NAMIC Wiki - User contributions [en]

Downloads

2010-02-04T20:19:28Z

Gcasey:

The following is a collection of electronic resources provided by NA-MIC. This includes software, data, tutorials, presentations, and additional documentation.

==Software==

* Software 1
* Software 2

==Data==

* [[Data:DBP2:Harvard | Brain: Multi-Modality (DTI, fMRI, sMRI)]] (from Harvard) -> need to migrate to XNAT
* [[Data:DBP2:UNC | Brain: 2 autistic children and 2 normal controls scanned at 2 years with follow up at 4 years]] (from UNC) -> need to migrate to XNAT
* [[Data:DBP2:Queens | Prostate: Trans-rectal biopsy (tutorial)]] (from Queens University) -> need to migrate to XNAT
* [[Data:DBP2:Queens | Prostate: Perk Station (tutorial)]] (from Queens University) -> need to migrate to XNAT
* [https://mri.radiology.uiowa.edu//visible_human_datasets.html Visible Human Datasets] (from Iowa University)
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]
* [[Projects:RegistrationDocumentation:UseCaseInventory | Registration Use Case Library]]

==Tutorials==

* [[Training:Slicer|Slicer Training]]
* [[NA-MIC_Training_Toolkit|NA-MIC Training Toolkit]]
* [[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration ]] (Guorong Wu)
* [[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]] (Daniel Haehn)
* [[AHM 2010 Tutorial Contest - Port of Slicer to Qt| Port of Slicer to Qt]] (Julien Finet)
* [[AHM 2010 Tutorial Contest - EM Fiber Clustering| EM Fiber Clustering]] (Mahnaz Maddah)
* [[Slicer3:Training | Slicer3 Training 101]]
* [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]
* [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]

Downloads

2010-02-04T20:19:12Z

Gcasey: added registration use case library to data

The following is a collection of electronic resources provided by NA-MIC. This includes software, data, tutorials, presentations, and additional documentation.

==Software==

* Software 1
* Software 2

==Data==

* [[Data:DBP2:Harvard | Brain: Multi-Modality (DTI, fMRI, sMRI)]] (from Harvard) -> need to migrate to XNAT
* [[Data:DBP2:UNC | Brain: 2 autistic children and 2 normal controls scanned at 2 years with follow up at 4 years]] (from UNC) -> need to migrate to XNAT
* [[Data:DBP2:Queens | Prostate: Trans-rectal biopsy (tutorial)]] (from Queens University) -> need to migrate to XNAT
* [[Data:DBP2:Queens | Prostate: Perk Station (tutorial)]] (from Queens University) -> need to migrate to XNAT
* [https://mri.radiology.uiowa.edu//visible_human_datasets.html Visible Human Datasets] (from Iowa University)
* [http://insight-journal.org/midas/community/view/21?path_navigation=19-15 Head MRI, MRA, DTI from 100 healthy volunteers]
* [[Projects:RegistrationDocumentation:UseCaseInventory Registration Use Case Library]]

==Tutorials==

* [[Training:Slicer|Slicer Training]]
* [[NA-MIC_Training_Toolkit|NA-MIC Training Toolkit]]
* [[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration ]] (Guorong Wu)
* [[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]] (Daniel Haehn)
* [[AHM 2010 Tutorial Contest - Port of Slicer to Qt| Port of Slicer to Qt]] (Julien Finet)
* [[AHM 2010 Tutorial Contest - EM Fiber Clustering| EM Fiber Clustering]] (Mahnaz Maddah)
* [[Slicer3:Training | Slicer3 Training 101]]
* [[Media:ARCTIC-Slicer3-Tutorial.pdf|‏ ARTIC (Automatic Regional Cortical Thickness) Tutorial]]
* [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]

ITK Registration Optimization

2010-01-21T14:23:42Z

Gcasey:

{|border=1
|This page contains a record of the development of RegisterImages. For user documentation please see [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.4 RegisterImages-Documentation-3.4]
|}

= Slicer3 Module: RegisterImages =

The RegisterImages module is the product of the research discussed below.

== Major Features ==

The major features of the module include:
* Default parameters register many full-head and skull-stripped MRI: rigid, affine, and BSpline
* Offers a complete, pipeline-based registration solution
** Load and apply existing transforms
** Compute rigid, affine, and bspline transforms in sequence with a single command
* Intuitive parameters
** Instead of setting obscure "scales" for parameters, you set global values for "Expected Offset", "Expected Rotation", ... to indicate how much mis-registration is anticipated in the data being registered
* MinimizeMemory option provides a way to compute bspline registrations using a dense set of control points and a large number of samples on "normal" computers (albeit computation time increases)
* SampleFromOverlap option allows images of vastly different sizes to be registered
** Helps to avoid (but does not completely eliminate) the annoying ITK exception, "too many samples falls outside of the image"
* Incorporates testing
** Specify a baseline image, and modules will perform the requested registration, compare its results with the baseline image, and return success/failure
* Based on an extensible and re-usable class structure.

Each of these features is discussed next.

== Head MRI Registration ==

=== Example 1: Problem Cases ===

* Registers images which were not well resolved (or produced seg-faults) using other slicer registration modules:
** http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration

==== Difficult affine registration, Same subject, Different protocols: T2 and Fractional Anisotropy ====
{|
|-
| [[Image:RegisterImages-T2-fa-registration-setup-2008-07-30.png|thumb|250px|Setup: T2 (fixed) with FA (moving)]]
| [[Image:RegisterImages-T2-fa-registration-results-2008-07-30.png|thumb|250px|Affine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== Difficult affine registration, Same subject, Different protocols: T1 and Gradient ====

{|
|-
| [[Image:RegisterImages-Debrecen-affine-setup-2008-07-30.png|thumb|250px|Setup: T1 (fixed) with Gradient (moving)]]
| [[Image:RegisterImages-Debrecen-affine-results-2008-07-30.png|thumb|250px|Affine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

=== Example 2: Affine Registration ===

* Task:
** Affine registration of head MRI from two different subjects
* Data:
** Using cases UNC-Healthy-Normal002 (fixed) and UNC-Healthy-Normal004 (moving)
** Data provided by Dr. Bullitt at UNC.
** Data is available from Kitware's MIDAS archive at http://hdl.handle.net/1926/542
** Data can be automatically downloaded into ${RegisterImages_BINARY_DIR}/Testing/Data directory by enabling the CMake variable "BUILD_REGISTER_IMAGES_REAL_WORLD_TESTING"
*** Warning this also enables additional tests that can take 4+ hours to complete.
*** To see the code for automatically downloading from MIDAS (via svn), see Slicer3/Applications/CLI/RegisterImagesModule/Applications/CMakeLists.txt

==== Affine registration of head MRI from two difference subjects ====

{|
|-
| [[Image:RegisterImages-Normal002-004-affine-setup-2008-07-30.png|thumb|250px|Setup: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-affine-results-2008-07-30.png|thumb|250px|PipelineAffine Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== Affine registration of skull-stripped head MRI from two difference subjects ====

{|
|-
| [[Image:RegisterImages-Normal002-004-stripped-affine-setup-2008-07-30.png|thumb|250px|Setup: Skull Stripped: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-stripped affine-results-2008-07-30.png|thumb|250px|PipelineAffine Results: Skull Stripped RegisterImages, Default Options (2008-07-30)]]
|-
|}

=== Example 3: BSpline Registration ===

* Task:
** BSpline registration of head MRI from two different subjects
* Data:
** Using cases UNC-Healthy-Normal002 (fixed) and UNC-Healthy-Normal004 (moving)
** Data provided by Dr. Bullitt at UNC.
** Data is available from Kitware's MIDAS archive at http://hdl.handle.net/1926/542
** Data can be automatically downloaded into ${RegisterImages_BINARY_DIR}/Testing/Data directory by enabling the CMake variable "BUILD_REGISTER_IMAGES_REAL_WORLD_TESTING"
*** Warning this also enables additional tests that can take 4+ hours to complete.
*** To see the code for automatically downloading from MIDAS (via svn), see Slicer3/Applications/CLI/RegisterImagesModule/Applications/CMakeLists.txt

==== BSpline, Default Options, Different Subjects, Same Protocol, Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-bspline-setup-2008-07-30.png|thumb|250px|Setup: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-bspline-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Default Options (2008-07-30)]]
|-
|}

==== BSpline, Dense Control-Point Grid, Different Subjects, Same Protocol, Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-bspline2-setup-2008-07-30.png|thumb|250px|PipelineBSpline Results: UNC Normal 002 (fixed) with UNC Normal 004 (moving), Default Options]]
| [[Image:RegisterImages-Normal002-004-bspline2-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Options: MinimizeMemory and ControlPointSpacing=15 pixels (vs. default ControlPointSpacing=40 pixels) (2008-07-30)]]
|-
|}

==== BSpline, (Default Options vs. Dense Control-Point Grid), Different Subjects, Same Protocol, Skull-Stripped Head MRI ====
{|
|-
| [[Image:RegisterImages-Normal002-004-stripped-bspline-setup-2008-07-30.png|thumb|250px|Setup: Skull Stripped: UNC Normal 002 (fixed) with UNC Normal 004 (moving)]]
| [[Image:RegisterImages-Normal002-004-stripped-bspline-results-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, Default Options (2008-07-30)]]
| [[Image:RegisterImages-Normal002-004-stripped bspline-results2-2008-07-30.png|thumb|250px|PipelineBSpline Results: RegisterImages, MinimizeMemeory and ControlPointSpacing=15 pixels (vs. default ControlPointSpacing=40 pixels) (2008-07-30)]]
|-
|}

== Pipeline Registration ==

The module implements a registration pipeline. The steps in that pipeline are as follows:

* Step 1: Loaded transform
** You may load a pre-computed transform to initialize the registration.
** If one is loaded, it is immediately applied (i.e., the moving image is resampled)
* Step 2: Initial registration
** Options are:
*** None (sets the center of rotation to the center of the moving image)
*** Landmark (uses N-pairs of landmarks (passed as vectors) and a least-squared error metric to register the images using a rigid transform
*** Image Centers (shifts the images to align their centers)
*** Centers of Mass (shifts the images to align their centers of mass)
*** Second Moments (shifts and rotates the images to align the 1st and 2nd moments)
* Step 3: Registration
** Options are:
*** None (applies the loaded transforms)
*** Initial
**** computes and applies the initial transform to the loaded registrations)
*** Rigid
**** computes a rigid transform and then applies it to the loaded registrations
*** Affine
**** computes an affine transform and then applies it to the loaded registrations
*** BSpline
**** computes a bspline transform and then applies it to the loaded registrations
*** PipelineRigid
**** computes a rigid transform (initialized using the results from the initial registration) and then applies it to the loaded registrations
*** PipelineAffine
**** computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations
*** PipelineBSpline
**** computes a rigid transform (initialized using the results from the initial registration), uses those results to initialize and compute an affine transform, and then applies it to the loaded registrations, THEN computes and applies a BSpline transform

== Intuitive Parameters ==

* In rare cases (given unusual acquisition conditions and/or highly inconsistent acquisition protocols) you will need to change the default parameters.
* More often you may wish to tweak parameters to achieve your application-specific speed-vs-accuracy tradeoff

=== IO Tab ===
* Set the fixed and moving images using images in the scene
* Optionally set the ResampleImage to store the output image
** If not set, registration won't conduct the final resampling, saving computation time

=== Registration Parameters Tab ===
* Load Transform
** provide the Loaded Transform for the loaded phase of registration
* Save Transform
** results of the entire registration pipeline will be saved here
* Initialization
** see registration pipeline discussion
* Registration
** see registration pipeline discussion
** For rigid and affine registrations, one-plus-one evoluation optimization is first applied for N iterations, and then FRPR gradient-line-search optimization is applied.
*** For more information, check the code: RegisterImagesModule/itkOptimizedImageToImageRegistrationmethod.h/txx
** For BSpline registration, a hierarchical registration scheme is used. An image pyramid having 3 levels is used to resample the images and the control grids. Heuristics are used to control the various resampling parameters. At each level, registration is conducted using FRPR gradient-line-search optimization.
*** For more information, check the code: RegisterImagesModule/itkBSplineImageToImageRegistrationMethod.h/txx
* Metric
** Use the Mutual Information metric. It is an multithreaded and optimized version of the Mattes MI method.
*** For more information, check the code; Insight/Code/Review/itkOptMattesMutualInformationImageMetric.h/txx
* "Expected" values
** For rigid, affine, and bspline registration, parameter scales (refer to the Insight Software Guide) are represented as hyper-parameters in the RegisterImages module.
*** "Expected Offset" controls the offset scales in rigid and affine registration the deformation vector scale in bspline registration
*** "Expected Rotation" is roughly in terms of radians. It controls the rotation angles in rigid and affine registration
*** "Expected Scale" is for scaling during affine registration
*** "Expected Skew" is for skew for affine registration

=== Advaned Registration Parameters Tab ===
* Verbosity level
** Controls the level of detail in the reports in the log file
* Sample from fixed/moving overlap
** When the fixed image is much larger than the moving image, it is CRITICAL to set this flag and to pick a good initialization method. In that way, only the portion of the fixed image that is initially covered by the moving image will be used during registration. This prevents ITK from throwing an exception (error) stating that too many fixed-image samples miss (map outside of) the moving image.
* Fixed image intensity percentage threshold
** A less robust way to overcome the image overlap issue discussed above, you can specify a threshold as a portion (0 to 1) of the fixed image intensity range that should be used to select fixed image samples for computing the metric. That is, by specifying 0.5, only the pixels in the upper half of the fixed-image's intensity range will be used during random sample selection.
** Remember, it is important to include pixels inside and outside of the object of interest, otherwise the fixed image histogram may be too homogeneous for mis-registrations to be detected.
* Random number seed
** To ensure consistent performance, you can set a seed - repeated runs should produce identical results.
* Number of threads
** Number of multi-core/mult-processor threads to use during metric value computations.
* MimimizeMemory
** Turns off caching of intermediate values during bspline registration
** Provides a way to compute bspline registrations using a dense set of control points and a large number of samples on "normal" computers (albeit computation time increases)
** Rule of thumb, if the BSpline registration crashes - re-run with this option enabled.
* use windowed sinc for final interpolation
** If you have time to kill. Extremely slow and only marginally better than bspline resampling (the default).

=== Registration Testing Parameters ===
* Baseline Image
** Set the image against which the Resampled Image (IO tab) will be compared after registration
* Number of Failed Pixels Tolerance
** Registration returns "failure" if this many pixels are different between the Resampled and Baseline images
* Intensity Tolerance
** Minimum intensity difference between corresponding Resampled and Baseline pixels for those pixels to be counted as failures
* Radius Tolerance
** The program will search this neighborhood size about each Resampled pixel to find the closest matching Baseline pixel. The closest matching pixels are compared using the Intensity Tolerance (above)
* Baseline Difference Image
** Result of subtracting the resampled image from the baseline image
* Baseline Resamples Moving Image
** resampled image, resampled into the space of the baseline image

=== Advanced Initial Registration Parameters ===
* Fixed / Moving Landmarks
** A vector string (comma separated base-3 list) of the indexes of corresponding points in the fixed and moving images
** If supplied, then choose "Landmarks" as the initial registration method (see discussion on registration pipeline)

=== Advanaced Rigid and Affine Parameters ===
* MaxIterations
** Number of iterations for one-plus-one and for FRPR registration
* Sampling Ratio
** Portion of the image pixels to be used when computing the metric

=== Advanced BSpline Parameters ===
* MaxIterations
** Number of iterations for one-plus-one and for FRPR registration
* Sampling Ratio
** Portion of the image pixels to be used when computing the metric
** Do the math...if you have 40 pixels between control points, then there will be 40^3 (64,000) pixels relevant to each control point. That excessive for directing one control point. Keep the sampling small. For 40 pixels between control points, a sampling density of 0.1 provide 6,400 pixels for metric computation at each control point - more than enough.
** When in doubt, turn on MinimizeMemory
* Control point spacing (pixels)
** Don't think about grid size - instead think about the level of detail that needs to be resolved (see discussion on sampling ratio).
** When in doubt, turn on MinimizeMemory

== Incorporates testing ==

* See discussion on the "Registration Testing Parameters" tab.

== Class structure ==

* Try it, you'll like it.
* Follows the coding style of itk
* Limited comments, but meaningful variable names
* No documentation is provided or planned - don't even ask.

= Instructions for Enabling the RegisterImages module =

This module should now be built and distributed by default. No special steps are needed to use this module.

= Background =

== Goals ==

There are two components to this research
# Identify registration algorithms that are suitable for non-rigid registration problems that are endemic to NA-MIC
# Develop implementations of those algorithms that take advantage of multi-core and multi-processor hardware

== Steps involved ==

# Modify ITK's registration framework to support oriented images
# Modify ITK's registration framework to be thread safe
# Develop multi-threaded versions of select registration modules
# Make everything backward compatible with ITK's existing registration methods and framework
# Deliver in ITK
# Develop helper classes and write IJ article

Target date for these deliverables: Jan 1, 2008

== Planned follow-on work ==

Devise a new metric for MI registration
# If we always use every voxel for the metric, then we can cache the weights by the voxel's position wrt the adjacent control points. For example, for Kilian's situation of a control point every 2 voxels, then there really are only a few unique weight sets that are repeated throughout the volume. Luis had already brought up a variation on this idea.
# This method could also be combined with the rule to not evaluate voxels or control points that fall on background voxels. This too has been discussed, but such a rule makes multi-threading tricky in that we don't want to waste threads by allocating them to image regions that contain only background voxels.
# The metric could be closely tied to a multiresolution registration scheme. In fact, the grid and the image resolutions should perhaps be linearly related. That is, we could tie the metric computation to the resolution of the deformation grid by subsampling the image. There are situations where this is not a right thing to do (just because the grid is coarse doesn't mean that a small movement isn't important); HOWEVER, as part of a multiresolution registration strategy, it is perhaps the viable option. This would need to be evaluated on the data.
# Have "don't-care" regions in which bspline control points are processed/don't move, e.g., no need to adjust ones that only contain background

== Status and News ==
Thanks (but not your questions or comments) go to
* Luis Ibanez, Matt Turek, Stephen Aylward
Questions and comments should go to the Slicer Developers' list

== Publications ==

# [http://insight-journal.org/InsightJournalManager/view_reviews.php?pubid=172 Aylward, Stephen; Jomier, Julien; Barre, Sebastien; Davis, Brad; Ibanez, Luis, "Optimizing ITK’s Registration Methods for Multi-processor, Shared-Memory Systems." MICCAI Open Source and Open Data Workshop, 2007] [http://insight-journal.org/InsightJournalManager/download_publication.php?pubid=172&revision=2&name=OptimizingITKRegistrationMethods.pdf&pdf=1 (Download PDF)]
# [[NAC_Grid_Enabled_ITK | BWH Neuroimaging Analysis Center (NAC), 2007-2008: Grid Enabled ITK]]
# IJ article on oriented images and registration in ITK
#* http://www.insight-journal.org/dspace/bitstream/1926/1293/2/Brooks_Arbel_FastOrientedImage_V1.pdf
#* Solution presented by the authors is closely related to the changes made in ITK

== Algorithmic Requirements and Use Cases ==

* Requirements
*# relatively robust, with few parameters to tweak
*# runs on grey scale images
*# has already been published
*# relatively fast (ideally speaking a few minutes for volume to volume).
*# not patented
*# can be implemented in ITK and parallelized.

* Use-cases
*# Intersubject mapping
*#* [[Intersubject|Example data set]] (Kilian)
*# fMRI to hi-res brain morphology mapping
*#* [[FMRI-to-hires|Example data set]] (Steve Pieper)
*# DTI: components of the diffusion tensor
*#* [[DTI-non-rigid|Example data]] (Sylvain)

== Hardware Platform Requirements and Use Cases ==

* Requirements
*# Shared memory
*# Single and multi-core machines
*# Single and multi-processor machines
*# AMD and Intel - Windows, Linux, and SunOS

* Use-cases
*# Intel Core2Duo
*# Intel quad-core Xeon processors, Visual Studio 8, Windows Vista (Kitware: redwall)
*# 6 CPU Sun, Solaris 8 (SPL: vision)
*# 12 CPU Sun, Solaris 8 (SPL: forest and ocean)
*# 16 core Opteron (SPL: john, ringo, paul, george)
*# 16 core, Sun Fire, AMDOpteron (UNC: Styner)

== Historic Results ==

January 5, 2008 - Note: "Opt" results are not using the OptLinearInterpolateImageFunction.

*[http://www.na-mic.org/Wiki/images/f/fe/MattesGetValue.pdf MattesMI GetValue Results]
*[http://www.na-mic.org/Wiki/images/1/1b/MattesBSplineGetValue.pdf MattesMI, b-spline interpolation and transform, GetValue Results]
*[http://www.na-mic.org/Wiki/images/1/16/MeanSquaresGetValue.pdf MeanSquares GetValue Results]
*[http://wiki.na-mic.org/Wiki/images/c/c5/MattesGetValueAndDerivative.pdf MattesMI GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/f/f6/MattesBSplineGetValueAndDerivative.pdf MattesMI, b-spline interpolation and transform, GetValueAndDerivative Results]
*[http://wiki.na-mic.org/Wiki/images/2/2d/MeanSquaresGetValueAndDerivative.pdf MeanSquares GetValueAndDerivative Results]

== Historic Events ==

* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-06-tcon April 6, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-12-tcon April 12, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-04-18-tcon April 18, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-05-01-tcon May 1, 2007: TCon]
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization/2007-06-27-tcon June 27, 2007: NAMIC Programmers' Week]
* [http://wiki.na-mic.org/Wiki/index.php/Registration_Update January, 2008: NAMIC AHM]

= Related Pages =

* [[Non Rigid Registration]]
* [http://www.slicer.org/slicerWiki/index.php/Slicer3:Performance_Analysis Slicer3:Performance_Analysis]
* [http://www.na-mic.org/Wiki/index.php/User:Barre/ITK_Registration_Optimization User:Barre/ITK Registration Optimization]
* [[ITK_Registration_Optimization/Testing_And_Backward_Forward_Compatibility | Testing and ITK Backward Forward Compatibility]]

= Notes on Software Profiling Tools =
* [http://www.lw-tech.com/index.php LTProf - simple profilter for Windows - Shareware]
* [http://www.intel.com/cd/software/products/asmo-na/eng/vtune/vlin/239145.htm Intel's VTune for Linux] ($)
* [http://www.cs.uoregon.edu/research/tau/home.php TAU]
* [http://www.cs.brown.edu/research/thmon/thmon.html Threadmon: Thread usage/blockage]
* [http://www.etnus.com/ TotalView] ($)
* [http://perfsuite.ncsa.uiuc.edu/ PerfSuite (POSIX Threads)]
* [http://sam.zoy.org/writings/programming/gprof.html GProf work-around for multi-threaded apps]
* References on multi-threaded profiling and code optimization
** [http://www.mactech.com/articles/mactech/Vol.11/11.04/ExtremeAdvantage/index.html General C++ performance optimization]
** [http://www.cs.princeton.edu/~mji/tmon.pdf Multi-threaded performance measurement (pdf document)]
** [http://en.wikipedia.org/wiki/Performance_analysis Wikipedia - General performance analysis]

Projects:RegistrationImprovement

2010-01-14T14:51:50Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= TODO =

* Documentation of RegisterImagesMultiRes, TransformFromFiducials
* Update documentation of RegisterImages
* Testing on TBI and Huntingtons data
* Box ROIs using Slicer ROI module (70% completed)

= Timeline of contributions =

== Jan 13, 2010 ==

* Mantis based tests for use case library
* XML description of presets (thanks to Jim Miller)
* Fixed some bugs in RegisterImagesMultiRes when dealing with images that have negative spacings.

== Jan 7, 2010 ==
Sped up compilation of command line modules by 40 minutes.

== Dec 15, 2009 ==
There is a new module "Transform from Fiducials" that computes a
linear transform from two fiducials lists with corresponding points.
Currently this can produce transformations which are translation only,
rigid, or similarity. The intent is for this to be used as a
preprocessing module for further registration. This is factored out
from the RegisterImages module so that you can see the result of the
fiducial based transform before using that as an initialization.

Development is continuing on RegisterImagesMultiRes to expose more
parameters of the algorithm to the user and to work with more types of
images.

== Nov 27, 2009 ==
I've merged several improvements into RegisterImagesMultiRes in SVN 11043

Better heuristic for downsampling images of different resolutions
and spacing. The actual heuristic is implemented in
DownsampleHeuristics.h. This should enable the algorithm to work on a
much wider range of images.

Heuristic for computing optimizer scales so the user only has to
select one global step size (in units of voxels). The dimensions of
the image are then used to compute the scalings for each component of
the transform.

support for saving the output transform in addition to the resampled image

== November 16, 2009 ==

Module committed to slicer. Currently only works on very specific images due to assumptions in the multi-resolution downsampling.

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2010-01-14T14:44:15Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= TODO =

* Documentation of RegisterImagesMultiRes, TransformFromFiducials
* Update documentation of RegisterImages
* Testing on TBI and Huntingtons data
* Box ROIs using Slicer ROI module (70% completed)

= Timeline of contributions =

== Jan 13, 2009 ==

* Mantis based tests for use case library
* XML description of presets (thanks to Jim Miller)
* Fixed some bugs in RegisterImagesMultiRes when dealing with images that have negative spacings.

== Jan 7, 2009 ==
Sped up compilation of command line modules by 40 minutes.

== Dec 15, 2009 ==
There is a new module "Transform from Fiducials" that computes a
linear transform from two fiducials lists with corresponding points.
Currently this can produce transformations which are translation only,
rigid, or similarity. The intent is for this to be used as a
preprocessing module for further registration. This is factored out
from the RegisterImages module so that you can see the result of the
fiducial based transform before using that as an initialization.

Development is continuing on RegisterImagesMultiRes to expose more
parameters of the algorithm to the user and to work with more types of
images.

== Nov 27, 2009 ==
I've merged several improvements into RegisterImagesMultiRes in SVN 11043

Better heuristic for downsampling images of different resolutions
and spacing. The actual heuristic is implemented in
DownsampleHeuristics.h. This should enable the algorithm to work on a
much wider range of images.

Heuristic for computing optimizer scales so the user only has to
select one global step size (in units of voxels). The dimensions of
the image are then used to compute the scalings for each component of
the transform.

support for saving the output transform in addition to the resampled image

== November 16, 2009 ==

Module committed to slicer. Currently only works on very specific images due to assumptions in the multi-resolution downsampling.

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2010-01-14T14:41:12Z

Gcasey: /* TODO */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= TODO =

* Documentation of RegisterImagesMultiRes, TransformFromFiducials
* Update documentation of RegisterImages
* Testing on TBI and Huntingtons data
* Box ROIs using Slicer ROI module (70% completed)

= Timeline of contributions =

== Jan 13, 2009 ==

* Mantis based tests for use case library
* XML description of presets (thanks to Jim Miller)
* Fixed some bugs in RegisterImagesMultiRes when dealing with images that have negative spacings.

== November 16, 2009 ==

Module committed to slicer. Currently only works on very specific images due to assumptions in the multi-resolution downsampling.

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2010-01-14T14:40:39Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= TODO =

* Documentation of RegisterImagesMultiRes, TransformFromFiducials
* Update documentation of RegisterImages
* Testing on TBI and Huntingtons data

= Timeline of contributions =

== Jan 13, 2009 ==

* Mantis based tests for use case library
* XML description of presets (thanks to Jim Miller)
* Fixed some bugs in RegisterImagesMultiRes when dealing with images that have negative spacings.

== November 16, 2009 ==

Module committed to slicer. Currently only works on very specific images due to assumptions in the multi-resolution downsampling.

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

2010 Winter Project Week RegistrationInfrastructure

2010-01-08T17:40:10Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:Fiducial_registration_before.jpg|Image test. Before registration.
Image:Fiducial_registration_after.jpg|Image test. After fiducial alignment.
Image:Fiducial_registration_after_multires.jpg|Image test. Image based alignment.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials
*During programming week
** Preset MRML (thanks to Jim Miller)
** Feedback on RegisterImagesMultiRes
** Improve testing (MIDAS based test)
** Compilation time improvements
** Identified and fixed some bugs in certain orientations.

</div>
</div>

<div style="width: 97%; float: left;">

=== Goals: Infrastructure ===
* Improvement of parameters UI
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-08T17:29:30Z

Gcasey:

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:Fiducial_registration_before.jpg|Image test. Before registration.
Image:Fiducial_registration_after.jpg|Image test. After fiducial alignment.
Image:Fiducial_registration_after_multires.jpg|Image test. Image based alignment.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials
*During programming week
** Preset MRML (thanks to Jim Miller)
** Feedback on RegisterImagesMultiRes
** Improve testing (MIDAS based test)
** Compilation time improvements

</div>
</div>

<div style="width: 97%; float: left;">

=== Goals: Infrastructure ===
* Improvement of parameters UI
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

File:Fiducial registration after multires.jpg

2010-01-08T17:29:02Z

Gcasey:

File:Fiducial registration after.jpg

2010-01-08T17:28:29Z

Gcasey:

File:Fiducial registration before.jpg

2010-01-08T17:26:55Z

Gcasey:

2010 Winter Project Week RegistrationInfrastructure

2010-01-07T21:24:56Z

Gcasey:

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials
*During programming week
** Preset MRML (thanks to Jim Miller)
** Feedback on RegisterImagesMultiRes
** Improve testing (MIDAS based test)
** Compilation time improvements

</div>
</div>

<div style="width: 97%; float: left;">

=== Goals: Infrastructure ===
* Improvement of parameters UI
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-06T16:03:44Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials
*During programming week
** Preset MRML (thanks to Jim Miller)
** Feedback on RegisterImagesMultiRes
** Improve testing (MIDAS based test)

</div>
</div>

<div style="width: 97%; float: left;">

=== Goals: Infrastructure ===
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation
* Plan for deformable registration

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-06T16:03:28Z

Gcasey:

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials
*During programming week
** Preset MRML
** Feedback on RegisterImagesMultiRes
** Improve testing (MIDAS based test)

</div>
</div>

<div style="width: 97%; float: left;">

=== Goals: Infrastructure ===
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation
* Plan for deformable registration

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:24:03Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer
*TransformFromFiducials

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastructure ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation
* Improve testing (Luis)
* Plan for deformable registration

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:12:13Z

Gcasey: /* Progress: Infrastructure */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastructure ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation
* Improve testing (Luis)
* Plan for deformable registration

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationCaseLibrary

2010-01-04T17:09:56Z

Gcasey:

__NOTOC__
<gallery>
Image:RegistrationCaseLibrary_snapshot.png‎|Example Snapshot of Registration Case Library Entry]]
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:SRegVar_Roll1.png|Example of Registration Parameter Exploration: registering a FLAIR brain to T1 at 1,2,5,10% sampling rates. Such explorations will be part of finding the optimal registration for a given scenario.
</gallery>

=The 3DSlicer Registration Case Library Project=

==Key Investigators==
* BWH: Dominik Meier, Ron Kikinis
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This work is part of a 2-year effort to supplement the 3DSlicer Registration Module with extensive set of documentation, tutorials and use case scenarios. We seek to build a comprehensive '''[[Projects:RegistrationDocumentation:UseCaseInventory|library of use cases ]]''' for every form of registration challenge using 3DSlicer. Each library entry will contain a dataset along with Registration Parameter Presets and a guided tutorial on how to successfully register the images.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The use case library relies mainly on user contributions for content. There is an [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''official call for datasets''']] to all slicer users to consider a unique time-limited service for any dataset/registration problem that is not yet in the library. Users who agree to share one '''anonymized''' dataset for the library will have that dataset registered by us and the solution and strategies posted. [[Projects:RegistrationDocumentation:UseCaseExample1b|Look here for an example of a library entry.]]
<br>
Our plan for the project week is to first get a survey of all projects using registration. We hope to catch most of these projects from reviewing these project description pages, so it is important that if you use registration in your procedure, please make sure to mention explicitly. We will collect as many example cases as possible, and select a few focus cases with particularly vexing registration challenges and begin to develop the appropriate tailored registration strategies.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*List of contacts for new use cases: [[2010_Winter_Project_Week_RegistrationCaseLibrary#Target Projects| see below]]
*insights/comments on registration settings/setting changes that made a difference go here
*Notes re. user insights/comments/wishes on registration go here

</div>
</div>

<div style="width: 97%; float: left;">
=== Progress: Target Projects ===
The projects below have been tentatively identified as having registration ties. We will seek discussion with these projects during the week. If your project is listed here, I will try to discuss the registration aspects at some point during the week. Type and length of discussion will vary greatly. Text next to each project below identifies the registration link.
*'''Segmentation''':
**[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully): uses register images to align atlas; functionality and compatibility considerations for RegisterImages redesign (both algorithm & GUI)
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully): uses ChangeTracker which in turn uses registration. From the [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4. documentation]: ChangeTracker is using Rigid Registration module through the CommandLineModule shared object invocation... "Rigid registration" *must* be available for ChangeTracker to function properly.
**[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami): employs its own shape-registration scheme: each shape is registered to a fixed arbitrary shape in the training set using a mean-square error registration scheme.
**[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa): includes registration in new (ABC) module: category: intra-subject multi-contrast reg.
**[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa): employs a label fusion segmentation algorithm which first registered all of the training images to the test one
*'''Registration'''
**[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski): co-registration of subject MRI with anatomical atlas; involves moving image with drastically clipped FOV, inter-subject registration
**[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Peter Risholm)
*'''IGT'''
** [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda): Transperineal device: includes registration, where accuracy should be improved; currently the registration is based on a single-slice image; it could possible to improve the accuracy by increasing the number of slices used for the registration.
*'''Radiotherapy'''
** [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov): Once segmentation is available, the goal is to register patient scans to account for anatomical changes between visits
*'''Analysis'''
**[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov): Register follow-up to baseline
*'''Informatics'''
**'''XNAT''' : discussion with XNAT group re. feasibility of using XNAT central as repository for use-case library.
**Processing and loading images in NRRD format: NRRD and NIFTI are the default formats for the image data in the registration case library.
* '''Diffusion'''
**[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell)
*'''NA-MIC Kit Internals'''
**[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin): SPECTRE: skull stripping is an important element for registration preprocessing, documentation and possibly GUI will link to this module.
*'''NA-MIC Outreach'''
**[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace): Insights/Guidelines for registration tutorials to be built.

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:09:28Z

Gcasey: /* Progress: Infrastructure */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastructure ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation
* Improve testing (Luis)

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:08:48Z

Gcasey: moved 2010 Winter Project Week RegistrationInfracstructure to 2010 Winter Project Week RegistrationInfrastructure

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastructure ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfracstructure

2010-01-04T17:08:48Z

Gcasey: moved 2010 Winter Project Week RegistrationInfracstructure to 2010 Winter Project Week RegistrationInfrastructure

#REDIRECT [[2010 Winter Project Week RegistrationInfrastructure]]

2010 Winter Project Week

2010-01-04T17:08:27Z

Gcasey: /* Registration */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__
[[Image:PW-SLC2010.png|300px]]

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates_Venue_Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)
#[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)
#[[2010_Winter_Project_Week_Musco_Skeletal_Segmentation | Rapid Segmentation of Knee Structures for Simulation]] (Harish Doddi, Saikat Pal, Luis Ibanez, Scott Delp)
#[[2010_Winter_Project_Week_WMLS | White Matter Lesion segmentation]] (Minjeong Kim UNC)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[2010_Winter_Project_Week_RegistrationInfrastructure|Registration Infrastructure]] (Casey Goodlett, Dominik Meier, Ron Kikinis)
#[[2010_Winter_Project_Week_Deformation_Field_Visualization|Deformation Field and Tensor Visualization]] (Garrett Larson, Martin Styner)
#[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski, Dominik Meier, Ron Kikinis)
# [[ 2010_Winter_Project_Week_testbed|Testbed for Evaluation, Comparison, and Parameter Exploration for 3D Registration]] (James Fishbaugh, Casey Goodlett, Guido Gerig)
# [[ 2010_Winter_Project_Week_HAMMER|HAMMER Registration Algorithm in Slicer 3]] (Guorong Wu, Xiaodong Tao, Jim Miller, and Dinggang Shen)

=== IGT ===
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters for Tumor Resection]] (Petter Risholm, Sandy Wells)
#[[2010_Winter_Project_Week_MRI_Reconstruction_by_Registration | MRI Reconstruction by Registration for Focused Ultrasound Therapy]] (Ben Schwartz, Sandy Wells)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation for Neurosurgical Planning]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI|Fast Imaging Library, and Siemens EPI for IGT]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin|DicomRT plugin for Slicer]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)
#[[2010_WinterProject_Week_CorticalThicknessAnalysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_WinterProject_Week_XNATUseforPopulationAnalysis|XNAT Use for Population Analysis]] (Corentin Hamel, Martin Styner, Clement Vachet)

=== Informatics ===
#[[2010_Winter_Project_Week_XND|XNAT Desktop User Interface]] (Dan M, Wendy P, Ron K)
#[[2010_Winter_Project_Week_Slicer_XNAT|Slicer 3 XNAT Performance Tuning]] (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#[[2010_Winter_Project_Week_catalyst|Harvard CTSC XNAT]] (Yong Gao, Dan M, Tim Olson, John Paulett)
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)
#[[2010_Winter_Project_Week_OAWMB|Open Access Whole body CT/MR data set]] (Dan Marcus, Steve Pieper)
#[[2010_Winter_Project_Week_mComment | Annotation of Medical Images]] (Kilian Pohl, Yong Zhang, Nicole Aucion, Wendy Plesniak, Steve Pieper)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller, Mahnaz Maddah, Nicole Aucoin, Wendy Plesniak, James Malcolm, Alex Yarmarkovich)
#[[ 2010_Winter_Project_Week_DTI_Fiber_Tract_Statistics|DTI Fiber-Tract Statistics]] (Anuja Sharma, Guido Gerig)

=== NA-MIC Kit Internals ===
#[[2010_Winter_Project_Week_Testing_for_Extensions|Testing for Extensions]] (Steve, Andriy Fedorov, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen, Jim Miller)
#[[2010_Winter_Project_Week_VTK_3D_Widgets_in_Slicer3|VTK 3D Widgets in Slicer3]] (Nicole Aucoin, Karthik, Will)
#[[2010_Winter_Project_Week_Slicer3_Colors_Module|Updates to Slicer3 Colors Module]] (Nicole Aucoin)
#[[2010_Winter_Project_Week_CMAKE_Build_process|CMAKE_Build_process]] (Dave Partyka, Katie Hayes)
#[[2010_Winter_Project_Week_XNAT_Packaging_For_Slicer | Integration of XNAT Packaging for Slicer Internals]] (Dan, Tim Olsen, Steve Pieper, Dave Partyka, Wendy, Randy)
#[[2010_Winter_Project_Week_Orthogonal_Planes_Issues|Orthogonal planes in reformat widget issues in Slicer3.5]] (Michal Depa, Steve Pieper)
#[[2010_Winter_Project_Week_Slicer_Dashboard|Slicer Dashboard]] (Luis, Steve, Bill & All)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller, Jean-Christophe Fillion-Robin, Julien Finet)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:06:55Z

Gcasey: /* Progress: Infrastrcuture */

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastructure ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationInfrastructure

2010-01-04T17:06:36Z

Gcasey: Created page with '__NOTOC__ <gallery> Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & com…'

__NOTOC__
<gallery>
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
</gallery>

=Slicer registration infrastructure=

==Key Investigators==
* Kitware: Casey Goodlett
* BWH: Dominik Meier, Ron Kikinis
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This project aims to provide the infrastructure necessary for robust interactive registration in Slicer.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

An experimental module RegisterImagesMultiRes is in development with the aim of providing robust linear registration.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">

=== Progress: Infrastrcuture ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationCaseLibrary

2010-01-04T16:59:24Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:RegistrationCaseLibrary_snapshot.png‎|Example Snapshot of Registration Case Library Entry]]
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:SRegVar_Roll1.png|Example of Registration Parameter Exploration: registering a FLAIR brain to T1 at 1,2,5,10% sampling rates. Such explorations will be part of finding the optimal registration for a given scenario.
</gallery>

=The 3DSlicer Registration Case Library Project=

==Key Investigators==
* BWH: Dominik Meier, Ron Kikinis
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This work is part of a 2-year effort to supplement the 3DSlicer Registration Module with extensive set of documentation, tutorials and use case scenarios. We seek to build a comprehensive '''[[Projects:RegistrationDocumentation:UseCaseInventory|library of use cases ]]''' for every form of registration challenge using 3DSlicer. Each library entry will contain a dataset along with Registration Parameter Presets and a guided tutorial on how to successfully register the images.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The use case library relies mainly on user contributions for content. There is an [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''official call for datasets''']] to all slicer users to consider a unique time-limited service for any dataset/registration problem that is not yet in the library. Users who agree to share one '''anonymized''' dataset for the library will have that dataset registered by us and the solution and strategies posted. [[Projects:RegistrationDocumentation:UseCaseExample1b|Look here for an example of a library entry.]]
<br>
Our plan for the project week is to first get a survey of all projects using registration. We hope to catch most of these projects from reviewing these project description pages, so it is important that if you use registration in your procedure, please make sure to mention explicitly. We will collect as many example cases as possible, and select a few focus cases with particularly vexing registration challenges and begin to develop the appropriate tailored registration strategies.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*List of contacts for new use cases: [[2010_Winter_Project_Week_RegistrationCaseLibrary#Target Projects| see below]]
*insights/comments on registration settings/setting changes that made a difference go here
*Notes re. user insights/comments/wishes on registration go here
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">
=== Progress: Target Projects ===
The projects below have been tentatively identified as having registration ties. We will seek discussion with these projects during the week. If your project is listed here, I will try to discuss the registration aspects at some point during the week. Type and length of discussion will vary greatly. Text next to each project below identifies the registration link.
*'''Segmentation''':
**[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully): uses register images to align atlas; functionality and compatibility considerations for RegisterImages redesign (both algorithm & GUI)
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully): uses ChangeTracker which in turn uses registration. From the [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4. documentation]: ChangeTracker is using Rigid Registration module through the CommandLineModule shared object invocation... "Rigid registration" *must* be available for ChangeTracker to function properly.
**[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami): employs its own shape-registration scheme: each shape is registered to a fixed arbitrary shape in the training set using a mean-square error registration scheme.
**[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa): includes registration in new (ABC) module: category: intra-subject multi-contrast reg.
**[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa): employs a label fusion segmentation algorithm which first registered all of the training images to the test one
*'''Registration'''
**[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski): co-registration of subject MRI with anatomical atlas; involves moving image with drastically clipped FOV, inter-subject registration
**[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Peter Risholm)
*'''IGT'''
** [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda): Transperineal device: includes registration, where accuracy should be improved; currently the registration is based on a single-slice image; it could possible to improve the accuracy by increasing the number of slices used for the registration.
*'''Radiotherapy'''
** [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov): Once segmentation is available, the goal is to register patient scans to account for anatomical changes between visits
*'''Analysis'''
**[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov): Register follow-up to baseline
*'''Informatics'''
**'''XNAT''' : discussion with XNAT group re. feasibility of using XNAT central as repository for use-case library.
**Processing and loading images in NRRD format: NRRD and NIFTI are the default formats for the image data in the registration case library.
* '''Diffusion'''
**[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell)
*'''NA-MIC Kit Internals'''
**[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin): SPECTRE: skull stripping is an important element for registration preprocessing, documentation and possibly GUI will link to this module.
*'''NA-MIC Outreach'''
**[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace): Insights/Guidelines for registration tutorials to be built.

=== Progress: Infrastrcuture ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard
* Reorganize Wiki documentation

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationCaseLibrary

2010-01-04T16:59:04Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:RegistrationCaseLibrary_snapshot.png‎|Example Snapshot of Registration Case Library Entry]]
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:SRegVar_Roll1.png|Example of Registration Parameter Exploration: registering a FLAIR brain to T1 at 1,2,5,10% sampling rates. Such explorations will be part of finding the optimal registration for a given scenario.
</gallery>

=The 3DSlicer Registration Case Library Project=

==Key Investigators==
* BWH: Dominik Meier, Ron Kikinis
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This work is part of a 2-year effort to supplement the 3DSlicer Registration Module with extensive set of documentation, tutorials and use case scenarios. We seek to build a comprehensive '''[[Projects:RegistrationDocumentation:UseCaseInventory|library of use cases ]]''' for every form of registration challenge using 3DSlicer. Each library entry will contain a dataset along with Registration Parameter Presets and a guided tutorial on how to successfully register the images.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The use case library relies mainly on user contributions for content. There is an [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''official call for datasets''']] to all slicer users to consider a unique time-limited service for any dataset/registration problem that is not yet in the library. Users who agree to share one '''anonymized''' dataset for the library will have that dataset registered by us and the solution and strategies posted. [[Projects:RegistrationDocumentation:UseCaseExample1b|Look here for an example of a library entry.]]
<br>
Our plan for the project week is to first get a survey of all projects using registration. We hope to catch most of these projects from reviewing these project description pages, so it is important that if you use registration in your procedure, please make sure to mention explicitly. We will collect as many example cases as possible, and select a few focus cases with particularly vexing registration challenges and begin to develop the appropriate tailored registration strategies.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*List of contacts for new use cases: [[2010_Winter_Project_Week_RegistrationCaseLibrary#Target Projects| see below]]
*insights/comments on registration settings/setting changes that made a difference go here
*Notes re. user insights/comments/wishes on registration go here
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">
=== Progress: Target Projects ===
The projects below have been tentatively identified as having registration ties. We will seek discussion with these projects during the week. If your project is listed here, I will try to discuss the registration aspects at some point during the week. Type and length of discussion will vary greatly. Text next to each project below identifies the registration link.
*'''Segmentation''':
**[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully): uses register images to align atlas; functionality and compatibility considerations for RegisterImages redesign (both algorithm & GUI)
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully): uses ChangeTracker which in turn uses registration. From the [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4. documentation]: ChangeTracker is using Rigid Registration module through the CommandLineModule shared object invocation... "Rigid registration" *must* be available for ChangeTracker to function properly.
**[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami): employs its own shape-registration scheme: each shape is registered to a fixed arbitrary shape in the training set using a mean-square error registration scheme.
**[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa): includes registration in new (ABC) module: category: intra-subject multi-contrast reg.
**[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa): employs a label fusion segmentation algorithm which first registered all of the training images to the test one
*'''Registration'''
**[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski): co-registration of subject MRI with anatomical atlas; involves moving image with drastically clipped FOV, inter-subject registration
**[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Peter Risholm)
*'''IGT'''
** [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda): Transperineal device: includes registration, where accuracy should be improved; currently the registration is based on a single-slice image; it could possible to improve the accuracy by increasing the number of slices used for the registration.
*'''Radiotherapy'''
** [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov): Once segmentation is available, the goal is to register patient scans to account for anatomical changes between visits
*'''Analysis'''
**[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov): Register follow-up to baseline
*'''Informatics'''
**'''XNAT''' : discussion with XNAT group re. feasibility of using XNAT central as repository for use-case library.
**Processing and loading images in NRRD format: NRRD and NIFTI are the default formats for the image data in the registration case library.
* '''Diffusion'''
**[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell)
*'''NA-MIC Kit Internals'''
**[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin): SPECTRE: skull stripping is an important element for registration preprocessing, documentation and possibly GUI will link to this module.
*'''NA-MIC Outreach'''
**[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace): Insights/Guidelines for registration tutorials to be built.

=== Progress: Infrastrcuture ===
* Preset MRML
* Feedback on RegisterImagesMultiRes
* Improvement of parameters UI
* Brainstorm on Wizard

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationCaseLibrary

2010-01-04T16:57:56Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:RegistrationCaseLibrary_snapshot.png‎|Example Snapshot of Registration Case Library Entry]]
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:SRegVar_Roll1.png|Example of Registration Parameter Exploration: registering a FLAIR brain to T1 at 1,2,5,10% sampling rates. Such explorations will be part of finding the optimal registration for a given scenario.
</gallery>

=The 3DSlicer Registration Case Library Project=

==Key Investigators==
* BWH: Dominik Meier, Ron Kikinis
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This work is part of a 2-year effort to supplement the 3DSlicer Registration Module with extensive set of documentation, tutorials and use case scenarios. We seek to build a comprehensive '''[[Projects:RegistrationDocumentation:UseCaseInventory|library of use cases ]]''' for every form of registration challenge using 3DSlicer. Each library entry will contain a dataset along with Registration Parameter Presets and a guided tutorial on how to successfully register the images.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The use case library relies mainly on user contributions for content. There is an [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''official call for datasets''']] to all slicer users to consider a unique time-limited service for any dataset/registration problem that is not yet in the library. Users who agree to share one '''anonymized''' dataset for the library will have that dataset registered by us and the solution and strategies posted. [[Projects:RegistrationDocumentation:UseCaseExample1b|Look here for an example of a library entry.]]
<br>
Our plan for the project week is to first get a survey of all projects using registration. We hope to catch most of these projects from reviewing these project description pages, so it is important that if you use registration in your procedure, please make sure to mention explicitly. We will collect as many example cases as possible, and select a few focus cases with particularly vexing registration challenges and begin to develop the appropriate tailored registration strategies.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*List of contacts for new use cases: [[2010_Winter_Project_Week_RegistrationCaseLibrary#Target Projects| see below]]
*insights/comments on registration settings/setting changes that made a difference go here
*Notes re. user insights/comments/wishes on registration go here
*RegisterImagesMultiRes in Slicer

</div>
</div>

<div style="width: 97%; float: left;">
=== Progress: Target Projects ===
The projects below have been tentatively identified as having registration ties. We will seek discussion with these projects during the week. If your project is listed here, I will try to discuss the registration aspects at some point during the week. Type and length of discussion will vary greatly. Text next to each project below identifies the registration link.
*'''Segmentation''':
**[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully): uses register images to align atlas; functionality and compatibility considerations for RegisterImages redesign (both algorithm & GUI)
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully): uses ChangeTracker which in turn uses registration. From the [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4. documentation]: ChangeTracker is using Rigid Registration module through the CommandLineModule shared object invocation... "Rigid registration" *must* be available for ChangeTracker to function properly.
**[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami): employs its own shape-registration scheme: each shape is registered to a fixed arbitrary shape in the training set using a mean-square error registration scheme.
**[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa): includes registration in new (ABC) module: category: intra-subject multi-contrast reg.
**[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa): employs a label fusion segmentation algorithm which first registered all of the training images to the test one
*'''Registration'''
**[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski): co-registration of subject MRI with anatomical atlas; involves moving image with drastically clipped FOV, inter-subject registration
**[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Peter Risholm)
*'''IGT'''
** [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda): Transperineal device: includes registration, where accuracy should be improved; currently the registration is based on a single-slice image; it could possible to improve the accuracy by increasing the number of slices used for the registration.
*'''Radiotherapy'''
** [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov): Once segmentation is available, the goal is to register patient scans to account for anatomical changes between visits
*'''Analysis'''
**[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov): Register follow-up to baseline
*'''Informatics'''
**'''XNAT''' : discussion with XNAT group re. feasibility of using XNAT central as repository for use-case library.
**Processing and loading images in NRRD format: NRRD and NIFTI are the default formats for the image data in the registration case library.
* '''Diffusion'''
**[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell)
*'''NA-MIC Kit Internals'''
**[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin): SPECTRE: skull stripping is an important element for registration preprocessing, documentation and possibly GUI will link to this module.
*'''NA-MIC Outreach'''
**[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace): Insights/Guidelines for registration tutorials to be built.

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week RegistrationCaseLibrary

2010-01-04T16:57:39Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:RegistrationCaseLibrary_snapshot.png‎|Example Snapshot of Registration Case Library Entry]]
Image:Registration_ExamplePresetMenu.png|Example Preset Menu. Presets will be a new feature implemented into the RegisterImage module to organize, share & communicate regisration input parameters tailored to a specific scenario.
Image:SRegVar_Roll1.png|Example of Registration Parameter Exploration: registering a FLAIR brain to T1 at 1,2,5,10% sampling rates. Such explorations will be part of finding the optimal registration for a given scenario.
</gallery>

=The 3DSlicer Registration Case Library Project=

==Key Investigators==
* BWH: Dominik Meier, Ron Kikinis
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
This work is part of a 2-year effort to supplement the 3DSlicer Registration Module with extensive set of documentation, tutorials and use case scenarios. We seek to build a comprehensive '''[[Projects:RegistrationDocumentation:UseCaseInventory|library of use cases ]]''' for every form of registration challenge using 3DSlicer. Each library entry will contain a dataset along with Registration Parameter Presets and a guided tutorial on how to successfully register the images.

We also have a [[AHM2010:RegistrationBreakout|''Registration Breakout Session'']] on Tuesday 1-2pm (Amethyst Room). If registration is on your processing list, please drop in, have a look at what's new, and share your thoughts.

A new robust affine registration is also under development named RegisterImagesMultiRes. Feedback on this module would be appreciated to facilitate development.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The use case library relies mainly on user contributions for content. There is an [[Projects:RegistrationDocumentation:UseCaseAdvertisement|'''official call for datasets''']] to all slicer users to consider a unique time-limited service for any dataset/registration problem that is not yet in the library. Users who agree to share one '''anonymized''' dataset for the library will have that dataset registered by us and the solution and strategies posted. [[Projects:RegistrationDocumentation:UseCaseExample1b|Look here for an example of a library entry.]]
<br>
Our plan for the project week is to first get a survey of all projects using registration. We hope to catch most of these projects from reviewing these project description pages, so it is important that if you use registration in your procedure, please make sure to mention explicitly. We will collect as many example cases as possible, and select a few focus cases with particularly vexing registration challenges and begin to develop the appropriate tailored registration strategies.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
*List of contacts for new use cases: [[2010_Winter_Project_Week_RegistrationCaseLibrary#Target Projects| see below]]
*insights/comments on registration settings/setting changes that made a difference go here
*Notes re. user insights/comments/wishes on registration go here

</div>
</div>

<div style="width: 97%; float: left;">
=== Progress: Target Projects ===
The projects below have been tentatively identified as having registration ties. We will seek discussion with these projects during the week. If your project is listed here, I will try to discuss the registration aspects at some point during the week. Type and length of discussion will vary greatly. Text next to each project below identifies the registration link.
*'''Segmentation''':
**[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully): uses register images to align atlas; functionality and compatibility considerations for RegisterImages redesign (both algorithm & GUI)
**[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully): uses ChangeTracker which in turn uses registration. From the [http://www.slicer.org/slicerWiki/index.php/Modules:ChangeTracker-Documentation-3.4. documentation]: ChangeTracker is using Rigid Registration module through the CommandLineModule shared object invocation... "Rigid registration" *must* be available for ChangeTracker to function properly.
**[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso): Does this involve co-registration of an atlas?
**[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami): employs its own shape-registration scheme: each shape is registered to a fixed arbitrary shape in the training set using a mean-square error registration scheme.
**[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa): includes registration in new (ABC) module: category: intra-subject multi-contrast reg.
**[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa): employs a label fusion segmentation algorithm which first registered all of the training images to the test one
*'''Registration'''
**[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski): co-registration of subject MRI with anatomical atlas; involves moving image with drastically clipped FOV, inter-subject registration
**[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Peter Risholm)
*'''IGT'''
** [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda): Transperineal device: includes registration, where accuracy should be improved; currently the registration is based on a single-slice image; it could possible to improve the accuracy by increasing the number of slices used for the registration.
*'''Radiotherapy'''
** [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov): Once segmentation is available, the goal is to register patient scans to account for anatomical changes between visits
*'''Analysis'''
**[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov): Register follow-up to baseline
*'''Informatics'''
**'''XNAT''' : discussion with XNAT group re. feasibility of using XNAT central as repository for use-case library.
**Processing and loading images in NRRD format: NRRD and NIFTI are the default formats for the image data in the registration case library.
* '''Diffusion'''
**[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation]] (Lauren O'Donnell)
*'''NA-MIC Kit Internals'''
**[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin): SPECTRE: skull stripping is an important element for registration preprocessing, documentation and possibly GUI will link to this module.
*'''NA-MIC Outreach'''
**[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace): Insights/Guidelines for registration tutorials to be built.

==References==
*[[2010_Winter_Project_Week#Projects|back to AHM_2010 project list]]
*[[Projects:RegistrationDocumentation|Link to the RegistrationDocumentation Project Wiki]]
*[[Projects:RegistrationImprovement|Link to Kitware Registration Developer Efforts]]

</div>

2010 Winter Project Week

2010-01-04T16:23:50Z

Gcasey: /* Registration */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__
[[Image:PW-SLC2010.png|300px]]

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates_Venue_Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)
#[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)
#[[2010_Winter_Project_Week_Musco_Skeletal_Segmentation | Rapid Segmentation of Knee Structures for Simulation]] (Harish Doddi, Saikat Pal, Luis Ibanez, Scott Delp)
#[[2010_Winter_Project_Week_WMLS | White Matter Lesion segmentation]] (Minjeong Kim UNC)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[2010_Winter_Project_Week_Deformation_Field_Visualization|Deformation Field and Tensor Visualization]] (Garrett Larson, Martin Styner)
#[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski, Dominik Meier, Ron Kikinis)
# [[ 2010_Winter_Project_Week_testbed|Testbed for Evaluation, Comparison, and Parameter Exploration for 3D Registration]] (James Fishbaugh, Casey Goodlett, Guido Gerig)
# [[ 2010_Winter_Project_Week_HAMMER|HAMMER Registration Algorithm in Slicer 3]] (Guorong Wu, Xiaodong Tao, Jim Miller, and Dinggang Shen)

=== IGT ===
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters for Tumor Resection]] (Petter Risholm, Sandy Wells)
#[[2010_Winter_Project_Week_MRI_Reconstruction_by_Registration | MRI Reconstruction by Registration for Focused Ultrasound Therapy]] (Ben Schwartz, Sandy Wells)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation for Neurosurgical Planning]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI|Fast Imaging Library, and Siemens EPI for IGT]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin|DicomRT plugin for Slicer]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)
#[[2010_WinterProject_Week_CorticalThicknessAnalysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_WinterProject_Week_XNATUseforPopulationAnalysis|XNAT Use for Population Analysis]] (Corentin Hamel, Martin Styner, Clement Vachet)

=== Informatics ===
#[[2010_Winter_Project_Week_XND|XNAT Desktop User Interface]] (Dan M, Wendy P, Ron K)
#[[2010_Winter_Project_Week_Slicer_XNAT|Slicer 3 XNAT Performance Tuning]] (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#[[2010_Winter_Project_Week_catalyst|Harvard CTSC XNAT]] (Yong Gao, Dan M, Tim Olson, John Paulett)
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)
#[[2010_Winter_Project_Week_OAWMB|Open Access Whole body CT/MR data set]] (Dan Marcus, Steve Pieper)
#[[2010_Winter_Project_Week_mComment | Annotation of Medical Images]] (Kilian Pohl, Yong Zhang, Nicole Aucion, Wendy Plesniak, Steve Pieper)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller, Mahnaz Maddah, Nicole Aucoin, Wendy Plesniak, James Malcolm, Alex Yarmarkovich)
#[[ 2010_Winter_Project_Week_DTI_Fiber_Tract_Statistics|DTI Fiber-Tract Statistics]] (Anuja Sharma, Guido Gerig)

=== NA-MIC Kit Internals ===
#[[2010_Winter_Project_Week_Testing_for_Extensions|Testing for Extensions]] (Steve, Andriy Fedorov, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen, Jim Miller)
#[[2010_Winter_Project_Week_VTK_3D_Widgets_in_Slicer3|VTK 3D Widgets in Slicer3]] (Nicole Aucoin, Karthik, Will)
#[[2010_Winter_Project_Week_Slicer3_Colors_Module|Updates to Slicer3 Colors Module]] (Nicole Aucoin)
#[[2010_Winter_Project_Week_CMAKE_Build_process|CMAKE_Build_process]] (Dave Partyka, Katie Hayes)
#[[2010_Winter_Project_Week_XNAT_Packaging_For_Slicer | Integration of XNAT Packaging for Slicer Internals]] (Dan, Tim Olsen, Steve Pieper, Dave Partyka, Wendy, Randy)
#[[2010_Winter_Project_Week_Orthogonal_Planes_Issues|Orthogonal planes in reformat widget issues in Slicer3.5]] (Michal Depa, Steve Pieper)
#[[2010_Winter_Project_Week_Slicer_Dashboard|Slicer Dashboard]] (Luis, Steve, Bill & All)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller, Jean-Christophe Fillion-Robin, Julien Finet)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2010 Winter Project Week testbed

2010-01-04T16:23:29Z

Gcasey: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utah: James Fishabugh, Guido Gerig
* Kitware: Casey Goodlett

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

We are interested in comparing existing registration packages to determine how registration in Slicer3 can be improved. This work focuses on examining various packages researchers are currently using for registration and comparing results on a set of examples representative of common registration tasks. We propose the development of a testbed, where registration packages can be compared and parameters suitable for a given domain (e.g. multi-modal brain registration) can be determined.

The focus for comparison will be challenging applications of 3D linear and non-linear
registration. For example, pre and post treatment T1 images of hearts or multi-modal images of individual subjects with traumatic brain injuries (TBI).

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

The testbed provides a common interface for conducting experiments with various registration applications. We propose a database of known registration application definitions. The set of definitions in the database represents the currently available registration packages in the testbed. Adding a new definition to the database consists of defining the parameters for the desired registration application in an XML format.

The testbed is similar in spirit to BatchMake. In the same way that BatchMake provides a wrapper for command line applications, the registration testbed provides a wrapper for command line registration applications. This allows
for experiments to be scripted, and run across several registration packages. The user can define the registration task they would like to perform, or choose from a set of representative examples. Additionally, the testbed can be used for exploratory experiments, where the goal is to find good parameters for a given registration task.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

Currently working on a proof of concept prototype.

</div>
</div>

2010 Winter Project Week

2010-01-03T14:31:16Z

Gcasey: /* Registration */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__
[[Image:PW-SLC2010.png|300px]]

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates_Venue_Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)
#[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)
#[[2010_Winter_Project_Week_Musco_Skeletal_Segmentation | Knee Segmentation]] (Harish Doddi, Saikat Pal, Luis Ibanez, Scott Delp)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[2010_Winter_Project_Week_Deformation_Field_Visualization|Deformation Field and Tensor Visualization]] (Garrett Larson, Martin Styner)
#[[2010_Winter_Project_Week_ThalamicNucleiAtlas | Fusion of Anatomy,MRI and Electrophysiology in Parkinson's]] (Andrzej Przybyszewski, Dominik Meier, Ron Kikinis)
# [[ 2010_Winter_Project_Week_testbed|Testbed for Evaluation, Comparison, and Parameter Exploration for 3D Registration]] (James Fishbaugh, Guido Gerig)

=== IGT ===
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters for Tumor Resection]] (Petter Risholm, Sandy Wells)
#[[2010_Winter_Project_Week_MRI_Reconstruction_by_Registration | MRI Reconstruction by Registration for Focused Ultrasound Therapy]] (Ben Schwartz, Sandy Wells)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation for Neurosurgical Planning]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI|Fast Imaging Library, and Siemens EPI for IGT]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin|DicomRT plugin for Slicer]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)
#[[2010_WinterProject_Week_CorticalThicknessAnalysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_WinterProject_Week_XNATUseforPopulationAnalysis|XNAT Use for Population Analysis]] (Corentin Hamel, Martin Styner, Clement Vachet)

=== Informatics ===
#[[2010_Winter_Project_Week_XND|XNAT Desktop User Interface]] (Dan M, Wendy P, Ron K)
#[[2010_Winter_Project_Week_Slicer_XNAT|Slicer 3 XNAT Performance Tuning]] (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#[[2010_Winter_Project_Week_catalyst|Harvard CTSC XNAT]] (Yong Gao, Dan M, Tim Olson, John Paulett)
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)
#[[2010_Winter_Project_Week_OAWMB|Open Access Whole body CT/MR data set]] (Dan Marcus, Steve Pieper)
#[[2010_Winter_Project_Week_mComment | Annotation of Medical Images]] (Kilian Pohl, Yong Zhang, Nicole Aucion, Wendy Plesniak, Steve Pieper)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller, Mahnaz Maddah, Nicole Aucoin, Wendy Plesniak, James Malcolm, Alex Yarmarkovich)
#[[ 2010_Winter_Project_Week_DTI_Fiber_Tract_Statistics|DTI Fiber-Tract Statistics]] (Anuja Sharma, Guido Gerig)

=== NA-MIC Kit Internals ===
#[[2010_Winter_Project_Week_Testing_for_Extensions|Testing for Extensions]] (Steve, Andriy Fedorov, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen, Jim Miller)
#[[2010_Winter_Project_Week_VTK_3D_Widgets_in_Slicer3|VTK 3D Widgets in Slicer3]] (Nicole Aucoin, Karthik, Will)
#[[2010_Winter_Project_Week_Slicer3_Colors_Module|Updates to Slicer3 Colors Module]] (Nicole Aucoin)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#[[2010_Winter_Project_Week_XNAT_Packaging_For_Slicer | Integration of XNAT Packaging for Slicer Internals]] (Dan, Tim Olsen, Steve Pieper, Dave Partyka, Wendy, Randy)
#[[2010_Winter_Project_Week_Orthogonal_Planes_Issues|Orthogonal planes in reformat widget issues in Slicer3.5]] (Michal Depa, Steve Pieper)
#[[2010_Winter_Project_Week_Slicer_Dashboard|Slicer Dashboard]] (Luis, Steve, Bill & All)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller, Jean-Christophe Fillion-Robin, Julien Finet)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2010 Winter Project Week

2009-12-17T20:36:01Z

Gcasey: /* Registration */

Back to [[Project Events]], [[AHM_2010]], [[Events]]

__NOTOC__

==Background==

From January 4-8, 2010, the tenth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience applications will be hosted in Salt Lake City, Utah. Participant engange in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Dates.Venue.Registration ==

Please [[AHM_2010#Dates_Venue_Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2010#Agenda|click here for the agenda for AHM 2010 and Project Week]].

== Modules and extensions==

* [[Media:3DSlicer-Modules%2BExtensions-2009-11-27.ppt|Overview]]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Requirements_for_Modules Requirements for modules]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation-3.5#Introduction User-side explanations]
* [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Extensions Developer-side explanations]

==Projects==

=== Segmentation ===
#[[2010_Winter_Project_Week_Spine_Segmentation_Module_in_Slicer3|Spine Segmentation Module in Slicer3]] (Martin Loepprich, Sylvain Jaume, Polina Golland, Ron Kikinis, Steve Pieper)
#[[2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Steve Pieper)
#[[2010_Winter_Project_Week_RobustStatisticsDrivenActiveContourSegmentation|Active contour segmentation using robust statistics]] (Yi Gao, Allen Tannenbaum, GT; Andriy Fedorov, Katie Hayes Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_SegmentationWizard|High Level Wizard for Segmentation of Images]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_LongitudinalLupusAnalyses|Longitudinal Analyses of Lesions in Lupus]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_MultiscaleLupusAnalyses|Multiscale Analyses of Lupus Patients]] (Mark Scully, Jeremy Bockholt, Steve Pieper)
#[[2010_Winter_Project_Week_ProstateSeg|Prostate segmentation using shape-based method]] (Andras Lasso, Gabor Fichtinger, Yi Gao, Allen Tannenbaum, Andriy Fedorov)
#[[2010_Winter_Project_Week_TubularTreeSeg|Tubular Tree Segmentation for brain and cardiac imagery]] (Vandana Mohan, Allen Tannenbaum, GT; Marek Kubicki, BWH)
#[[2010_Winter_Project_Week_SegmentationEpicardialWall|Epicardial Wall Segmentation]] (Behnood Gholami, Yi Gao, Allen Tannenbaum, GT; Rob MacLeod, Josh Blauer, University of Utah)
#[[2010_Winter_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Matias Perez, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Winter_Project_Week_TBISegmentation|Segmentation of TBI (Traumatic Brain Injury) Subjects from Multimodal MRI]] (Marcel Prastawa, Guido Gerig, Ron Kikinis)
#[[2010_Winter_Project_Week_Cardiac_Ablation_Scar_Segmentation|Cadiac Ablation Scar Segmentation]] (Michal Depa, Polina Golland, Ehud Schmidt, Ron Kikinis)

=== Registration ===
#[[2010_Winter_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library Project]] (Dominik Meier, Casey Goodlett, Ron Kikinis)
#[[2010_Winter_Project_Week_RegistrationInfrastructure|Improvements to the infrastructure for Registration in Slicer]] (Casey Goodlett, Dominik Meier, Ron Kikinis)
#[[Tissue_Dependent_Registration|Registration with Varying Elastic Parameters]] (Petter Risholm, Sandy Wells)
#[[2010_Winter_Project_Week_Deformation_Field_Visualization|Deformation Field and Tensor Visualization]] (Garrett Larson, Martin Styner)

=== IGT ===
# [[2010_Winter_Project_Week_Fast_Imaging_Library_%2B_Siemens_EPI]] (Scott Hoge, Nick Todd, Dennis Parker, Katie Hayes)
# [[2010_Winter_Project_Week_MRI_Guided_Robotic_Prostate_Intervention| MRI-guided Robotic Prostate Intervention]] (Andras Lasso and Junichi Tokuda)
#[[ 2010_Winter_Project_Week_WM_ATLAS|Atlas-Based White Matter Segmentation for Neurosurgical Planning]] (Lauren O'Donnell, C-F Westin, Alexandra J. Golby)

=== Radiotherapy ===
# [[2010_Winter_Project_Week_DicomRT_Plugin|DicomRT plugin for Slicer]] (Greg Sharp, others)
# [[Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Vandana Mohan, Greg Sharp, Allen Tannenbaum )

=== Analysis ===
#[[2010_Winter_Project_Week_VervetMRILongitudinalAnalysis|Vervet MRI Longitudinal Analysis]] (Andriy Fedorov, Ron Rikinis, Ginger Li, Chris Wyatt)
#[[2010_WinterProject_Week_MRSIModule|MRSI Module]] (Bjoern Menze, Polina Golland)
#[[2010_WinterProject_Week_CorticalThicknessAnalysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_WinterProject_Week_XNATUseforPopulationAnalysis|XNAT Use for Population Analysis]] (Corentin Hamel, Martin Styner, Clement Vachet)

=== Informatics ===
#XNAT Desktop User Interface (Dan M, Wendy P, Ron K)
#Slicer 3 XNAT Performance Tuning (Wendy P, Dan M, Tim Olson, Nicole Aucoin)
#Harvard CTSC XNAT (Yong Gao, Dan M, Tim Olson, John Paulett)
##Contributing SubjectHandler Yong wrote into DicomServer release.
##Scan Level search capabilities for queries like "find all mr sessions with a usable MPRAGE scan". According to Tim, this is not an out-of-the-box thing offered by the REST API.
##Processing and loading images in NRRD format.
#[[2010_Winter_Project_Week_xnatfs|xnatfs Integration into XNAT core]] (Dan Blezek, John Paulett, Tim Olsen)
#Whole body CT/MR open access data set publishing (Dan Marcus)

=== Diffusion ===
#[[ 2010_Winter_Project_Week_HARDI_RSH|Integration of Real Spherical Harmonic basis for HARDI models]] (Luke Bloy, C-F Westin)
#[[ 2010_Winter_Project_Week_Tractography|Filtered tractography]] (James Malcolm, Peter Savadjiev, Yogesh Rathi, C-F Westin, Casey Goodlett)
#[[ 2010_Winter_Project_Week_HARDI_CONNECTIVITY|Connectivity Study of Neonatal Brain Data using HARDI Techniques]] ( Yundi(Wendy) Shi, Deepika Mahalingam, Martin Styner )
#[[2010_Winter_Project_Week_TractographyPickingEditing|Tractography Picking and Bundle Editing]] (Jim Miller)
#[[ 2010_Winter_Project_Week_DTI_Fiber_Tract_Statistics|DTI Fiber-Tract Statistics]] (Anuja Sharma, Guido Gerig)

=== Python ===

=== NA-MIC Kit Internals ===
#Testing for Extensions (Steve, Andre, Jim, Julien Jomier, Katie Hayes, Stuart Wallace)
#[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration|Integration of SPECTRE Java module into 3D Slicer]] (Nicole Aucoin, Aaron Carass, Min Chen)
#[[2010_Winter_Project_Week_VTK_3D_Widgets_in_Slicer3|VTK 3D Widgets in Slicer3]] (Nicole Aucoin, Karthik, Will)
#[[2010_Winter_Project_Week_Slicer3_Colors_Module|Updates to Slicer3 Colors Module]] (Nicole Aucoin)
#CMAKE Build process (Dave Partyka, Katie Hayes)
#Integration of XNAT Packaging for Slicer Internals (Dan, Tim Olsen, Dave Partyka, Wendy, Randy)
#[[2010_Winter_Project_Week_Orthogonal_Planes_Issues|Orthogonal planes in reformat widget issues in Slicer3.5]] (Michal Depa, Steve Pieper)

(Other possibilities: Plotting, Layouts)

=== NA-MIC Outreach ===
#[[AHM 2010 Tutorial Polishing | Tutorial Polishing]] (Stuart Wallace, Randy Gollub, Sonia Pujol, all contributing tutorial contest developers)

=== Execution Model ===
# [[2010_Winter_Project_Week_Qt-ing the Command Line Module | Qt-ing the Command Line Module]] (Jim Miller)
# [[2010_Winter_Project_Week_Command Line Module Simple Return Types | Simple Return Types]] (Jim Miller)

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# Starting Thursday, October 15th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 15: Engineering Infrastructure Projects
#*October 22: Funded External Collaboration Projects
#*October 29: Funded External Collaboration Projects
#*November 5: DPB Projects
#*November 19: DPB Projects
#*December 3: Other/new collaborations
#*December 10: Finalize Engineering Projects
#*December 17: Loose Ends
#By December 17, 2010: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By December 17, 2009: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

Projects:RegistrationImprovement

2009-11-18T19:59:35Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= Timeline of contributions =

== November 16, 2009 ==

Module committed to slicer. Currently only works on very specific images due to assumptions in the multi-resolution downsampling.

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2009-11-06T15:12:03Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= Timeline of contributions =

== November 6, 2009 ==

New registration module called MoreSearch implemented in NAMIC sandbox. A new registration module that is now in a rough draft stage for testing and further improvment. The improvements in this module are user of multi-resolution, a new set of ITK transforms that decomposes the parameter space into rotation, translation, scale, and skew, and an initializer based on ideas from the FSL algorithm.

{|
|-
|[[Image:Cbg_registration_algorithm_test.png|thumb|500px| Vervet data registration]]
| [[Image:Cbg_registration_algorithm_test2.png|thumb|500px| Vervet data registration]]
|-
|}

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

File:Cbg registration algorithm test2.png

2009-11-06T15:03:37Z

Gcasey:

File:Cbg registration algorithm test.png

2009-11-06T14:55:41Z

Gcasey:

Projects:RegistrationImprovement

2009-10-22T17:34:29Z

Gcasey: /* October 22, 2009 */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= Timeline of contributions =

== October 22, 2009 ==

Investigating MRML Presets. The following can be saved as a .mrml scene and loaded into slicer to populate the parameter sets of RegisterImages.
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2009-10-22T17:33:40Z

Gcasey: /* Timeline of contributions */

= Registration Improvements =
This page will describe registration improvements made within Slicer3 to improve the usability and robustness of registration algorithms so they may be used in an interactive clinical setting.

= Key Contributors =
*Kitware: Casey Goodlett with consultation from Will Schroeder and Stephen Aylward
*BWH: Ron Kikinis, Dominik Meier, Andriy Fedorov

= RegisterImages Algorithm =

*ITK Metrics used: [http://www.itk.org/Doxygen/html/classitk_1_1MattesMutualInformationImageToImageMetric.html MattesMutualInformation]
*Optimizer: [http://www.itk.org/Doxygen/html/classitk_1_1OnePlusOneEvolutionaryOptimizer.html OnePlusOne Evolutionary Optimizer] followed by [http://www.itk.org/Doxygen/html/classitk_1_1FRPROptimizer.html FRPR] in fletcher reeves mode
*Transform Types: Rigid transform [http://www.itk.org/Doxygen/html/classitk_1_1VersorRigid3DTransform.html VersorRigid3DTransform], Affine transform [http://www.itk.org/Doxygen/html/classitk_1_1AffineTransform.html AffineTransform], B-spline transform [http://www.itk.org/Doxygen/html/classitk_1_1BSplineDeformableTransform.html BSplineDeformableTransform]
*Initialization types, details on landmark-based initialization

A user should typically one of the Pipeline methods (PipelineRigid, PipelineAffine, PipelineBspline) as these will run Initalization -> Rigid -> Affine -> Bspline to the specified level. These are run in order to convergence or maximum # of iterations. Within each pipeline step there is a two stage optimization. First the evolution optmizer is run to stochastically chose a starting location for optimization. After this the FRPR optimizer is used. Currently multi-resolution optimization is only used in the bspline level.

== Improvement Ideas ==
* Use multi-resolution at all stages
**Both multi-resolution and the sequence of calls with increasing DOF could be implemented as a single recursive scheme. The caller provides an array of DOF and a matching array of resolution levels, which is processed by recursive calls with the first/last element taken from the list. A simulation Matlab program and example is here: [[Projects:RegistrationImprovement:RecursiveScheme]]
**The GUI can list the many combination as a single list of checkboxes for increasing DOF. The full list would be 3,6,7,9,12,b . The checked boxes provide the input string for the recursive call. [[Media:DOFHierarchy_GUI.jpg‎ ]]
* The prestage to affine maybe should be similarity not rigid (based on assumption that its hard to optimize rotation without scale change).
* Learn from FSL flirt to make an extensive test of a grid of possible rotations to get a good initialization for rotations.
* Ability to specify masks that are used to limit were samples are drawn (this should ultimately be both a label image or a user drawn box)

= Timeline of contributions =

== October 22, 2009 ==

Investigating MRML Presets
<pre>
<MRML version="" userTags="">
<CommandLineModule
id="vtkMRMLCommandLineModuleNode1" name="Register Images Set 1"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineAffine" metric="MattesMI" expectedOffset="10"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.04" affineMaxIterations="50"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40" ></CommandLineModule>
<CommandLineModule
id="vtkMRMLCommandLineModuleNode2" name="Register Images Set 2"
hideFromEditors="true" selectable="true" selected="false"
title="Register%20Images"
version="0.1.0.$Revision:%202104%20$(alpha)" resampledImage=""
loadTransform="" saveTransform="" initialization="CentersOfMass"
registration="PipelineRigid" metric="MattesMI" expectedOffset="20"
expectedRotation="0.1" expectedScale="0.05" expectedSkew="0.01"
verbosityLevel="Standard" sampleFromOverlap="false" fixedImageMask=""
randomNumberSeed="0" numberOfThreads="0" minimizeMemory="false"
interpolation="Linear" baselineImage=""
baselineNumberOfFailedPixelsTolerance="1000"
baselineIntensityTolerance="10" baselineRadiusTolerance="0"
baselineDifferenceImage="" baselineResampledMovingImage=""
fixedLandmarks="" movingLandmarks="" rigidMaxIterations="100"
rigidSamplingRatio="0.03" affineMaxIterations="80"
affineSamplingRatio="0.02" bsplineMaxIterations="20"
bsplineSamplingRatio="0.1" controlPointSpacing="40"></CommandLineModule>
</MRML>
</pre>

== October 16 2009 ==
Found some bugs in ITK similarity transform with Luis

== October 6, 2009 ==
Preliminary version of brute force rotation initializer implemented. TODO save in sandbox then merge to Slicer module.

== September 22, 2009 ==
Committed ability to use a label image to act as a mask for drawing samples for image match calculation.

== September 11, 2009 ==
Merge two new modules that present a simplified view of RegisterImages into Slicer3 to show up in Modules Menu hierarchy
[http://www.slicer.org/slicerWiki/index.php/File:Registration-module-hierarchy-prototype.png Menu hierarchy screenshot]

== September 9, 2009 ==
Sync default parameters between GUI and command line version of RegisterImages

== August 21, 2009 ==
[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

== August 18, 2009 ==
*Link landmark initalization with fiducials framework in Slicer3
*Link transform save and load with TransformIO in Slicer3

= Links =
*Project describing improvements to multi-threading of ITK Metrics and initial version of RegisterImages [[ITK_Registration_Optimization]]
*[[Events:Registration_Summit_August_2009 | Initial Project Meeting ]]

= Registration Documentation =
Efforts re. documentation, use case collection, user perspectives, troubleshooting etc. will be consolidated here: [[Projects:RegistrationDocumentation]]

Projects:RegistrationImprovement

2009-10-16T16:44:21Z

Gcasey: /* Timeline of contributions */

Projects:RegistrationImprovement

2009-10-06T19:32:00Z

Gcasey: /* Timeline of contributions */

Projects:RegistrationImprovement

2009-09-22T15:45:47Z

Gcasey:

Projects:RegistrationImprovement

2009-09-17T19:50:21Z

Gcasey: /* RegisterImages Algorithm */

Projects:RegistrationImprovement

2009-09-17T19:31:13Z

Gcasey: /* RegisterImages Algorithm */

Projects:RegistrationImprovement

2009-09-17T19:13:51Z

Gcasey:

Projects:RegistrationImprovement

2009-09-17T18:20:22Z

Gcasey: /* August 18, 2009 */

Projects:RegistrationImprovement

2009-09-17T18:11:38Z

Gcasey:

Projects:RegistrationImprovement

2009-09-17T18:11:25Z

Gcasey: Page to document experiences and improvements in improving the registration framework in Slicer

User:Gcasey

2009-09-07T14:48:42Z

Gcasey: /* Registration Links */

= Casey Goodlett =

==About me==
R&D Engineer - Kitware, Inc.
[http://www.kitware.com/company/team/goodlett.html Homepage]

*PhD in Computing from University of Utah (advisor: Guido Gerig)
** DTI
** Statistical analysis
** Registration and atlas building
*MS from University of North Carolina - Chapel Hill
*BS from Clemson University

==Registration work blog==
===September 7, 2009===

===Registration Links===
*[[Slicer3:Registration]]
*[[ITK_Registration_Optimization]]
*[[Modules:RegisterImages-Documentation-3.4]]
*Feedback from users
**[[Projects:DBP2:Harvard:Registration_Documentation]]
**[[Summer2009:Registration_reproducibility_in_Slicer]]
**From Andriy
***[[MeningiomaMRIRegistrationStudy]]
***[[Vervet_MRI_registration]]
*Other registration tools
**[http://www.fmrib.ox.ac.uk/fsl/flirt/index.html FLIRT]
**[http://www.doc.ic.ac.uk/~dr/software/ IRTK]
**[http://www.nitrc.org/projects/multimodereg/ BRAINSfit]
**[http://www.bioimagesuite.org/ BioImageSuite]

User:Gcasey

2009-09-07T14:47:35Z

Gcasey:

= Casey Goodlett =

==About me==
R&D Engineer - Kitware, Inc.
[http://www.kitware.com/company/team/goodlett.html Homepage]

*PhD in Computing from University of Utah (advisor: Guido Gerig)
** DTI
** Statistical analysis
** Registration and atlas building
*MS from University of North Carolina - Chapel Hill
*BS from Clemson University

==Registration work blog==
===September 7, 2009===

===Registration Links===
*[[ITK_Registration_Optimization]]
*[[Slicer3:Registration]]
*[[Modules:RegisterImages-Documentation-3.4]]
*[[Projects:DBP2:Harvard:Registration_Documentation]]
*[[Summer2009:Registration_reproducibility_in_Slicer]]
*From Andriy
**[[MeningiomaMRIRegistrationStudy]]
**[[Vervet_MRI_registration]]
*Other registration tools
**[http://www.fmrib.ox.ac.uk/fsl/flirt/index.html FLIRT]
**[http://www.doc.ic.ac.uk/~dr/software/ IRTK]
**[http://www.nitrc.org/projects/multimodereg/ BRAINSfit]
**[http://www.bioimagesuite.org/ BioImageSuite]

User:Gcasey

2009-09-07T14:43:34Z

Gcasey: