Procrustes registration<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
* Future: support for mesh representation, GPU<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41274Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T18:00:44Z<p>Cates: /* Overlap and Similarity */</p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery <br />
== Overlap and Similarity ==<br />
* Level of integration questions.<br />
* Bridges to 3rd party libs<br />
* Distribution questions: How to build/package with 3rd party libs. How to distribute data.<br />
<br />
== ITKv4 Features ==<br />
* GPU<br />
* Registration framework<br />
<br />
<br />
== PBMNRRegistration ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
* Future: support for mesh representation, GPU<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41273Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:59:41Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery <br />
== Overlap and Similarity ==<br />
* Level of integration questions.<br />
* Distribution questions: How to build/package with 3rd party libs. How to distribute data.<br />
<br />
== ITKv4 Features ==<br />
* GPU<br />
* Registration framework<br />
<br />
<br />
== PBMNRRegistration ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
* Future: support for mesh representation, GPU<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41272Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:59:04Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery <br />
== Overlap and Similarity ==<br />
* Level of integration questions.<br />
* Distribution questions: How to build/package with 3rd party libs. How to distribute data.<br />
<br />
== ITKv4 Features ==<br />
* GPU<br />
* Registration framework<br />
<br />
<br />
(PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
* Future: support for mesh representation, GPU<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41271Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:50:59Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
<b>Distribution:</b><br />
External module?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<b>Distribution:</b> Currently external module. More integration?<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.<br />
<br />
<b>Distribution:</b><br />
ITK Module. Test applications. Integration with third party applications (ShapeWorks)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41270Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:46:07Z<p>Cates: /* Lesion Sizing Toolkit */</p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
* Annotations / metadata<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41267Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:36:35Z<p>Cates: /* Lesion Sizing Toolkit */</p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit and application. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41266Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:31:59Z<p>Cates: /* ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling */</p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Uses the core of an existing code base built from ITK: [http://www.nitrc.org/projects/shapeworks ShapeWorks NITRC Repository]<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
* Generic infrastructure for point-based surface representations<br />
* Cross-sectional and longitudinal analysis<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41265Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:27:43Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br><br />
<b>Inputs:</b> a segmentation mask, a mesh <br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs <br><br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br><br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41263Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:24:43Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Contributions:</b> New filters, classes. Application?<br />
<b>Inputs:</b> a segmentation mask, a mesh<br><br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Contributions:</b> Functioning toolkit. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs<br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41262Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:23:22Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Inputs:</b> a segmentation mask, a mesh<br><br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
<b>Contributions:</b> New filters, classes. Application?<br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br><br />
<b>Contributions:</b> Functioning toolkit. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs<br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br><br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41261Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:22:15Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Inputs:</b> a segmentation mask, a mesh<br><br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
<b>Contributions:</b> New filters, classes. Application?<br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br />
<b>Contributions:</b> Functioning toolkit. Possibly new ITK filters classes. Data.<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs<br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Inputs:</b> Segmentations<br />
<b>Outputs:</b> Point sets<br />
<b>Contributions:</b> New ITK module (particle system), filters, classes.<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41260Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T17:01:43Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Inputs:</b> a segmentation mask, a mesh<br><br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br />
<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs<br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Inputs:</b>Segmentations<br />
<b>Outputs:</b>Point sets<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module. New ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41259Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T16:56:47Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br><br><br />
<b>Inputs:</b> a segmentation mask, a mesh<br><br />
<b>Outputs:</b> deformation field, transformed image(s)<br><br />
<br><br />
# FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
# BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
# PBMSolver: PETSc dependence<br />
# ImageWarp: Already in ITK<br />
<br />
<b>What support is needed?</b><br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
<b>Gaps:</b><br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
<br />
<b>Data:</b><br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
<b>Inputs:</b> DICOM<br />
<b>Outputs:</b> Lesion volume measurements and segmentations.<br />
<br />
* Already in ITK as an external module. Contract is to port to use ITKv4 and distribute.<br />
* Using spatial objects as inputs and outputs<br />
<br />
<b>What support is needed?</b><br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups. e.g. Enhanced canny edge detection<br />
<br />
<b>Gaps:</b><br />
* Representing measures as a concept in ITK<br />
<br />
<b>Data:</b> 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<b>Inputs:</b>Segmentations<br />
<b>Outputs:</b>Point sets<br />
* Existing code base mostly ITK<br />
* Port significant portions to ITKv4<br />
* New ParticleSystem module, new ITK filter process objects.<br />
<br />
<b>What support is needed?</b><br />
* Logistics of integration and distribution, including data.<br />
<br />
<b>Data:</b> <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
<b>Gaps:</b> <br />
* Multivariate stats: Bridge to R for complex statistical analysis without going to file system. Only implement what is needed for within ITK algorithms.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41258Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T16:46:49Z<p>Cates: </p>
<hr />
<div>== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
The following is a rough pipeline of the method with proposed classes.<br />
<br />
Inputs: a segmentation mask, a mesh<br />
Outputs: deformation field, transformed image(s)<br />
<br />
1) FeaturePointSelection3dFilter: No dependencies. Plan to start implementation with this filter. <br />
2) BlockMatching3Dfilter: Similar to Penn FEM registration classes? Perhaps only need to implement a new metric? Plan to use the GPU infrastructure, but also have a non GPU version.<br />
3) PBMSolver: PETSc dependence<br />
4) ImageWarp: Already in ITK<br />
<br />
<br />
Gaps:<br />
* Mesh generation. Tetmesh reader / converter? Use Biomesh3D and bridge to ITK?<br />
* Self-updating transform object<br />
* PETSc & MPI within an ITK filter?<br />
<br />
What support is needed?<br />
* CMake integration w/ PETSc and MPI. Build / distribution issues.<br />
* Further discussion and collaboration with the FEM, registration, and GPU groups.<br />
<br />
Data:<br />
* ?<br />
<br />
== Lesion Sizing Toolkit ==<br />
Inputs: DICOM<br />
Outputs: Lesion volume measurements and segmentations.<br />
<br />
* Already in ITK as an external module. Contract is to reimplement with ITKv4 and distribute.<br />
<br />
* Using spatial objects as inputs and outputs<br />
* Should some of these algorithms be migrated into ITK proper? (e.g. enhanced canny edge detection)<br />
<br />
What support it needed?<br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups.<br />
<br />
Gaps:<br />
* Representing measures as a concept in ITK<br />
<br />
Data: 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<br />
Data: <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
Gaps: <br />
* Multivariate stats.<br />
* Bridge to R for complex statistical analysis without going to file system.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41257Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T16:39:40Z<p>Cates: </p>
<hr />
<div>== Lesion Sizing Toolkit ==<br />
Inputs: dicom<br />
Outputs: measures of volumes, segmentations<br />
<br />
* Already in ITK as an external module. Contract is to reimplement with ITKv4 and distribute.<br />
<br />
* Using spatial objects as inputs and outputs<br />
* Should some of these algorithms be migrated into ITK proper? (e.g. enhanced canny edge detection)<br />
<br />
What support it needed?<br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups.<br />
<br />
Gaps:<br />
* Representing measures as a concept in ITK<br />
<br />
Data: 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
== 3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration) ==<br />
<br />
The following is a rough pipeline of the method with proposed classes.<br />
(segmentation -> mesh gen -> registration -> petsc -> generate image (deformation field))<br />
Inputs: a mask, a mesh<br />
<br />
1) FeaturePointSelection3dFilter(mask, fixed image): start with this filter <br />
2) BlockMatching3Dfilter(fixed, moving, metrics,feature points) -- GPU, similar to penn fem registration classes, maybe metric plug in<br />
3) PBMSolver(displacement vector, mesh) --petsc dependence<br />
4) ImageWarp--already in ITK<br />
<br />
Outputs: deformation field, transformed image(s)<br />
<br />
Gaps:<br />
* Mesh generation, tetmesh reader / converter: Biomesh3D and bridge to ITK?<br />
* ITK Mesh<br />
* Self-updating transform object<br />
* Integration of solver<br />
* MPI with ITK?<br />
<br />
What support is needed?<br />
* CMake integration w/ petsc (uses MPI). Build / distribution<br />
* Interface w/ FEM guys, registration & GPU guys<br />
<br />
<br />
== ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling ==<br />
<br />
Data: <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
Gaps: <br />
* Multivariate stats.<br />
* Bridge to R for complex statistical analysis without going to file system.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Summer_ITKv4_ClinicalGroupMeetingNotes&diff=41256Summer ITKv4 ClinicalGroupMeetingNotes2011-06-27T16:39:07Z<p>Cates: Created page with "== Lesion Sizing Toolkit == Inputs: dicom Outputs: measures of volumes, segmentations * Already in ITK as an external module. Contract is to reimplement with ITKv4 and distribu..."</p>
<hr />
<div>== Lesion Sizing Toolkit ==<br />
Inputs: dicom<br />
Outputs: measures of volumes, segmentations<br />
<br />
* Already in ITK as an external module. Contract is to reimplement with ITKv4 and distribute.<br />
<br />
* Using spatial objects as inputs and outputs<br />
* Should some of these algorithms be migrated into ITK proper? (e.g. enhanced canny edge detection)<br />
<br />
What support it needed?<br />
* Does ITK want a tighter integration of these classes, and in this same form? Does this cover more general concepts useful to other groups.<br />
<br />
Gaps:<br />
* Representing measures as a concept in ITK<br />
<br />
Data: 60 datasets. Chest CT scans 1mm resolution. 200mb each. MIDAS? Store as DICOM? Automatically download using CTest.<br />
<br />
##3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery (PBMNRRegistration)<br />
<br />
The following is a rough pipeline of the method with proposed classes.<br />
(segmentation -> mesh gen -> registration -> petsc -> generate image (deformation field))<br />
Inputs: a mask, a mesh<br />
<br />
1) FeaturePointSelection3dFilter(mask, fixed image): start with this filter <br />
2) BlockMatching3Dfilter(fixed, moving, metrics,feature points) -- GPU, similar to penn fem registration classes, maybe metric plug in<br />
3) PBMSolver(displacement vector, mesh) --petsc dependence<br />
4) ImageWarp--already in ITK<br />
<br />
Outputs: deformation field, transformed image(s)<br />
<br />
Gaps:<br />
* Mesh generation, tetmesh reader / converter: Biomesh3D and bridge to ITK?<br />
* ITK Mesh<br />
* Self-updating transform object<br />
* Integration of solver<br />
* MPI with ITK?<br />
<br />
What support is needed?<br />
* CMake integration w/ petsc (uses MPI). Build / distribution<br />
* Interface w/ FEM guys, registration & GPU guys<br />
<br />
<br />
##ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling<br />
<br />
Data: <br />
* 25 longitudinal cardiac DE-MRI (1.25mm in-plane, 2.5mm thick) with segmentations of the left atrium. 2-4 datapoints each (pre ablation, 3mo, 6mo, 1 year)<br />
* Need IRB to release image data<br />
<br />
Gaps: <br />
* Multivariate stats.<br />
* Bridge to R for complex statistical analysis without going to file system.</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Summer_v4_2011_Meeting&diff=41244ITK/Summer v4 2011 Meeting2011-06-27T15:22:01Z<p>Cates: /* Monday Afternoon */</p>
<hr />
<div>ITKv4 Summer Meeting<br />
<br />
*'''Dates: June 27-29, 2011''' <br />
*'''City: Chapel Hill, NC'''<br />
*'''Location: Franklin Hotel<br />
<br />
== Travel / Hotel Information ==<br />
<br />
The Meeting will take place at the Franklin Hotel.<br />
<br />
* http://franklinhotelnc-px.trvlclick.com/index.html<br />
<br />
Since the meeting starts at<br />
<br />
* 8 am on June 27th,<br />
<br />
we recommend people to arrange their hotel accommodation for the previous night!<br />
<br />
* Use the room group 'ITKV4'<br />
** Reservation line: 866.831.5999<br />
** Ask for the "room block" reserved under 'ITKV4'<br />
* The rate is $129 / Night<br />
<br />
== Registration Information ==<br />
<br />
* Download [[Media:ITKv4 Summer2011Meeting Registration.pdf |Registration Form]]<br />
* It is a fillable PDF form<br />
* Fill it up please.<br />
** Indicate the number of days that you are attending.<br />
** Registration fee = ( NumberOfDays * $65 );<br />
** Print it as a PDF file<br />
*** since otherwise the form is still modifiable<br />
* Send the processed form back to Kitware<br />
** email it at: admin at kitware dot com<br />
<br />
== Meeting Room ==<br />
<br />
<br />
== Meeting Agenda ==<br />
<br />
* '''WARNING : THE AGENDA WAS REORGANIZED ON MAY 27th : PLEASE REVIEW'''<br />
<br />
=== Must See Topics ===<br />
<br />
* BETA Release<br />
* GPU<br />
* Modularization<br />
* SimpleITK<br />
* DICOM<br />
* Registration Refactoring<br />
* LevelSet Refactoring<br />
<br />
=== Monday June 27th - A2D2 Summit ===<br />
<br />
* [[ITK_Release_4/The Team/A2D2 Development Team|A2D2 Development Team]]<br />
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]<br />
<br />
==== Monday Morning ====<br />
<br />
* 8:30 am Welcome: Terry Yoo<br />
* 8:50 am State of the Toolkit: Hans Johnson [[http://www.vtk.org/Wiki/File:20110627ITKToolKitStatus.pdf#filelinks]] [[http://www.vtk.org/Wiki/File:20110627ITKToolKitStatus.pptx#filelinks]]<br />
* 9:10 am [[ITK_Release_4/New_Code_Contribution_Process|Procedures for integrating A2D2 contributions]] (Bill/Luis)<br />
* 9:30 am Split in to Focus Groups<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 10:00 Break<br />
* 10:30 am Working Groups (continuation)<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 12:00 pm Lunch<br />
<br />
==== Monday Afternoon ====<br />
<br />
* 1:00 pm Plenary: '''Group 1''' : 20min presentation + discussion<br />
* 2:00 pm Plenary: '''Group 2''' : 20min presentation + discussion [[Summer_ITKv4_ClinicalGroupMeetingNotes | Group 2 notes]]<br />
* 2:45 pm Break<br />
* 3:15 pm Plenary: '''Group 3''' : 20min presentation + discussion<br />
* 4:00 pm Plenary: '''Group 4''' : 20min presentation + discussion<br />
* 4:45 pm Adjourn<br />
<br />
==== Group Details ====<br />
<br />
===== Group 1: Microscopy and Histology =====<br />
<br />
# '''Ross Whitaker''' (designated speaker) ''Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics.''<br />
# '''Marc Niethammer''' ''Adding Deconvolution Algorithms to ITK'' [[Summer_ITKv4_2011_Meeting/A2D2/Deconvolution| Pre-Meeting Document]]<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies''<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Large Histology Segmentation and Visualization''<br />
<br />
===== Group 2: Clinical Applications and CADs =====<br />
<br />
# '''Thomas Fletcher''' (designated speaker) ''ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling''<br />
# '''Ricardo Avila''' ''Fostering Open Science for Lung Cancer Lesion Sizing''<br />
# '''Nikos Chrisochoides''' ''3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery''<br />
<br />
===== Group 3: Video =====<br />
<br />
# '''Amitha Perera''' and '''Patrick Reynolds''' (designated speakers) ''ITKExtensions for Video Processing'' [[Summer_ITKv4_2011_Meeting/A2D2/VideoExtensions| Pre-Meeting Document]]<br />
# '''Kevin Cleary''' ''Real-Time Image Capture for ITK through a Video Grabber''<br />
# '''John Galeotti''' ''Methods in Medical Image Analysis: An ITK-Based Course with Deliverable Algorithms that extends and evaluates ITK while broadening its developer base''<br />
<br />
===== Group 4: Data and Web-based Applications =====<br />
<br />
# '''Sean Megason''' (designated speaker) ''SCORE++: Crowd source data, automatic segmentation and ground truth for ITK4''<br />
# '''Marcel Prastawa''' ''SCORE: Systematic Comparison through Objective Rating and Evaluation''<br />
# '''Ziv Yaniv''' ''Framework for automated parameter tuning of ITK registration pipelines''<br />
<br />
===== Working Groups Tasks =====<br />
<br />
* Each PI or representative will share a brief summary (max 5min) of their proposal with the other members of the group.<br />
* Things to Discuss:<br />
*# How the A2D2s will advance the subject under consideration.<br />
*# Find possible overlaps and similarities between the A2D2s - solve them.<br />
*# Decide how the software will be distributed. (e.g. ITK module, ITK classes, independent software, IJ, etc...)<br />
*# List all the new classes/modules that will be contributed to ITK<br />
*# Discuss the design, architecture, and dependencies<br />
*# List ITKv4 features that you might need to use (e.g. GPU? Multi-thread? Streaming?)<br />
*# Discuss how each member of the group can help/assist each other<br />
*# Come-up with a plan of action and '''time-line'''<br />
*# Combine slides into a single presentation showing all the points that were discussed<br />
<br />
===== Plenary Sessions =====<br />
<br />
* Designated speaker will present<br />
* Each of the other members should be available to anser questions and/or provide additional explanation<br />
* Discuss possible problems and challenges<br />
<br />
==== Dinner ====<br />
==== Arrival Group Dinner ====<br />
<br />
<br />
* Hackfest at Kitware NC Office (KRS)<br />
<br />
* Location:<br />
<br />
Suite G-4<br />
101 East Weaver St<br />
Carrboro, North Carolina<br />
27510 USA<br />
518-371-3971 (voice/fax)<br />
<br />
http://www.kitware.com/company/NC_mapsdirections.html<br />
<br />
This is at walking distance from the Franklin Hotel.<br />
<br />
* Date: Monday June 27th<br />
* Time: 6pm-10pm<br />
<br />
* Hands Raised so Far:<br />
<br />
Terry, Bill, Stephen, Luis, Nick, Hans, Bill(ret), Arnaud, Cory<br />
<br />
=== Tuesday June 28th ===<br />
<br />
<br />
==== Tuesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Working Groups<br />
** '''Group 1''' ITK Revise<br />
** '''Group 2''' DICOM<br />
* 10:30 am Break<br />
* 11:00 am Working Groups<br />
** '''Group 3''' GPU and Multithreading<br />
** '''Group 4''' Simplify<br />
* 12:30 pm Lunch<br />
<br />
==== Tuesday Afternoon ====<br />
<br />
* 1:30 pm Plenary Session: '''Revise'''<br />
** 20min presentations and the discussion about Registration, FEM, LevelSets.<br />
* 3:00 pm Break<br />
* 3:30 pm Plenary Session: '''Simplify'''<br />
** 20min presentations and the discussion about SimpleITK, WrapITK, Doxygen for SimpleITK<br />
* 4:30 pm Plenary Session: '''GPU & Multithreading'''<br />
** 20min presentations and discussion<br />
* 5:30 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER<br />
** Mama Dip's<br />
*** http://www.mamadips.com/<br />
<br />
=== Wednesday June 29th ===<br />
<br />
==== Wednesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Plenary Session: '''DICOM'''<br />
** 20min presentation and discussion DCMTK, GDCM<br />
* 9:30 am Modularization (Bill Hoffman)<br />
* 10:00 am Break<br />
* 10:30 am Migration Guide (Gabe Hart / Dave Cole)<br />
* 11:00 am Road Ahead (What's Next ?) (Terry Yoo)<br />
<br />
* 12:00 pm Lunch<br />
<br />
==== Wednesday Afternoon ====<br />
<br />
* 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)<br />
* 1:30 pm Integration (Slicer/Wiki Examples/OTB/ImageJ/ICY/OME/V3D) (Bill Lorensen / Luis Ibanez)<br />
* 2:00 pm Code Revisions (Jim Miller)<br />
* 2:30 pm Break<br />
* 3:00 pm New Process for New Incoming Code (Bill Lorensen)<br />
* 3:30 pm Doxygen Documentation (Arnaud Gelas)<br />
* 4:00 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER for Survivors<br />
** Carolina Brewery.<br />
<br />
== Attendees ==<br />
<br />
Please add your name to the list below if you are planning to attend.<br />
<br />
=== Kitware ===<br />
<br />
* Luis Ibanez<br />
* Bill Hoffman<br />
* Stephen Aylward<br />
* David Cole <br />
* Marcus Hanwell<br />
* Xiaoxiao Liu (Lesion Sizing Toolkit)<br />
* Andinet Enquobahrie (A2D2 Registration)<br />
* Michel Audette (A2D2 Meshes)<br />
* Amitha Perera (A2D2 Video)<br />
* Gabe Hart (A2D2 Video / Simple ITK)<br />
* Patrick Reynolds (A2D2 Video/SCORE/SCORE++)<br />
* Brad Davis<br />
* Mike Grauer (SCORE/SCORE++/A2D2 Registration)<br />
* Jean-Christophe Fillion-Robin<br />
<br />
=== University of Iowa ===<br />
* Vincent Magnotta<br />
* Hans Johnson<br />
<br />
=== University of Pennsylvania ===<br />
*Brian Avants<br />
*James C. Gee<br />
*Nick Tustison<br />
<br />
=== Harvard University ===<br />
* Sean Megason<br />
* Arnaud Gelas<br />
* Won-Ki Jeong (SEAS)<br />
<br />
=== The Ohio State University ===<br />
<br />
* Raghu Machiraju<br />
* Kun Huang<br />
* Zhi Han<br />
<br />
=== College of William and Mary ===<br />
<br />
* Nikos Chrisochoides<br />
* Dr. Kot<br />
* Dr. Liu<br />
<br />
=== University of Utah ===<br />
<br />
* Ross Whitaker<br />
* Marcel Prastawa<br />
* Josh Cates<br />
* Kris Zygmunt<br />
<br />
=== Cosmo Software===<br />
<br />
* Drew Wasem<br />
* Ashish Sharma<br />
* Alex Gouaillard [A*STAR] (over the phone / internet)<br />
<br />
=== GE ===<br />
* Jim Miller<br />
* Dirk Padfield<br />
<br />
=== Mayo Clinic ===<br />
* Dan Blezek<br />
<br />
=== University of North Carolina ===<br />
<br />
* Cory Quammen<br />
* Marc Niethammer<br />
<br />
=== National Library of Medicine ===<br />
* Terry Yoo<br />
* Bradley Lowekamp<br />
* Jesus Caban<br />
<br />
=== Georgetown University / CNMC ===<br />
* Ziv Yaniv<br />
<br />
=== Noware ===<br />
* Bill Lorensen<br />
<br />
=== Bioscan ===<br />
* John McInerney<br />
<br />
=== Attendance Matrix ===<br />
<br />
{| border="1"<br />
|- bgcolor="#abcdef"<br />
! Name !! Monday June 27 !! Tuesday June 28 !! Wednesday June 29<br />
|-<br />
| Luis Ibanez || X || X || X<br />
|-<br />
| Bill Hoffman || || || <br />
|-<br />
| Stephen Aylward || || || <br />
|-<br />
| David Cole || || || <br />
|-<br />
| Marcus Hanwell || X || X || X <br />
|-<br />
| Xiaoxiao Liu || || || <br />
|-<br />
| Andinet Enquobahrie || || || <br />
|-<br />
| Michel Audette || || || <br />
|-<br />
| Amitha Perera || || || <br />
|-<br />
| Gabe Hart || || || <br />
|-<br />
| Patrick Reynolds || || || <br />
|-<br />
| Brad Davis || || || <br />
|-<br />
| Vincent Magnotta || || x || X<br />
|-<br />
| Hans Johnson || x || X || X <br />
|-<br />
| Brian Avants || || || <br />
|-<br />
| James C. Gee || || || <br />
|-<br />
| Nick Tustison || x || x || x <br />
|-<br />
| Sean Megason || x || x || x <br />
|-<br />
| Arnaud Gelas || x || x || x <br />
|-<br />
| Won-Ki Jeong || X || X || X <br />
|-<br />
| Raghu Machiraju || x || x || x<br />
|-<br />
| Kun Huang || || || <br />
|-<br />
| Zhi Han || || || <br />
|-<br />
| Nikos Chrisochoides || || || <br />
|-<br />
| Dr. Kot || || || <br />
|-<br />
| Dr. Liu || || || <br />
|-<br />
| Ross Whitaker || || || <br />
|-<br />
| Drew Wasem || X || X || X <br />
|-<br />
| Ashish sharma || X || X || X <br />
|-<br />
| Alex Gouaillard (remote) || || || <br />
|-<br />
| Jim Miller || X || X || X <br />
|-<br />
| Dirk Padfield || X || X || X <br />
|-<br />
| Dan Blezek || X || X || X <br />
|-<br />
| Cory Quammen || || || <br />
|-<br />
| Marc Niethammer || || || <br />
|-<br />
| Terry Yoo || || || <br />
|-<br />
| Bradley Lowekamp || || || <br />
|-<br />
| Jesus Caban || || || <br />
|-<br />
| Ziv Yaniv || X || X || <br />
|-<br />
| Bill Lorensen || X || X || X <br />
|-<br />
| Marcel Prastawa || X || || <br />
|-<br />
| Josh Cates || X || X || <br />
|-<br />
| Kris Zygmunt || X || X || X <br />
|-<br />
| Jean-Christophe Fillion-Robin || X || || <br />
|-<br />
<br />
|}</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Summer_v4_2011_Meeting&diff=40842ITK/Summer v4 2011 Meeting2011-06-16T17:40:02Z<p>Cates: /* Attendance Matrix */</p>
<hr />
<div>ITKv4 Summer Meeting<br />
<br />
*'''Dates: June 27-29, 2011''' <br />
*'''City: Chapel Hill, NC'''<br />
*'''Location: Franklin Hotel<br />
<br />
== Travel / Hotel Information ==<br />
<br />
The Meeting will take place at the Franklin Hotel.<br />
<br />
* http://franklinhotelnc-px.trvlclick.com/index.html<br />
<br />
Since the meeting starts at<br />
<br />
* 8 am on June 27th,<br />
<br />
we recommend people to arrange their hotel accommodation for the previous night!<br />
<br />
* Use the room group 'ITKV4'<br />
** Reservation line: 866.831.5999<br />
** Ask for the "room block" reserved under 'ITKV4'<br />
* The rate is $129 / Night<br />
<br />
== Registration Information ==<br />
<br />
* Download [[Media:ITKv4 Summer2011Meeting Registration.pdf |Registration Form]]<br />
* It is a fillable PDF form<br />
* Fill it up please.<br />
** Indicate the number of days that you are attending.<br />
** Registration fee = ( NumberOfDays * $65 );<br />
** Print it as a PDF file<br />
*** since otherwise the form is still modifiable<br />
* Send the processed form back to Kitware<br />
** email it at: admin at kitware dot com<br />
<br />
== Meeting Room ==<br />
<br />
<br />
== Meeting Agenda ==<br />
<br />
* '''WARNING : THE AGENDA WAS REORGANIZED ON MAY 27th : PLEASE REVIEW'''<br />
<br />
=== Must See Topics ===<br />
<br />
* BETA Release<br />
* GPU<br />
* Modularization<br />
* SimpleITK<br />
* DICOM<br />
* Registration Refactoring<br />
* LevelSet Refactoring<br />
<br />
=== Monday June 27th - A2D2 Summit ===<br />
<br />
* [[ITK_Release_4/The Team/A2D2 Development Team|A2D2 Development Team]]<br />
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]<br />
<br />
==== Monday Morning ====<br />
<br />
* 8:30 am Welcome: Terry Yoo<br />
* 8:50 am State of the Toolkit: Hans Johnson<br />
* 9:10 am Procedures for integrating A2D2 contributions (Bill/Luis)<br />
* 9:30 am Split in to Focus Groups<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 10:00 Break<br />
* 10:30 am Working Groups (continuation)<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 12:00 pm Lunch<br />
<br />
==== Monday Afternoon ====<br />
<br />
* 1:00 pm Plenary: '''Group 1''' : 20min presentation + discussion<br />
* 2:00 pm Plenary: '''Group 2''' : 20min presentation + discussion<br />
* 2:45 pm Break<br />
* 3:15 pm Plenary: '''Group 3''' : 20min presentation + discussion<br />
* 4:00 pm Plenary: '''Group 4''' : 20min presentation + discussion<br />
* 4:45 pm Adjourn<br />
<br />
==== Group Details ====<br />
<br />
===== Group 1: Microscopy and Histology =====<br />
<br />
# '''Ross Whitaker''' (designated speaker) ''Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics.''<br />
# '''Marc Niethammer''' ''Adding Deconvoltion Algorithms to ITK''<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies''<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Large Histology Segmentation and Visualization''<br />
<br />
===== Group 2: Clinical Applications and CADs =====<br />
<br />
# '''Thomas Fletcher''' (designated speaker) ''ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling''<br />
# '''Ricardo Avila''' ''Fostering Open Science for Lung Cancer Lesion Sizing''<br />
# '''Nikos Chrisochoides''' ''3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery''<br />
<br />
===== Group 3: Video =====<br />
<br />
# '''Amitha Perera''' and '''Patrick Reynolds''' (designated speakers) ''ITKExtensions for Video Processing''<br />
# '''Kevin Cleary''' ''Real-Time Image Capture for ITK through a Video Grabber''<br />
# '''John Galeotti''' ''Methods in Medical Image Analysis: An ITK-Based Course with Deliverable Algorithms that extends and evaluates ITK while broadening its developer base''<br />
<br />
===== Group 4: Data and Web-based Applications =====<br />
<br />
# '''Sean Megason''' (designated speaker) ''SCORE++: Crowd source data, automatic segmentation and ground truth for ITK4''<br />
# '''Marcel Prastawa''' ''SCORE: Systematic Comparison through Objective Rating and Evaluation''<br />
# '''Ziv Yaniv''' ''Framework for automated parameter tuning of ITK registration pipelines''<br />
<br />
===== Working Groups Tasks =====<br />
<br />
* Each PI or representative will share a brief summary (max 5min) of their proposal with the other members of the group.<br />
* Things to Discuss:<br />
*# How the A2D2s will advance the subject under consideration.<br />
*# Find possible overlaps and similarities between the A2D2s - solve them.<br />
*# Decide how the software will be distributed. (e.g. ITK module, ITK classes, independent software, IJ, etc...)<br />
*# List all the new classes/modules that will be contributed to ITK<br />
*# Discuss the design, architecture, and dependencies<br />
*# List ITKv4 features that you might need to use (e.g. GPU? Multi-thread? Streaming?)<br />
*# Discuss how each member of the group can help/assist each other<br />
*# Come-up with a plan of action and '''time-line'''<br />
*# Combine slides into a single presentation showing all the points that were discussed<br />
<br />
===== Plenary Sessions =====<br />
<br />
* Designated speaker will present<br />
* Each of the other members should be available to anser questions and/or provide additional explanation<br />
* Discuss possible problems and challenges<br />
<br />
==== Dinner ====<br />
==== Arrival Group Dinner ====<br />
<br />
* Irish Pub<br />
<br />
=== Tuesday June 28th ===<br />
<br />
<br />
==== Tuesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Working Groups<br />
** '''Group 1''' ITK Revise<br />
** '''Group 2''' DICOM<br />
* 10:30 am Break<br />
* 11:00 am Working Groups<br />
** '''Group 3''' GPU and Multithreading<br />
** '''Group 4''' Simplify<br />
* 12:30 pm Lunch<br />
<br />
==== Tuesday Afternoon ====<br />
<br />
* 1:30 pm Plenary Session: '''Revise'''<br />
** 20min presentations and the discussion about Registration, FEM, LevelSets.<br />
* 3:00 pm Break<br />
* 3:30 pm Plenary Session: '''Simplify'''<br />
** 20min presentations and the discussion about SimpleITK, WrapITK, Doxygen for SimpleITK<br />
* 4:30 pm Plenary Session: '''GPU & Multithreading'''<br />
** 20min presentations and discussion<br />
* 5:30 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER<br />
** Mama Dip's<br />
*** http://www.mamadips.com/<br />
<br />
=== Wednesday June 29th ===<br />
<br />
==== Wednesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Plenary Session: '''DICOM'''<br />
** 20min presentation and discussion DCMTK, GDCM<br />
* 9:30 am Modularization (Bill Hoffman)<br />
* 10:00 am Break<br />
* 10:30 am Migration Guide (Gabe Hart / Dave Cole)<br />
* 11:00 am Road Ahead (What's Next ?) (Terry Yoo)<br />
<br />
* 12:00 pm Lunch<br />
<br />
==== Wednesday Afternoon ====<br />
<br />
* 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)<br />
* 1:30 pm Integration (Slicer/Wiki Examples/OTB/ImageJ/ICY/OME/V3D) (Bill Lorensen / Luis Ibanez)<br />
* 2:00 pm Code Revisions (Jim Miller)<br />
* 2:30 pm Break<br />
* 3:00 pm New Process for New Incoming Code (Bill Lorensen)<br />
* 3:30 pm Doxygen Documentation (Arnaud Gelas)<br />
* 4:00 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER for Survivors<br />
** Carolina Brewery.<br />
<br />
== Attendees ==<br />
<br />
Please add your name to the list below if you are planning to attend.<br />
<br />
=== Kitware ===<br />
<br />
* Luis Ibanez<br />
* Bill Hoffman<br />
* Stephen Aylward<br />
* David Cole <br />
* Marcus Hanwell<br />
* Xiaoxiao Liu (Lesion Sizing Toolkit)<br />
* Andinet Enquobahrie (A2D2 Registration)<br />
* Michel Audette (A2D2 Meshes)<br />
* Amitha Perera (A2D2 Video)<br />
* Gabe Hart (A2D2 Video / Simple ITK)<br />
* Patrick Reynolds (A2D2 Video/SCORE/SCORE++)<br />
* Brad Davis<br />
* Mike Grauer (SCORE/SCORE++/A2D2 Registration)<br />
<br />
=== University of Iowa ===<br />
* Vincent Magnotta<br />
* Hans Johnson<br />
<br />
=== University of Pennsylvania ===<br />
*Brian Avants<br />
*James C. Gee<br />
*Nick Tustison<br />
<br />
=== Harvard University ===<br />
* Sean Megason<br />
* Arnaud Gelas<br />
* Won-Ki Jeong (SEAS)<br />
<br />
=== The Ohio State University ===<br />
<br />
* Raghu Machiraju<br />
* Kun Huang<br />
* Zhi Han<br />
<br />
=== College of William and Mary ===<br />
<br />
* Nikos Chrisochoides<br />
* Dr. Kot<br />
* Dr. Liu<br />
<br />
=== University of Utah ===<br />
<br />
* Ross Whitaker<br />
* Marcel Prastawa<br />
* Josh Cates<br />
<br />
=== Cosmo Software===<br />
<br />
* Drew Wasem<br />
* Ashish Sharma<br />
* Alex Gouaillard [A*STAR] (over the phone / internet)<br />
<br />
=== GE ===<br />
* Jim Miller<br />
* Dirk Padfield<br />
<br />
=== Mayo Clinic ===<br />
* Dan Blezek<br />
<br />
=== University of North Carolina ===<br />
<br />
* Cory Quammen<br />
* Marc Niethammer<br />
<br />
=== National Library of Medicine ===<br />
* Terry Yoo<br />
* Bradley Lowekamp<br />
* Jesus Caban<br />
<br />
=== Georgetown University / CNMC ===<br />
* Ziv Yaniv<br />
<br />
=== Noware ===<br />
* Bill Lorensen<br />
<br />
=== Bioscan ===<br />
* John McInerney<br />
<br />
=== Attendance Matrix ===<br />
<br />
{| border="1"<br />
|- bgcolor="#abcdef"<br />
! Name !! Monday June 27 !! Tuesday June 28 !! Wednesday June 29<br />
|-<br />
| Luis Ibanez || X || X || X<br />
|-<br />
| Bill Hoffman || || || <br />
|-<br />
| Stephen Aylward || || || <br />
|-<br />
| David Cole || || || <br />
|-<br />
| Marcus Hanwell || || || <br />
|-<br />
| Xiaoxiao Liu || || || <br />
|-<br />
| Andinet Enquobahrie || || || <br />
|-<br />
| Michel Audette || || || <br />
|-<br />
| Amitha Perera || || || <br />
|-<br />
| Gabe Hart || || || <br />
|-<br />
| Patrick Reynolds || || || <br />
|-<br />
| Brad Davis || || || <br />
|-<br />
| Vincent Magnotta || || || <br />
|-<br />
| Hans Johnson || || || <br />
|-<br />
| Brian Avants || || || <br />
|-<br />
| James C. Gee || || || <br />
|-<br />
| Nick Tustison || x || x || x <br />
|-<br />
| Sean Megason || x || x || x <br />
|-<br />
| Arnaud Gelas || x || x || x <br />
|-<br />
| Won-Ki Jeong || X || X || X <br />
|-<br />
| Raghu Machiraju || x || x || x<br />
|-<br />
| Kun Huang || || || <br />
|-<br />
| Zhi Han || || || <br />
|-<br />
| Nikos Chrisochoides || || || <br />
|-<br />
| Dr. Kot || || || <br />
|-<br />
| Dr. Liu || || || <br />
|-<br />
| Ross Whitaker || || || <br />
|-<br />
| Drew Wasem || X || X || X <br />
|-<br />
| Ashish sharma || X || X || X <br />
|-<br />
| Alex Gouaillard (remote) || || || <br />
|-<br />
| Jim Miller || X || X || X <br />
|-<br />
| Dirk Padfield || X || X || X <br />
|-<br />
| Dan Blezek || X || X || X <br />
|-<br />
| Cory Quammen || || || <br />
|-<br />
| Marc Niethammer || || || <br />
|-<br />
| Terry Yoo || || || <br />
|-<br />
| Bradley Lowekamp || || || <br />
|-<br />
| Jesus Caban || || || <br />
|-<br />
| Ziv Yaniv || X || X || <br />
|-<br />
| Bill Lorensen || X || X || X <br />
|-<br />
| Marcel Prastawa || X || || <br />
|-<br />
| Josh Cates || X || X || <br />
|-<br />
<br />
|}</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Summer_v4_2011_Meeting&diff=40841ITK/Summer v4 2011 Meeting2011-06-16T17:38:22Z<p>Cates: /* University of Utah */</p>
<hr />
<div>ITKv4 Summer Meeting<br />
<br />
*'''Dates: June 27-29, 2011''' <br />
*'''City: Chapel Hill, NC'''<br />
*'''Location: Franklin Hotel<br />
<br />
== Travel / Hotel Information ==<br />
<br />
The Meeting will take place at the Franklin Hotel.<br />
<br />
* http://franklinhotelnc-px.trvlclick.com/index.html<br />
<br />
Since the meeting starts at<br />
<br />
* 8 am on June 27th,<br />
<br />
we recommend people to arrange their hotel accommodation for the previous night!<br />
<br />
* Use the room group 'ITKV4'<br />
** Reservation line: 866.831.5999<br />
** Ask for the "room block" reserved under 'ITKV4'<br />
* The rate is $129 / Night<br />
<br />
== Registration Information ==<br />
<br />
* Download [[Media:ITKv4 Summer2011Meeting Registration.pdf |Registration Form]]<br />
* It is a fillable PDF form<br />
* Fill it up please.<br />
** Indicate the number of days that you are attending.<br />
** Registration fee = ( NumberOfDays * $65 );<br />
** Print it as a PDF file<br />
*** since otherwise the form is still modifiable<br />
* Send the processed form back to Kitware<br />
** email it at: admin at kitware dot com<br />
<br />
== Meeting Room ==<br />
<br />
<br />
== Meeting Agenda ==<br />
<br />
* '''WARNING : THE AGENDA WAS REORGANIZED ON MAY 27th : PLEASE REVIEW'''<br />
<br />
=== Must See Topics ===<br />
<br />
* BETA Release<br />
* GPU<br />
* Modularization<br />
* SimpleITK<br />
* DICOM<br />
* Registration Refactoring<br />
* LevelSet Refactoring<br />
<br />
=== Monday June 27th - A2D2 Summit ===<br />
<br />
* [[ITK_Release_4/The Team/A2D2 Development Team|A2D2 Development Team]]<br />
* [[ITK_Release_4/The Team/ITKv4 Development Team|ITKv4 Development Team]]<br />
<br />
==== Monday Morning ====<br />
<br />
* 8:30 am Welcome: Terry Yoo<br />
* 8:50 am State of the Toolkit: Hans Johnson<br />
* 9:10 am Procedures for integrating A2D2 contributions (Bill/Luis)<br />
* 9:30 am Split in to Focus Groups<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 10:00 Break<br />
* 10:30 am Working Groups (continuation)<br />
** '''Group1''' : Microscopy<br />
** '''Group2''' : Clinical Applications<br />
** '''Group3''' : Video<br />
** '''Group4''' : Data and Web-based Applications<br />
* 12:00 pm Lunch<br />
<br />
==== Monday Afternoon ====<br />
<br />
* 1:00 pm Plenary: '''Group 1''' : 20min presentation + discussion<br />
* 2:00 pm Plenary: '''Group 2''' : 20min presentation + discussion<br />
* 2:45 pm Break<br />
* 3:15 pm Plenary: '''Group 3''' : 20min presentation + discussion<br />
* 4:00 pm Plenary: '''Group 4''' : 20min presentation + discussion<br />
* 4:45 pm Adjourn<br />
<br />
==== Group Details ====<br />
<br />
===== Group 1: Microscopy and Histology =====<br />
<br />
# '''Ross Whitaker''' (designated speaker) ''Fast Nonlocal Algorithms for Denoising Microscopy, MRI, and Ultrasound Images Using Nonparametric Neighborhood Statistics.''<br />
# '''Marc Niethammer''' ''Adding Deconvoltion Algorithms to ITK''<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Robust Characterization of Microstructure for Cancer Studies''<br />
# '''Raghu Machiraju''' ''A Comprehensive Workflow for Large Histology Segmentation and Visualization''<br />
<br />
===== Group 2: Clinical Applications and CADs =====<br />
<br />
# '''Thomas Fletcher''' (designated speaker) ''ITK Algorithms for Analyzing Time-Varying Shape with Application to Longitudinal Heart Modeling''<br />
# '''Ricardo Avila''' ''Fostering Open Science for Lung Cancer Lesion Sizing''<br />
# '''Nikos Chrisochoides''' ''3D Real-Time Physics-Based Non-Rigid Registration for Image Guided Neurosurgery''<br />
<br />
===== Group 3: Video =====<br />
<br />
# '''Amitha Perera''' and '''Patrick Reynolds''' (designated speakers) ''ITKExtensions for Video Processing''<br />
# '''Kevin Cleary''' ''Real-Time Image Capture for ITK through a Video Grabber''<br />
# '''John Galeotti''' ''Methods in Medical Image Analysis: An ITK-Based Course with Deliverable Algorithms that extends and evaluates ITK while broadening its developer base''<br />
<br />
===== Group 4: Data and Web-based Applications =====<br />
<br />
# '''Sean Megason''' (designated speaker) ''SCORE++: Crowd source data, automatic segmentation and ground truth for ITK4''<br />
# '''Marcel Prastawa''' ''SCORE: Systematic Comparison through Objective Rating and Evaluation''<br />
# '''Ziv Yaniv''' ''Framework for automated parameter tuning of ITK registration pipelines''<br />
<br />
===== Working Groups Tasks =====<br />
<br />
* Each PI or representative will share a brief summary (max 5min) of their proposal with the other members of the group.<br />
* Things to Discuss:<br />
*# How the A2D2s will advance the subject under consideration.<br />
*# Find possible overlaps and similarities between the A2D2s - solve them.<br />
*# Decide how the software will be distributed. (e.g. ITK module, ITK classes, independent software, IJ, etc...)<br />
*# List all the new classes/modules that will be contributed to ITK<br />
*# Discuss the design, architecture, and dependencies<br />
*# List ITKv4 features that you might need to use (e.g. GPU? Multi-thread? Streaming?)<br />
*# Discuss how each member of the group can help/assist each other<br />
*# Come-up with a plan of action and '''time-line'''<br />
*# Combine slides into a single presentation showing all the points that were discussed<br />
<br />
===== Plenary Sessions =====<br />
<br />
* Designated speaker will present<br />
* Each of the other members should be available to anser questions and/or provide additional explanation<br />
* Discuss possible problems and challenges<br />
<br />
==== Dinner ====<br />
==== Arrival Group Dinner ====<br />
<br />
* Irish Pub<br />
<br />
=== Tuesday June 28th ===<br />
<br />
<br />
==== Tuesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Working Groups<br />
** '''Group 1''' ITK Revise<br />
** '''Group 2''' DICOM<br />
* 10:30 am Break<br />
* 11:00 am Working Groups<br />
** '''Group 3''' GPU and Multithreading<br />
** '''Group 4''' Simplify<br />
* 12:30 pm Lunch<br />
<br />
==== Tuesday Afternoon ====<br />
<br />
* 1:30 pm Plenary Session: '''Revise'''<br />
** 20min presentations and the discussion about Registration, FEM, LevelSets.<br />
* 3:00 pm Break<br />
* 3:30 pm Plenary Session: '''Simplify'''<br />
** 20min presentations and the discussion about SimpleITK, WrapITK, Doxygen for SimpleITK<br />
* 4:30 pm Plenary Session: '''GPU & Multithreading'''<br />
** 20min presentations and discussion<br />
* 5:30 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER<br />
** Mama Dip's<br />
*** http://www.mamadips.com/<br />
<br />
=== Wednesday June 29th ===<br />
<br />
==== Wednesday Morning ====<br />
<br />
* 8:30 am Welcome, Questions, Concerns<br />
* 9:00 am Plenary Session: '''DICOM'''<br />
** 20min presentation and discussion DCMTK, GDCM<br />
* 9:30 am Modularization (Bill Hoffman)<br />
* 10:00 am Break<br />
* 10:30 am Migration Guide (Gabe Hart / Dave Cole)<br />
* 11:00 am Road Ahead (What's Next ?) (Terry Yoo)<br />
<br />
* 12:00 pm Lunch<br />
<br />
==== Wednesday Afternoon ====<br />
<br />
* 1:00 pm Testing Data (Patric Reynolds / Bill Hoffman)<br />
* 1:30 pm Integration (Slicer/Wiki Examples/OTB/ImageJ/ICY/OME/V3D) (Bill Lorensen / Luis Ibanez)<br />
* 2:00 pm Code Revisions (Jim Miller)<br />
* 2:30 pm Break<br />
* 3:00 pm New Process for New Incoming Code (Bill Lorensen)<br />
* 3:30 pm Doxygen Documentation (Arnaud Gelas)<br />
* 4:00 pm Adjourn<br />
<br />
==== Dinner ====<br />
<br />
* GROUP DINNER for Survivors<br />
** Carolina Brewery.<br />
<br />
== Attendees ==<br />
<br />
Please add your name to the list below if you are planning to attend.<br />
<br />
=== Kitware ===<br />
<br />
* Luis Ibanez<br />
* Bill Hoffman<br />
* Stephen Aylward<br />
* David Cole <br />
* Marcus Hanwell<br />
* Xiaoxiao Liu (Lesion Sizing Toolkit)<br />
* Andinet Enquobahrie (A2D2 Registration)<br />
* Michel Audette (A2D2 Meshes)<br />
* Amitha Perera (A2D2 Video)<br />
* Gabe Hart (A2D2 Video / Simple ITK)<br />
* Patrick Reynolds (A2D2 Video/SCORE/SCORE++)<br />
* Brad Davis<br />
* Mike Grauer (SCORE/SCORE++/A2D2 Registration)<br />
<br />
=== University of Iowa ===<br />
* Vincent Magnotta<br />
* Hans Johnson<br />
<br />
=== University of Pennsylvania ===<br />
*Brian Avants<br />
*James C. Gee<br />
*Nick Tustison<br />
<br />
=== Harvard University ===<br />
* Sean Megason<br />
* Arnaud Gelas<br />
* Won-Ki Jeong (SEAS)<br />
<br />
=== The Ohio State University ===<br />
<br />
* Raghu Machiraju<br />
* Kun Huang<br />
* Zhi Han<br />
<br />
=== College of William and Mary ===<br />
<br />
* Nikos Chrisochoides<br />
* Dr. Kot<br />
* Dr. Liu<br />
<br />
=== University of Utah ===<br />
<br />
* Ross Whitaker<br />
* Marcel Prastawa<br />
* Josh Cates<br />
<br />
=== Cosmo Software===<br />
<br />
* Drew Wasem<br />
* Ashish Sharma<br />
* Alex Gouaillard [A*STAR] (over the phone / internet)<br />
<br />
=== GE ===<br />
* Jim Miller<br />
* Dirk Padfield<br />
<br />
=== Mayo Clinic ===<br />
* Dan Blezek<br />
<br />
=== University of North Carolina ===<br />
<br />
* Cory Quammen<br />
* Marc Niethammer<br />
<br />
=== National Library of Medicine ===<br />
* Terry Yoo<br />
* Bradley Lowekamp<br />
* Jesus Caban<br />
<br />
=== Georgetown University / CNMC ===<br />
* Ziv Yaniv<br />
<br />
=== Noware ===<br />
* Bill Lorensen<br />
<br />
=== Bioscan ===<br />
* John McInerney<br />
<br />
=== Attendance Matrix ===<br />
<br />
{| border="1"<br />
|- bgcolor="#abcdef"<br />
! Name !! Monday June 27 !! Tuesday June 28 !! Wednesday June 29<br />
|-<br />
| Luis Ibanez || X || X || X<br />
|-<br />
| Bill Hoffman || || || <br />
|-<br />
| Stephen Aylward || || || <br />
|-<br />
| David Cole || || || <br />
|-<br />
| Marcus Hanwell || || || <br />
|-<br />
| Xiaoxiao Liu || || || <br />
|-<br />
| Andinet Enquobahrie || || || <br />
|-<br />
| Michel Audette || || || <br />
|-<br />
| Amitha Perera || || || <br />
|-<br />
| Gabe Hart || || || <br />
|-<br />
| Patrick Reynolds || || || <br />
|-<br />
| Brad Davis || || || <br />
|-<br />
| Vincent Magnotta || || || <br />
|-<br />
| Hans Johnson || || || <br />
|-<br />
| Brian Avants || || || <br />
|-<br />
| James C. Gee || || || <br />
|-<br />
| Nick Tustison || x || x || x <br />
|-<br />
| Sean Megason || x || x || x <br />
|-<br />
| Arnaud Gelas || x || x || x <br />
|-<br />
| Won-Ki Jeong || X || X || X <br />
|-<br />
| Raghu Machiraju || x || x || x<br />
|-<br />
| Kun Huang || || || <br />
|-<br />
| Zhi Han || || || <br />
|-<br />
| Nikos Chrisochoides || || || <br />
|-<br />
| Dr. Kot || || || <br />
|-<br />
| Dr. Liu || || || <br />
|-<br />
| Ross Whitaker || || || <br />
|-<br />
| Drew Wasem || X || X || X <br />
|-<br />
| Ashish sharma || X || X || X <br />
|-<br />
| Alex Gouaillard (remote) || || || <br />
|-<br />
| Jim Miller || X || X || X <br />
|-<br />
| Dirk Padfield || X || X || X <br />
|-<br />
| Dan Blezek || X || X || X <br />
|-<br />
| Cory Quammen || || || <br />
|-<br />
| Marc Niethammer || || || <br />
|-<br />
| Terry Yoo || || || <br />
|-<br />
| Bradley Lowekamp || || || <br />
|-<br />
| Jesus Caban || || || <br />
|-<br />
| Ziv Yaniv || X || X || <br />
|-<br />
| Bill Lorensen || X || X || X <br />
|-<br />
| Marcel Prastawa || X || || <br />
|-<br />
<br />
|}</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8292ITK/Copyright Transfers Status2007-02-21T17:50:22Z<p>Cates: /* Copyright Transfer Agreed by Authors */</p>
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<div>= Copyright Transfer Status Page =<br />
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This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)<br />
* Gaetan Lehmann : ModulusImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : InvertIntensityImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : WrapITK (received 2/14/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8291ITK/Copyright Transfers Status2007-02-21T17:50:06Z<p>Cates: /* Copyright Transfer Received by the ISC */</p>
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<div>= Copyright Transfer Status Page =<br />
<br />
This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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<br />
In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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* Alex Gouillard : itkQMesh<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)<br />
* Gaetan Lehmann : ModulusImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : InvertIntensityImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : WrapITK (received 2/14/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8258ITK/Copyright Transfers Status2007-02-08T22:01:03Z<p>Cates: /* Copyright Transfer Agreed by Authors */</p>
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<div>= Copyright Transfer Status Page =<br />
<br />
This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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<br />
In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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The process of transferring copyright is tracked here through three stages:<br />
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* The ISC request an author to transfer the copyright of a specific group of files<br />
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* Alex Gouillard : itkQMesh<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
<br />
This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)<br />
* Gaetan Lehmann : ModulusImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : InvertIntensityImageFilter (received 2/8/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8257ITK/Copyright Transfers Status2007-02-08T22:00:42Z<p>Cates: /* Copyright Transfer Received by the ISC */</p>
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<div>= Copyright Transfer Status Page =<br />
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This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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* Gaetan Lehmann : InvertIntensityImageFilter<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)<br />
* Gaetan Lehmann : ModulusImageFilter (received 2/8/2007)<br />
* Gaetan Lehmann : InvertIntensityImageFilter (received 2/8/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8256ITK/Copyright Transfers Status2007-02-07T23:25:55Z<p>Cates: /* Copyright Transfer Aggreed by Authors */</p>
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<div>= Copyright Transfer Status Page =<br />
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In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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* Gaetan Lehmann : InvertIntensityImageFilter<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8255ITK/Copyright Transfers Status2007-02-07T23:25:28Z<p>Cates: /* Copyright Transfer Status Page */</p>
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<div>= Copyright Transfer Status Page =<br />
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This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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The authors listed here have verbally or by email aggreed to transfer the copyright of their code to the ISC. Their copyright transfer aggreements are in the process of being sent, or are already in the mail.<br />
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* Gaetan Lehmann : InvertIntensityImageFilter<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
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* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code (received 2/1/2007)<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter (received 2/7/2007)<br />
* Gaetan Lehmann : Morphological Reconstruction Filters (received 2/7/2007)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Copyright_Transfers_Status&diff=8254ITK/Copyright Transfers Status2007-02-07T17:51:42Z<p>Cates: /* Copyright Transfer Received by the ISC */</p>
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<div>= Copyright Transfer Status Page =<br />
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This page summarizes the Status of Copyright Transfer letters associated to code that is under consideration for inclusion in the Insight Toolkit. <br />
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In most cases this code is contributed as part of submissions to the Insight Journal.<br />
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The authors listed here have verbally or by email aggreed to transfer the copyright of their code to the ISC. Their copyright transfer aggreements are in the process of being sent, or are already in the mail.<br />
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* Alex Gouillard : itkQMesh<br />
* Gaetan Lehmann : ModulusImageFilter<br />
* Gaetan Lehmann : InvertIntensityImageFilter<br />
* Gaetan Lehmann : ReconstructionByDilationImageFilter<br />
* Gaetan Lehmann : MorphologicalGradientImageFilter<br />
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== Copyright Transfer Received by the ISC ==<br />
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This list states the authors and code items for which the ISC has received copyright transfer aggreements.<br />
<br />
* Hans Johnson : Octree classes<br />
* Su Yong : 'How to Use ITK and MFC' source code</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Conference_2005&diff=2035ITK/Conference 20052005-09-22T18:11:13Z<p>Cates: /* Program */</p>
<hr />
<div>= ITK Conference - October 2005 - Bethesda Maryland =<br />
<br />
== Organization ==<br />
<br />
The Insight Software Consortium and the National Library of Medicine are organizing the first ITK Conference to be held in Bethesda Maryland on October 12-14 2005.<br />
<br />
== Context ==<br />
<br />
The ITK Conference will reunite developers and users of the Insight Toolkit and will provide an environment for discussing the use of the toolkit and its future development. We expect 50-100 attendees including NIH and other Federal Program Managers, ITK developers, and those interested in the future of the Insight Segmentation and Registration Toolkit (http://www.itk.org).<br />
<br />
== Program ==<br />
<br />
* Thursday 13 October 2005<br />
** 8:30 - 9:00 Introduction<br />
** 9:00 - 11:00 Key Note Panel: "Open Source Software Licensing." Speakers include Lawrence Rosen, lawyer and author of the text "Open Source Licensing" [[http://www.rosenlaw.com/oslbook.htm]]<br />
** 11:00 - 11:30 Break<br />
** 11:30 - 12:30 Presentations by A2D2 contractors awarded in 2004 (20 minutes per awardee)<br />
** 12:30 - 13:30 Lunch<br />
** 13:30 - 15:30 Presentations by A2D2 contractors awarded in 2004 (20 minutes per awardee)<br />
** ISC Administrative meeting (attendence limited; agenda is available [[http://www.insightsoftwareconsortium.org/wiki/index.php/AdministrationMeeting-2005.10.12 HERE]])<br />
<br />
* Friday 14 October 2005<br />
** 9:00 - 10:00 ISC Discussion on licensing and backward compatibility (open to all)<br />
** 10:00 - 10:30 Break<br />
** 10:30 - 12:30 Presentations "Challenges to the Biological Imaging Community." We are expecting to have 3-5 speakers describing challenges to the ITK community.<br />
** 12:30 - 13:30 Lunch<br />
** 13:30 - 15:30 Envisioning ITK: Toolkit Road map for 2005-2006 and into the future<br />
<br />
== Venue ==<br />
<br />
=== Location ===<br />
<br />
The ITK Conference will be held at the NIH Campus in Bethesda Maryland. <br />
<br />
Lister Hill Center Auditorium<br />
National Library of Medicine<br />
National Institutes of Health (NIH) <br />
8600 Rockville Pike<br />
Bethesda<br />
Maryland 20894<br />
<br />
<br />
<br />
http://www.nlm.nih.gov/<br />
<br />
<br />
http://www.nlm.nih.gov/about/lhcaud_full.pdf<br />
<br />
<br />
Visitor information is available at <br />
<br />
http://www.nih.gov/about/visitor/index.htm<br />
<br />
in particular the visitor map<br />
<br />
http://dtts.ors.od.nih.gov/visitor_access_map.htm<br />
<br />
==== Security ====<br />
<br />
Given that the NIH campus is a Federal Building, certain security procedures are in place for getting access to the building<br />
<br />
Details on the security procedures can be found at<br />
<br />
http://www.nih.gov/about/visitorsecurity.htm<br />
<br />
Note in particular that you MUST bring a photo identification in order to enter NIH facilities.<br />
<br />
<br />
==== Laptops ====<br />
<br />
If you bring computers/laptops to the NIH campus, please make sure that you register them with the security officer upon entering the building. You will receive a tag for your computer, that you should present againt when leaving the building with your computer.<br />
<br />
<br />
==== Parking ====<br />
<br />
Please be advised that Parking spaces are very limited at the NIH campus. <br />
<br />
If you are in town you may want take the Metro up to the station "Medical Center" that is just next to the NIH campus.<br />
<br />
Information about the Metro schedules and stations can be found at<br />
http://www.wmata.com/<br />
<br />
If you stay in any of the hotels suggested below, you will be at walking distance from the campus entrance.<br />
<br />
=== Hotels ===<br />
<br />
The following hotels are suggested for their proximity to the NIH campus.<br />
<br />
This suggestion is subject to the NIH disclaimer<br />
<br />
http://www.nih.gov/about/disclaim.htm<br />
<br />
<br />
The following link will show you hotels close to the NIH campus.<br />
<br />
* [http://maps.google.com/maps?q=hotels&ll=38.999254,-77.096530&spn=0.046322,0.081050&t=k&near=9000+Rockville+pike+Bethesda+maryland+20892&num=10&start=0&hl=en Hotels in Google Maps / Satelite view]<br />
<br />
* [http://maps.google.com/maps?q=hotels&ll=38.999254,-77.096530&spn=0.046322,0.081050&near=9000+Rockville+pike+Bethesda+maryland+20892&num=10&start=0&hl=en Hotels in Google Maps / Map view]<br />
<br />
The following link will show you the location of the NIH campus in Earth Google<br />
<br />
* [http://earth.google.com/ Download Earth Google]<br />
<br />
* [http://www.itk.org/Wiki/images/e/e0/NIH_Bethesda_Campus_GoogleEarth_Image.jpg Aerial view of the NIH Campus and nearby hotels]</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Conference_2005&diff=1950ITK/Conference 20052005-08-10T23:47:43Z<p>Cates: /* Organization */</p>
<hr />
<div>= ITK Conference - October 2005 - Bethesda Maryland =<br />
<br />
== Organization ==<br />
<br />
The Insight Software Consortium and the National Library of Medicine are organizing the first ITK Conference to be held in Bethesda Maryland on October 12-14 2005.<br />
<br />
== Context ==<br />
<br />
The ITK Conference will reunite developers and users of the Insight Toolkit and will provide an environment for discussing the use of the toolkit and its future development.<br />
<br />
<br />
== Program (Tentative) ==<br />
<br />
This is a first Draft of the programm<br />
<br />
* Wednesday 12 October 2005<br />
** Meeting of the Insight Software Consortium (ISC) Board.<br />
*** Agenda is available [[http://www.insightsoftwareconsortium.org/wiki/index.php/AdministrationMeeting-2005.10.12 HERE]]<br />
* Thursday 13 October 2005<br />
** Key Note: "Open Source Software Licensing"<br />
** Presentations by A2D2 contractors awarded in 2004<br />
* Friday 14 October 2005<br />
** Applications: How is ITK being used<br />
** Toolkit Road map for 2005-2006<br />
<br />
== Venue ==<br />
<br />
=== Hotels ===<br />
=== Location ===</div>Cateshttps://public.kitware.com/Wiki/index.php?title=Proposals:DeprecationProcedure&diff=2771Proposals:DeprecationProcedure2005-05-03T23:19:47Z<p>Cates: /* The following is the draft of the policy on backward compatibility from the ISC */</p>
<hr />
<div>== Backward Compatibility ==<br />
<br />
=== The following is the draft of the policy on backward compatibility from the ISC ===<br />
<br />
The developers of open-source software toolkits should make every effort to maintain backward compatibility within its major versions (e.g., from Version 1.2 to 1.3). Specifically, the API of the existing methods should not change, the API of technologies used internal to the methods (e.g., the streaming system) will not change, and the API of new methods will conform to that of the existing methods.<br />
<br />
Across major versions (e.g. from Version 1.x to 2.0), the APIs of the toolkit may change if it is in the best interest of the toolkit so as to provide effective and consistent implementations of the methods and features that are being sought by its users. When making a major version release, the following should be considered:<br />
<br />
* Intent to release a major update must be announced to the developers 3 months in advance<br />
* Every API change will be well documented in a single descriptive file, included with the distribution<br />
* Every effort will be made to provide scripts to facilitate user software updating<br />
* Deprecated files will be moved to a deprecated directory.<br />
* Files in the deprecated directory from the last major update will be removed.<br />
* Deprecated methods will display an appropriate warning at runtime when used within a program. The warning should describe the means of fixing the compatibility issue.<br />
* Deprecated methods from the last major revision will be removed.<br />
<br />
Bug fixed should be applied to a branch of an old version only when specifically requested, when it will benefit a sufficient number of users, and when it will not cause an API change. Users should instead be encouraged to adopt the current release.<br />
<br />
Users are strongly encouraged to consult a toolkit’s web pages and join its user’s list to stay current on the changes occurring within the toolkit. Archiving your installation prior to upgrading to a new major version is also recommended.<br />
<br />
This policy is being reviewed and modified by an ISC subcommittee, consisting of Ross Whitaker, Bill Lorensen, and Will Schroeder. Comments/suggestions are welcome!</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/FAQ&diff=906ITK/FAQ2005-02-28T21:32:20Z<p>Cates: /* Build->Rebuild All in MS VC++ reloads all projects */</p>
<hr />
<div>== General information and availability ==<br />
=== Do I need FLTK to build ITK ? ===<br />
No,<br />
<br />
ITK does not require FLTK. FLTK is only used in particular demo applications in the InsightApplications directory.<br />
<br />
ITK does not provide any GUI functionality. When building full applications, the GUI is provided by other libraries such as Qt (http://www.trolltech.com/products/qt/index.html), FLTK (http://www.fltk.org/) Gtk+ (http://www.gtk.org/) or wxWidgets (http://www.wxwidgets.org/, which used to be called wxWindows).<br />
<br />
If you want to build the demo applications that require FLTK, you must install FLTK in your system. The recommended version is 1.1.4 that can be obtained from ftp.fltk.org and from the "RelatedSoftware" page in www.itk.org.<br />
<br />
Once FLTK is installed in your system, you will have to enable the USE_FLTK option when you run CMake to configure InsightApplications.<br />
<br />
=== Do I need VTK to build ITK ? ===<br />
No,<br />
<br />
ITK does not require VTK.<br />
<br />
VTK is only used by specific demo applications in the Insight/Applications directory. These applications will simply not be build if VTK is not available in your system.<br />
<br />
ITK does not provide any visualization functionalities. Applications requiring visualization should implement those functionalities from internal code or libraries like OpenGL, GLUT or VTK.<br />
<br />
In order to use ITK with VTK you must build VTK from sources and make sure that it is configured with the flag USE_ANSI_STDLIB enabled.<br />
<br />
Then you have to reconfigure ITK making sure that the option USE_VTK is enabled.<br />
<br />
=== Do I need GLUT/OpenGL to build ITK ===<br />
No,<br />
<br />
ITK does not depend on GLUT not OpenGL.<br />
<br />
GLUT and OpenGL are only used by specific demo applications in the Insight/Applications directory.<br />
<br />
ITK does not provide any visualization functionalities. Applications requiring visualization should obtain these services from external libraries like OpenGL, GLUT or VTK.<br />
<br />
=== Do I need Tcl to build ITK ===<br />
No,<br />
<br />
ITK does not depend on Tcl.<br />
<br />
However, there are three ways in which ITK is related to Tcl:<br />
<br />
# The testing system used by ITK dashboard is managed by Dart which is writen mostly in Tcl. If you want to configure experimental, continuous or nightly builds in your system using Dart. You will need Tcl installed.<br />
# ITK can be wrapped in order to be used from Tcl.<br />This is done using "Cable". That gives ITK the versatility needed for developing rapid prototyping, and facilitating interactive teaching and experimentaion with ITK classes.<br />
# Some demo applications in the Insight/Applications directory have configured their visualization by using VTK. These demo-applications have packaged ITK filters inside VTK filters and then wrapped those into Tcl using the traditional Tcl wrapping mechanism of VTK.<br />
<br />
=== What version of FLTK is required by ITK demo applications ===<br />
The recommended version of fltk is 1.1.4.<br />
<br />
The sources can be obtained from ftp.fltk.org <br />
<br />
ftp://ftp.fltk.org/pub/fltk/1.1.4/<br />
<br />
or from the "Related Software" page in www.itk.org.<br />
<br />
FLTK is not needed for building ITK itself. FLTK is only used by<br />
some of the demo applications distributed in InsightApplications<br />
<br />
FLTK is in continuous development and it has been quite difficult to keep track of its configuration changes.<br />
<br />
Also note that InsightApplications is not any more part of the core Insight Toolkit but is a standalone package.<br />
<br />
=== What additional packages are required by each demo-application ===<br />
The following list rapidly summarizes the additional pacakges required by demo applications in the Insight/Applications directory.<br />
<br />
The following applications require VTK wrapped for Tcl. These applications insert ITK filters into VTK objects and then wrapp them to be used from Tcl.<br />
<br />
* MRIRegistration<br />
* SegmentationEditor<br />
* vtkITK<br />
<br />
This wrapping is done with the traditional VTK wrapping mechanism which is totally independdent of ITK mechanism based on Cable.<br />
<br />
FLTK is used in the following demo applications to implement their GUI. The recommended version can be downloaded from http://www.itk.org/HTML/DownloadRelatedSoftware.htm<br />
<br />
* DistanceMapFilter<br />
* DicomImageViewer<br />
* GaussianFilter<br />
* GradientRecursiveGaussianFilter<br />
* Curves2DExtractor<br />
* Morphogenesis<br />
* MutualInformationEuler2DRegistration<br />
* ImageRegistration<br />
* ImageRegistration2D<br />
* RawImageReaderViewer<br />
* RegionGrowingSegmentation<br />
* ThresholdSegmentationLevelSet<br />
* FastMarchingLevelSet<br />
* ShapeDetectionLevelSet<br />
* MetaImageViewer<br />
* MetaImageColorViewer<br />
* SurfaceGenerator<br />
<br />
Among the applications using FLTK for GUI, the following applications also require VTK for visualizing segmented images in 3D:<br />
<br />
* RegionGrowingSegmentation<br />
* ThresholdSegmentationLevelSet<br />
* FastMarchingLevelSet<br />
* ShapeDetectionLevelSet<br />
<br />
There is also an example of how to use Qt for GUI along with ITK:<br />
<br />
* QtITK<br />
<br />
=== What 3D file formats can ITK import and export? ===<br />
<br />
The following table identifies the file formats that ITK can read/write via a factory mechanism based on the file extension (itk::ImageIOFactory). Some proprietary files format are only imported. More information on [[ITK File Formats]] is available, including data types supported.<br />
<br />
A very nice tool for viewing all of these images is ImageViewer which can be found in the InsightApplication package (fltk is required).<br />
<br />
{| border="1" cellpadding="2" cellspacing="0"<br />
|- bgcolor="#abcdef"<br />
! File Format<br />
! Read/Write<br />
! Import<br />
|-<br />
| Analyze 7.5 || AnalyzeImageIO ||<br />
|-<br />
| BMP &dagger; || BMPImageIO ||<br />
|-<br />
| Dicom || || DicomImageIO<br />
|-<br />
| GE 4x || || GE4ImageIO<br />
|-<br />
| GE 5x || || GE5ImageIO<br />
|-<br />
| GE Advantage Windows || || GEAdwImageIO<br />
|-<br />
| Gipl (.gipl) || GiplImageIO ||<br />
|-<br />
| IPLCommon || || IPLCommonImageIO<br />
|-<br />
| JPEG &dagger; || JPEGImageIO ||<br />
|-<br />
| MetaImage (.mha/.mhd) || MetaImageIO ||<br />
|-<br />
| PNG &dagger; || PNGImageIO ||<br />
|-<br />
| Raw &Dagger; || RawImageIO ||<br />
|-<br />
| Siemens Vision || || SiemensVisionImageIO<br />
|-<br />
| Stimulate (spr/sdt) || StimulateImageIO ||<br />
|-<br />
| TIFF || TIFFImageIO ||<br />
|-<br />
| VTK Structured Points || VTKImageIO ||<br />
|}<br />
<br />
&dagger; BMP, PNG and JPEG are not very good formats for 3D medical images. They only support 2D images and a limited set of pixel types such as unsigned char, and unsigned short. The great advantage of BMP, PNG and JPEG is that you can view them with almost any image viewer. It is possible to read/write 3D datasets as collections of 2D slices each one in an independent BMP, PNG or JPEG file by using the ImageSerierReader and ImageSeriesWriter.<br />
<br />
&Dagger; It is higly recommended not using this format. RAW is not a format, it is insufficient, inconsistent and simply dangerous. A RAW file without a header is useless, and once you add a header, it is not RAW anymore.<br />
<br />
=== What if my file format is not supported by ITK ? ===<br />
If ITK doesn't have a specific file format reader at this point.<br />
<br />
You may try converting this specific file format image to a format like PNG, for which ITK has readers.<br />
<br />
A good set of tools for performing such conversions is available in ImageMagick. It can be downloaded it for free from: http://www.imagemagick.org/<br />
<br />
You can also take advantage of the VTK readers/importers. All you need is then use the VTKImageToImage adaptor in order to convert the vtkImageData into an itk::Image.<br />
<br />
Supported VTK file formats can be found here: [[VTK_FAQ#What_image_file_formats_can_VTK_read_and_write.3F|What image file formats can VTK read and write?]] and [[VTK_FAQ#What_3D_file_formats_can_VTK_import_and_export.3F|What 3D file formats can VTK import and export]]<br />
<br />
=== How to read a volume from a DICOM series ===<br />
The following are alternative options for reading DICOM series. The first one in the list is the recommended option. The others are provided in case of desperation.<br />
<br />
# Use the itk::ImageSeriesReader<> in combination with the DicomSeriesFileNames<>. For a full example on how to do this, please look at the source code under Insight/Code/Examples/IO/DicomSeriesReadImageWrite.cxx.<br />
# Write a MetaImageHeader<br>This is a small text file holding information about the image: spacing, dimensions, pixelt type... This header can hold the list of dicom files you want to read. The only restriction is that the files must be uncompressed.<br>The easy way to create a MetaImage header is to use the application: MetaImageImporter that is available in: InsightApplications/MetaImageImporter. you can also take an existing metaimage reader and modify it in order to fit your needs. Please find attached one file that you can edit it with your favorite text editor.<br />
# Use MRIConvert<br>Jolinda Smith from the Lewis Center for Neuroimaging at the University of Oregon has developed a nice application that allows you to load DICOM series and export them in MetaImage and Analyze format (among others).<br>She graciously has made this application publicly available at: http://lcni.uoregon.edu/~jolinda/MRIConvert There is a fresh version updated in april 14th.<br />
# Jeff Brubaker and Stephen R. Aylward, at the UNC<br>CADDLab developed a DICOM query/move application called "MIND" (whit the motto: "MIND is not DICOM"). This application loads DICOM files over the network and export them in MetaImage format. This application is open source and it is available at: http://www.jeffro.net/mind/ and http://caddlab.rad.unc.edu/software/MIND/<br />
<br />
=== How to write a volume as DICOM series ===<br />
Use ITK in combination with gdcm <br />
<br />
http://www.creatis.insa-lyon.fr/Public/Gdcm/<br />
<br />
GDCM is an open source package developed by the Creatis team at INSA-Lyon. It is distributed under a license similar to ITK.<br />
<br />
http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html<br />
<br />
GCDM uses CMake in order to configure its build process, so you will find a familiar setup. Once you download, configure and buid GDCM, you can reconfigure ITK by running CMake in your ITK build, going into the Advanced options and enabling USE_GDCM. <br />
<br />
For a code example on how to use GDCM for reading and writing DICOM series, please refer to the source code in<br />
<br />
Insight/Examples/IO/DicomSeriesReadImageWrite2.cxx<br />
<br />
=== Interpreted languages supported by ITK ===<br />
Currently ITK supports the following language bindings:<br />
<br />
* Tcl<br />
* Python <br />
* Java<br />
<br />
Java was added in February 2004, it will not be found in the ITK release 1.6. You will need a CVS checkout with a data posterior to February 25 2004.<br />
<br />
=== How do I cite the use of ITK in a publication? ===<br />
The Insight software may be cited by referencing the paper, the books, and/or the web site.<br />
<br />
A) The paper:<br />
<br />
T.S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxes, R. Whitaker. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit. In Proc. of Medicine Meets Virtual Reality, J. Westwood, ed., IOS Press Amsterdam pp 586-592 (2002).<br />
<br />
B) The books:<br />
<br />
"Insight into Images"<br />
edited by Terry Yoo<br />
published by A.K. Peters 2004<br />
ISBN: 1-56881-217-5<br />
<br />
"The ITK Software Guide"<br />
Ibanez, Schroeder, Ng, Cates.<br />
published by Kitware Inc.<br />
ISBN: 1-930934-10-6<br />
<br />
"Mastering CMake,<br />
A Cross-Platform Build System"<br />
K. Martin and B. Hoffman<br />
published by Kitware Inc.<br />
ISBN: 1-930934-09-2<br />
<br />
C) The Web sites:<br />
<br />
"The Insight Segmentation and Registration Toolkit"<br />
www.itk.org<br />
<br />
"CMake: Cross Platform Make"<br />
www.cmake.org<br />
<br />
If you want to include ITK in an acknowledment section, a phrase similar to the following may be used:<br />
<br />
"This work benefited from the use of the Insight Segmentation<br />
and Registration Toolkit (ITK), an open source software<br />
developed as an initiative of the U.S. National Library<br />
of Medicine and available at www.itk.org."<br />
<br />
and<br />
<br />
"The multi-platform configuration tool CMake was used for<br />
configuring ITK and facilitating its use from our project.<br />
CMake was partially funded by the U.S. National Library of<br />
Medicine as part of the Insight Toolkit project. CMake is an <br />
open source system and it is freely available at www.cmake.org."<br />
<br />
=== I got the message: "Could not create IO object for file" ===<br />
Question:<br />
<br />
When trying to read or write a file using the ImageFileReader or the ImageFileWriter I got an exception with the following message:<br />
<br />
itk::ImageFileReaderException (00F7F494)<br />
Location: "Unknown"<br />
File: C:\ITK\InsightToolkit-1.6.0\Code\IO\itkImageFileReader.txx<br />
Line: 101<br />
Description: Could not create IO object for file c:\t1.mnc<br />
<br />
What is going wrong ?<br />
<br />
Answer:<br />
<br />
This exception is thrown when ITK does not recognize the fileformat that you are trying to read or write. When reading, ITK recognize file formats by asking a set of internal readers to attempt to read your file. If none of the registered readers accept your file, then the exception above is thrown. When writing, ITK uses the extension of the filename in order to chose the fileformat to be used. You must make sure that you use one of the filename extensions recognized by ITK. Please look at FAQ entry 1.7 for a full list of those extensions and associated fileformats.<br />
<br />
Additional details on the ITK Input/Output architecture are available in the ITK Software Guide: http://www.itk.org/ItkSoftwareGuide.pdf.<br />
<br />
<br />
<br />
=== Is ITK FDA-Approved ? ===<br />
<br />
Question: <br />
<br />
Has the Insight Toolkit been FDA approved? <br />
<br />
Answer: <br />
<br />
Given the fact that ITK is a software toolkit, it cannot be the<br />
subject of FDA approval as a medical device. We have discussed<br />
this topic in several occasions and received advice from FDA<br />
representatives, that can be summarized as follow:<br />
<br />
<br />
ITK is to be considered as an off-the-shelf (OTS) product that<br />
is used for supporting a higher level medical application/product.<br />
The developer of such application/product will be responsible for<br />
performing the validation processes described in FDA published<br />
guidelines for the development of software-related medical devices.<br />
<br />
For mode details see the page [[FDA Guidelines for Software Developement]]<br />
<br />
== Language bindings ==<br />
=== Error opening hint file NOTFOUND ===<br />
When you enable "USE_VTK" in the CMake configuration of ITK, and VTK was built with wrapping, CMake looks for a "hints" file.<br />
<br />
The "hints" file is on the VTK source tree under: VTK/Wrapping/hints<br />
<br />
Please switch CMake to "advanced", look for the VTK_WRAP_HINTS variable and set it to the full path to the "hints" file including the "hints" filename itself.<br />
<br />
here is how it looks in the CMakeCache.txt of a typical ITK installation:<br />
<br />
//Where can the hints file be found<br />
VTK_WRAP_HINTS:FILEPATH=/home/johndoe/src/VTK/Wrapping/hints<br />
<br />
== Using Insight ==<br />
<br />
=== How to combine ITK and VTK in my application ===<br />
<br />
A full tutorial on how to combine ITK and VTK is available at<br />
<br />
"Getting Started with ITK and VTK"<br />
http://www.itk.org/CourseWare/Training/GettingStarted-II.pdf<br />
<br />
You will need the auxiliary classes available at<br />
<br />
InsightApplications/Auxiliary/vtk<br />
<br />
For example, for converting ITK images into VTK images and back, you will find useful the files<br />
<br />
itkImageToVTKImageFilter.h<br />
itkImageToVTKImageFilter.txx<br />
itkVTKImageToImageFilter.h<br />
itkVTKImageToImageFilter.txx<br />
<br />
Simply copy those files into the source code directory of your project.<br />
<br />
For the full list of tutorials please look at<br />
<br />
http://www.itk.org/HTML/Tutorials.htm<br />
<br />
<br />
=== Compile/Link errors involving C++ streams library ===<br />
<br />
Compile and link errors involving the C++ streams library (ostream, istream, ifstream, ofstream, etc.) are usually the result of collisions between the old and new streams library. The C++ streams library in the Standard Library is different and usually imcompatible with the original C++ streams library. The new streams library is share the same class names as the old streams library but has a very different implementation (templates, thread safety, etc.). ITK can only be built using the Standard Library streams library.<br />
<br />
If the compile/link error is in an ITK file, the solution is usually to include the proper stream header file, i.e. <fstream> before any other include file. The forces the streams library used by all subsequent headers to be the Standard Library version.<br />
<br />
If the compile/link error is in an application that is trying to use ITK, the solution is usually to include an ITK header file before any other include file. This forces whatever include files that the application may use to use the Standard Library streams library.<br />
<br />
=== What is the difference between the CMake options ITK_WRAP_TCL and VTKITK_WRAP_TCL ? ===<br />
<br />
ITK_WRAP_TCL enables the official method of wrapping ITK into Tcl. This wrapping requires the installation of two external packages: Cable and GCC_XML. Information about these packages can be found at http://public.kitware.com/Cable/HTML/Index.html and http://www.gccxml.org/HTML/Index.html<br />
<br />
VTKITK_WRAP_TCL is not really part of ITK. It is only required to enable the build of some demo-applications in the Insight/Applications directory. These applications use VTK for visualization. ITK filter are packaged here inside VTK classes that are subsequently wrapped for Tcl using the traditional VTK wrapping mechanism (not Cable).<br />
<br />
=== EMACS configuration file : ITK coding style ===<br />
You can add the following codes into your .emacs file<br />
<br />
;;;;;;;;;;;;;;<br />
(c-add-style "itk"<br />
'("stroustrup" <br />
(c-basic-offset . 2)<br />
(c-offsets-alist<br />
(c . c-lineup-dont-change)<br />
(innamespace . 0)<br />
(inline-open . 0) <br />
(substatement-open . +)<br />
(statement-block-intro . 0) ) ) )<br />
(add-hook 'c++-mode-hook (function (lambda ()<br />
(c-set-style "itk")(turn-on-auto-fill))))<br />
(add-to-list 'auto-mode-alist '("\\.txx\\'" . c++-mode)) (add-to-list 'auto-mode-alist '("\\.h\\'" . c++-mode))<br />
;;;;;;;;;;;<br />
<br />
== VIM configuration file : ITK coding style ==<br />
for all of you who use VIM, here are just couple of things:<br />
<br />
set tabstop=2 " Tabs are two characters<br />
set shiftwidth=2 " Indents are two charactes too<br />
set expandtab " Do not use tabs<br />
set matchpairs+=<:> " To mach arguments of templates<br />
set cinoptions={1s,:0,l1,g0,c0,(0,(s,m1 " ITK/VTK style indenting<br />
<br />
Then you can also use CMake indentation and syntax file which are available on www.vim.org.<br />
<br />
This was contributed by Andy Cedilnik @kitware.com<br />
<br />
=== FLTK_WRAP_UI called with FLTK_WARP_UI undefined ===<br />
I use CMake to build the InsightApplications and the following error appears:<br />
<br />
CMake Error: Error in cmake code at<br />
../../CMakeLists.txt:20:<br />
FLTK_WRAP_UI called with FLTK_WARP_UI undefined<br />
<br />
I wonder where and how to define it.<br />
<br />
This error message<br />
<br />
"...FLTK_WARP_UI undefined"<br />
<br />
appears when you have missed to specify some of the FTLK components.<br />
<br />
Please run Cmake again, pass to "Advanced" mode and double check that you provided the right paths for the following components<br />
<br />
* FLTK_BASE_LIBRARY<br />
* FLTK_FLUID_EXECUTABLE<br />
* FLTK_FORMS_LIBRARY<br />
* FLTK_GL_LIBRARY<br />
* FLTK_INCLUDE_DIR<br />
<br />
Here is for example how they look in a typical Windows installation:<br />
<br />
FLTK_BASE_LIBRARY C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkd.lib<br />
FLTK_FLUID_EXECUTABLE C:/cygwin/home/ibanez/src/fltk-1.1.4/fluid/fluidd.exe<br />
FLTK_FORMS_LIBRARY C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkformsd.lib<br />
FLTK_GL_LIBRARY C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkgld.lib<br />
FLTK_IMAGES_LIBRARY C:/cygwin/home/ibanez/src/fltk-1.1.4/lib/fltkimagesd.lib<br />
FLTK_INCLUDE_DIR C:/cygwin/home/ibanez/src/fltk-1.1.4<br />
<br />
<br />
Here is an example for a Linux installation<br />
<br />
FLTK_BASE_LIBRARY /home/ibanez/local/lib/fltk.a<br />
FLTK_FLUID_EXECUTABLE /home/ibanez/local/bin/fluid<br />
FLTK_FORMS_LIBRARY /home/ibanez/local/lib/fltk_forms.a<br />
FLTK_GL_LIBRARY /home/ibanez/local/lib/fltk_gl.a<br />
FLTK_IMAGES_LIBRARY /home/ibanez/local/lib/fltk_images.a<br />
FLTK_INCLUDE_DIR /home/ibanez/local/include<br />
<br />
Note that FLTK on Unix/Linux *MUST* be installed. The reason is that FLTK<br />
has an inconsitent convention for the use of upper/lower case in file names <br />
and resolved this inconsistency by duplicating *ALL* the headers' filenames <br />
with symbolic links. These links are created during the installation process. <br />
If you don't install FLTK, you will not be able to find the headers because <br />
the case will not match the #includes in ITK.<br />
<br />
== Platform-specific questions ==<br />
=== Build->Rebuild All in MS VC++ reloads all projects ===<br />
When performing a "Rebuild All" from Microsoft Visual C++, every project prompts the user for a reload (and there are hundreds of projects).<br />
<br />
DO NOT USE "Rebuild All" or "Batch Build". Use the following recommended procedure.<br />
<br />
There is an ALL_BUILD target available in the MSVC++ workspace. The best way to build ITK is to set ALL_BUILD as the active project, then select the active configuration you want (DEBUG, etc).<br />
<br />
This can also be done from the command line like this: msdev ITK.dsw /MAKE "ALL_BUILD - Debug" /REBUILD<br />
<br />
=== Borland 5.5 Compiler Issues ===<br />
To build Insight using the (free) Borland 5.5 compiler:<br />
<br />
# Get the Borland compiler from http://www.borland.com and install it<br />
# Run cmakesetup and select the Borland Makefiles in the "Build For:" drop down.<br />
# Set the CMAKE_BUIlD_TYPE to MinSizeRel. This is required so that the Borland linker will stay below its size limit which is arounbd 35 meg for a tds file.<br />
<br />
=== Windows + FLTK: unresolved external symbol TrackMouseEvent ===<br />
This error is due to changes in FLTK and it is totally unrelated to ITK. The error only appears in ITK demo applications that are using FLTK for GUI.<br />
<br />
The library "comctl32" must be added to the link command line.<br />
<br />
You can solve this by editing the CMake file: CMake/Modules/FindFLTK.cmake and around line 39 add the comctl32 library.<br />
<br />
After the change the lines should look like:<br />
<br />
IF(WIN32)<br />
SET( FLTK_PLATFORM_DEPENDENT_LIBS wsock32 comctl32 )<br />
ENDIF(WIN32)<br />
<br />
This is already fixed in the CVS version of CMake FindFLTK.cmake.<br />
<br />
The CMake version 1.6 will have this issue solved.<br />
<br />
===Mac OS X ===<br />
<br />
====Getting Shared Libraries to work====<br />
There is a problem with the Mac OSX tool chain that prevents shared libraries <br />
from working. Fortunately, the Mac folks have fixed the problem. You have to <br />
update xcode, the compiler and as much stuff as possible, and it will work <br />
again, after you start from a clean build.<br />
<br />
If gcc -version reports any thing less than 3.3 build 1671, then you should update the compiler.<br />
From the apple developers download http://developer.apple.com/macosx/download/ you have to login to get the November2004GCCUpdater. <br />
<br />
<br />
====Under Mac OS X, when I try to run a program that builds successfully, the window is displayed but I can't interact with it.====<br />
<br />
This is caused by the fact that the application needs to be registered with the window manager for correct operation. There is an additional step that needs to be performed ''after'' the link step, in order to add the required resources to the binary. This can be done with a simple:<br />
<br />
% /Developer/Tools/Rez Carbon.r -o myapp<br />
<br />
For apps built with FLTK, you can use:<br />
<br />
% /Developer/Tools/Rez /usr/local/include/FL/mac.r -o myapp<br />
<br />
Here is an example of adding a custom command to do this automagically in your `CMakeList.txt` file:<br />
<br />
IF(APPLE)<br />
FIND_PROGRAM(APPLE_REZ Rez /Developer/Tools)<br />
ADD_CUSTOM_COMMAND(TARGET MyApplication<br />
POST_BUILD<br />
COMMAND ${APPLE_REZ}<br />
ARGS ${FLTK_INCLUDE_DIR}/mac.r -o MyApplication)<br />
ENDIF(APPLE)<br />
<br />
'''Note:''' This is ''not'' required for applcations build against X libraries; only for Carbon-based applications. If you have built FLTK for X rather than Carbon, the above does not apply.<br />
<br />
(Gavin Baker, 7-May-2004)<br />
<br />
=== How to set Windows DLL's on the Path ===<br />
<br />
==== In Windows 95 and 98 ====<br />
<br />
# Click on the "Start" button on the task bar.<br />
# Click on the "Run..." button<br />
# Type "sysedit". This is the editor of the system files, including the "autoexec.bat"<br />
# If you have already a PATH variable, then add the directory where the ITK DLLs are to that list. Use ";" as separators<br />
# If you don't have a PATH variable.... well... add one and put your directory there. It should look like<br />
<br />
PATH=C:\itkbin\bin\Release\<br />
<br />
==== In Windows XP Method A ====<br />
<br />
# Go to "Control Panel"<br />
# Select "System", <br />
# Take the "Advanced" tab<br />
# Click on the button "Environment Variables" on the bottom, <br />
# Select "PATH" <br />
# Add the full directory where you have your ITK .dlls. Pay attention to whether they are in the Release or Debug subdirectories.<br />
<br />
==== In Windows XP Method B ====<br />
<br />
# Right-Click on "My Computer" ( a popup menu should appear, the last option on it is "properties")<br />
#Select "properties" a new popup window appears with some tabs on it.<br />
# Select the tab "Advanced"<br />
# At the bottom you will se a button called "Environment Variables". Click on it.<br />
# A new popup window appears with a small browser with the list of environment variables. In this browser you will see the list of environment variables.<br />
# Select "path" and click on the "edit" button. A small new popup appears with two text fields: "Variable name" and "Variable value".<br />
# Go to the "Variable value" field, move to the end, add a ";" separator and type the directory where you have the VTK or ITK Dlls.<br />
# Add another ";" separator and type the directory where you have the ITK Dlls.<br />
# Click on "OK" to close the "Edit User Variable" window.<br />
# Click on "Ok" on the "Environment Variables" window.<br />
# Click on "Ok" on the "System Properties window".<br />
# Take a deep breath, cross you fingers and try to execute your program again.<br />
<br />
== Testing ==<br />
=== Is ITK tested regularly? ===<br />
ITK is tested throughout the day on machines distributed around the world. You can view the results at: http://public.kitware.com/Insight/Testing/HTML/TestingResults/Dashboard/MostRecentResults-Nightly/Dashboard.html<br />
<br />
ITK uses Dart to perform builds, run tests and generate dashboards. You can find more information about Dart at http://www.itk.org/Dart/<br />
<br />
=== What is the testing schedule? ===<br />
Dart opens a daily dashboard at 1:00AM Eastern Daylight Time and keeps that dashbooard open for 24 hours. Build/Test results submitted as "nightlies" will appear on the currently opened dashboard. Each test site can select a convenient time to run tests.<br />
<br />
Fresh dashboards are generated every hour, on the hour. They can also be generated on demand using the Rollup button on the dashboard. This button should be used sparingly since dashboard rollups can be time consuming.<br />
<br />
In addition to nightly testing, several sites run Continuous build/tests. These sites monitor cvs repository activity and begin a build/test sequence if there are updates to the repository. If a compile error is detected, the Dashboard server sends email to the "offending" party.<br />
<br />
=== What kind of testing is performed? ===<br />
ITK has three types of tests:<br />
<br />
# Unit Tests. Also called white box tests. These tests reside in the Testing/Code/XXX directories. There are meant to exercise a class's methods and verify that the code compiles, links and produces expected results. These tests do not need to produce results that are useful to a user. If a test returns a 0 status, it passes. A test fails if it returns a non-zero status.<br />
# Blackbox Tests. These tests are automatically (or semi-automatically) generated. For example, each Code directory has a test called itkXXXHeaderTest. This test is automatically created and has a "#include" for each file in the directory.<br />
# Regression Tests. These tests generate results and compare them with a known result. The purpose of regression testing is to detect changes in the output of the system. <br />
<br />
=== How Do I Add a Test? ===<br />
<br />
=== What is a continuous build and how can I contribute one? ===<br />
Continuous builds run throughout the day and report their output in the Continuous Builds portion of the dashboard. The most recent build is at the top of the list. The builds run periodically and check the status of the repository. If a file is added or changed since the last build, the working repository of the continuous build is updated, the code compiled and tests executed. Optional e-mail norifications can be sent if there are errors, warmings or test failures.<br />
<br />
You can set up a continuous build. This entails writing some small shell scripts and setting up a scheduler (Scheduler for Windows, cron for Linux/Unix). You will also need to install tcl, checkout Dart and configure your build for testing.<br />
<br />
For Windows 2000, here are three batch files that can be modified for your own environment.<br />
<br />
AllowInsightContinuous.bat<br />
BuildInsightContinuous.bat<br />
PreventInsightContinuous.bat<br />
<br />
The batch files use a lock to prevent/allow the continuous<br />
<br />
rem ************* AllowInsightContinuous.bat<br />
rem Allow the Continuous to run<br />
rem<br />
c:<br />
cd c:\lorensen\InsightContinuous\Insight-VC6<br />
if EXIST continuous.lock (<br />
del continuous.lock<br />
)<br />
cd ..<br />
rem ************* BuildInsightContinuous.bat<br />
rem DO a C++ Build Continuously<br />
rem<br />
c:<br />
rem Setup proxy it behind a firewall<br />
set HTTP_PROXY=webcache<br />
set HTTP_PROXY_PORT=8080<br />
rem<br />
rem Setup the path<br />
rem<br />
set PATH=c:/lorensen/InsightContinuous/Insight-VC6/bin/Release;%PATH%<br />
rem<br />
rem Tell cvs where .cvspass resides<br />
set HOME=c:/lorensen<br />
cd c:\lorensen\InsightContinuous\Insight-VC6<br />
if EXIST continuous.lock (<br />
exit /B<br />
) else (<br />
date /T > continuous.lock<br />
time /T >> continuous.lock<br />
cd c:\lorensen\InsightContinuous\Insight-VC6<br />
tclsh83 c:/lorensen/Dart/Source/Client/DashboardManager.tcl DartConfiguration.tcl Continuous Start Update Configure Build Test Submit<br />
cd c:\lorensen\InsightContinuous\Insight-VC6<br />
del continuous.lock<br />
cd ..<br />
)<br />
rem ***************** PreventInsightContinuous.bat<br />
rem Prevent the Continuous<br />
rem<br />
c:<br />
cd c:\lorensen\InsightContinuous\Insight-VC6<br />
if EXIST continuous.lock (<br />
exit /B<br />
) else (<br />
echo "Prevent continuous for nightly" > continuous.lock<br />
)<br />
cd ..<br />
<br />
Now you need to establish a schedule for the three batch jobs. Use the "Scheduled Tasks" on the "Control Panel" to access the Schedule Task Wizard. The following schedule runs the continuous every 10 minutes from 6:05AM until 12:00AM. The Allow and Prevent scripts turn the build ON/OFF at the appropriate time. Schedule each batch file as follows:<br />
<br />
AllowInsightContinuous.bat - Daily, Start 6:00AM<br />
BuildInsightContinuous.bat - Daily, Start 6:05AM, Advanced: Repeat Task every 10 minutes, duration 17 hours and 55 minutes<br />
PreventContinuous.bat - Daily, Start 12:00AM<br />
<br />
<br />
== Working with Image Data ==<br />
<br />
===How do I iterate through all the pixels in an image?===<br />
<br />
This requires the use of image iterators, which is explained in detail in the SoftwareGuide in Chapter 11, pdf-page 481.<br />
<br />
Examples are available in `Insight/Examples/Iterators`. You probably want to use the [http://www.itk.org/Insight/Doxygen/html/classitk_1_1ImageSliceIteratorWithIndex.html ImageSliceIterator].<br />
<br />
(Luis Ibanez, 7-Jun-2004)<br />
<br />
===What are Hounsfield Units?===<br />
<br />
Hounsfield units were defined by Sir Godfrey N. Hounsfield, on of the pioneers of Computer Tomography for clinical applications.<br />
<br />
The units represent the linear attenuation of X-Rays for a particular material. <br />
<br />
The units scale is defined in such a way that level for Water is 0 and the level for Air is -1000. <br />
<br />
The attenuation of any other material is mapped linearly into this range.<br />
<br />
A table of Hounsfield units for common human tissues is avalable in the following link [[ITK Hounsfield Units]]<br />
<br />
== Data Display ==<br />
<br />
===What imaging software is available for displaying medical image files?===<br />
<br />
Here are some viewing options for the image fileformats supported in ITK: <br />
<br />
1. Scalar images:<br />
<br />
* InsightApplications/ImageViewer<br />
* [http://www.paraview.org ParaView]<br />
* For 3D images: [http://www.kitware.com/products/volview.html VolView]<br />
<br />
2. Color Images:<br />
<br />
* InsightApplications/ColorImageViewer<br />
* [http://www.paraview.org ParaView]<br />
* For 3D images: [http://www.kitware.com/products/volview.html VolView]<br />
<br />
3. Vector Images:<br />
<br />
* [http://www.paraview.org ParaView] (glyphs, streamlines, composites).<br />
<br />
(Luis Ibanez, 9-Jun-2004)<br />
<br />
===When I view the output of my program, all I see is a black image. What went wrong?===<br />
<br />
ITK is capable of reading and writing data in a variety of formats and bit depths. However many 'consumer' image programs only work with 8-bit data, so when you try to display a 16-bit data file the image will appear black. The solution is to use an image display program that correctly handles these types of files. A small selection is listed above.<br />
<br />
[http://www.imagemagick.org/ ImageMagick] is a particularly useful set of tools for image display, manipulation and conversion.<br />
<br />
The `ImageViewer` program, part of InsightApplications, is capable of correctly loading and displaying all file types supported by ITK (including anisotropic images).<br />
<br />
(Gavin Baker, 24-Jun-2004)<br />
<br />
== Registration ==<br />
<br />
===Can ITK be used for multi-modal registration? For example, CT-MRI, or MRI-fMRI?===<br />
<br />
ITK provides several method for performing Multi-Modality registration. These methods are described in detail in the SoftwareGuide Chapter 8, pdf-page 241 to 340. In particular you will find interesting Section 8.4 in pdf-page 255 where the Mutual Information metrics are described.<br />
<br />
Examples on multimodality registration are available in `Insight/Examples/Registration`. A demo application using Mutual Information is available under `InsightApplications/LandmarkInitializedMutualInformationRegistration`.<br />
<br />
It is strongly recommended that you read the chapter on image resampling before you get involved with image<br />
registration methods. That will save you a lot of misunderstandings that are common in new users.<br />
<br />
You will also find useful the tutorial sessions, in particular [http://www.itk.org/CourseWare/Training/RegistrationMethodsOverview.pdf the overview].<br />
<br />
(Luis Ibanez, 7-June-2004)</div>Cateshttps://public.kitware.com/Wiki/index.php?title=ITK/Release_1_8&diff=2526ITK/Release 1 82004-08-06T18:00:51Z<p>Cates: </p>
<hr />
<div>= Support for BMP =<br />
= MetaIO supports zlib compression =<br />
= IO support for itkMeshSpatialObject via MetaIO =<br />
= IO support for "Nearly Raw Raster Data" image format (Nrrd) =<br />
= New itkTreeContainer and TreeIterators classes =<br />
= SpatialObjects supports TreeContainer =<br />
= New GaussianSpatialObject =<br />
= Many new examples =<br />
= Java wrapping =<br />
= List of new classes in ITK 1.8 =<br />
Code/Algorithms/itkDeformableSimplexMesh3DBalloonForceFilter.h<br />
Code/Algorithms/itkHistogramAlgorithmBase.h<br />
Code/Algorithms/itkImagePCADecompositionCalculator.h<br />
Code/Algorithms/itkIsolatedWatershedImageFilter.h<br />
Code/Algorithms/itkLevelSetMotionRegistrationFilter.h<br />
Code/Algorithms/itkLevelSetMotionRegistrationFunction.h<br />
Code/Algorithms/itkMatchCardinalityImageToImageMetric.h<br />
Code/Algorithms/itkOtsuMultipleThresholdsCalculator.h<br />
Code/Algorithms/itkOtsuThresholdImageFilter.h<br />
Code/Algorithms/itkPointSetToSpatialObjectDemonsRegistration.h<br />
Code/Algorithms/itkRegularSphereMeshSource.h<br />
Code/Algorithms/itkSTAPLEImageFilter.h<br />
<br />
Code/BasicFilters/itkAbsoluteValueDifferenceImageFilter.h<br />
Code/BasicFilters/itkBoundedReciprocalImageFilter.h<br />
Code/BasicFilters/itkGrayscaleGrindPeakImageFilter.h<br />
Code/BasicFilters/itkInverseDeformationFieldImageFilter.h<br />
Code/BasicFilters/itkIterativeInverseDeformationFieldImageFilter.h<br />
Code/BasicFilters/itkLabelStatisticsImageFilter.h<br />
Code/BasicFilters/itkLaplacianSharpeningImageFilter.h<br />
Code/BasicFilters/itkNaryMaximumImageFilter.h<br />
Code/BasicFilters/itkNotImageFilter.h<br />
Code/BasicFilters/itkRGBToLuminanceImageFilter.h<br />
Code/BasicFilters/itkSimplexMeshAdaptTopologyFilter.h<br />
Code/BasicFilters/itkSimplexMeshToTriangleMeshFilter.h<br />
Code/BasicFilters/itkThresholdLabelerImageFilter.h<br />
Code/BasicFilters/itkTileImageFilter.h<br />
Code/BasicFilters/itkTriangleMeshToSimplexMeshFilter.h<br />
Code/BasicFilters/itkVectorRescaleIntensityImageFilter.h<br />
Code/BasicFilters/itkWarpVectorImageFilter.h<br />
Code/BasicFilters/itkWeightedAddImageFilter.h<br />
<br />
Code/Common/itkAutoPointerDataObjectDecorator.h<br />
Code/Common/itkBinaryThresholdSpatialFunction.h<br />
Code/Common/itkCenteredEuler3DTransform.h<br />
Code/Common/itkCenteredVersorTransformInitializer.h<br />
Code/Common/itkChildTreeIterator.h<br />
Code/Common/itkDataObjectDecorator.h<br />
Code/Common/itkInOrderTreeIterator.h<br />
Code/Common/itkLeafTreeIterator.h<br />
Code/Common/itkLevelOrderTreeIterator.h<br />
Code/Common/itkPostOrderTreeIterator.h<br />
Code/Common/itkPreOrderTreeIterator.h<br />
Code/Common/itkRGBToLuminanceImageAdaptor.h<br />
Code/Common/itkRootTreeIterator.h<br />
Code/Common/itkSimpleDataObjectDecorator.h<br />
Code/Common/itkSimplexMesh.h<br />
Code/Common/itkSimplexMeshGeometry.h<br />
Code/Common/itkTreeChangeEvent.h<br />
Code/Common/itkTreeContainer.h<br />
Code/Common/itkTreeContainerBase.h<br />
Code/Common/itkTreeIteratorBase.h<br />
Code/Common/itkTreeIteratorClone.h<br />
Code/Common/itkTreeNode.h<br />
Code/Common/itkWindowedSincInterpolateImageFunction.h<br />
<br />
Code/IO/itkBMPImageIO.h<br />
Code/IO/itkBMPImageIOFactory.h<br />
Code/IO/itkGDCMImageIO.h<br />
Code/IO/itkGDCMSeriesFileNames.h<br />
Code/IO/itkNrrdImageIO.h<br />
Code/IO/itkNrrdImageIOFactory.h<br />
<br />
Code/Numerics/itkLBFGSBOptimizer.h<br />
Code/Numerics/Statistics/itkGreyLevelCooccurrenceMatrixTextureCoefficientsCalculator.h<br />
Code/Numerics/Statistics/itkImageToCooccurrenceListAdaptor.h<br />
Code/Numerics/Statistics/itkMaskedScalarImageToGreyLevelCooccurrenceMatrixGenerator.h<br />
Code/Numerics/Statistics/itkScalarImageTextureCalculator.h<br />
Code/Numerics/Statistics/itkScalarImageToGreyLevelCooccurrenceMatrixGenerator.h<br />
<br />
Code/SpatialObject/itkAffineGeometryFrame.h<br />
Code/SpatialObject/itkGaussianSpatialObject.h<br />
Code/SpatialObject/itkImageMaskSpatialObject.h<br />
Code/SpatialObject/itkMetaEvent.h<br />
Code/SpatialObject/itkMetaGaussianConverter.h<br />
Code/SpatialObject/itkMetaMeshConverter.h<br />
Code/SpatialObject/itkSpatialObjectTreeContainer.h<br />
Code/SpatialObject/itkSpatialObjectTreeNode.h</div>Cates