Difference between revisions of "2012 Summer Project Week:DifficultRegistration"

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<gallery>
 
<gallery>
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:Ct-body-atlas.jpg
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:Ct-body-cropped.jpg
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Image:Ct-body-legs.jpg
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Image:Mr-brain-atlas.jpg
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Image:Mr-brain-tbi.jpg
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Image:Mr-brain-rotated.jpg
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Image:Mr-brain-rhesus.jpg
 
</gallery>
 
</gallery>
  
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==Instructions for Use of this Template==
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==Registration Result Visualization==
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#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
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#Copy the entire text of this page into the page created above
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<b>Slicer:BRAINS<br>[[Image:IntraOp_Slicer-BRAINS_BSpline.gif|400px|lleft|IntraOp via BRAINS]]<br>
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#Link the created page into the list of projects for the project event
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NiftyReg<br>[[Image:mr-results-nifityreg.gif|400px|lleft|IntraOp via BRAINS]]<br>
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#Delete this section from the created page
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SIFT Landmark<br>[[Image:mr-results-sift.gif‎|200px|lleft|IntraOp via BRAINS]] [[Image:ct-results-sift.gif‎|200px|lleft|IntraOp via BRAINS]]</b><br>
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* Erasmus Medical Center: Stefan Klein
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* Utah: Tom Fletcher, Ross Whitaker
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* University College London: Marc Modat
 +
* UNC: Aditya Gupta, Martin Styner
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* BWH: Matthew Toews, Petter Risholm, Dominik Meier, William Wells
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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To identify solutions to difficult image registration problems that challenge the limits of current technology. Aspects of difficulty will include:
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<ul>
−
 
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<li>inter-subject registration
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+
<li>truncation, missing tissue
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+
<li>unknown initialization
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<li>inter-species registration
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<li>articulated deformation
 +
</ul>
 
</div>
 
</div>
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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+
A set of difficult pair-wise registration problems will be considered. Participants will discuss workable solutions based on their expertise and background, and these solutions will be documented.
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
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<br>
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Registration cases can be found [http://www.matthewtoews.com/namic2012 here].
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Our plan for the project week is to first try out <bar>,...
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<br>
−
 
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*CT: atlas and torso have flipped orientation: Correction Xforms here:  [[Media:FlipCT_Atlas+Torso.zip|Flip CT atlas&torso, zip file with 2 .tfm files]]
 
</div>
 
</div>
  
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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We held a general discussion of registration challenges in the community. Results were generated for head and neck data (Ivan Kolesov), three registration approaches were evaluated on challenging head and body images: (NiftyReg - Marc Modat), (Slicer:BRAINS - Dominik Meier), (SIFT Landmarks - Matthew Toews).
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+
<ul>
−
 
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<li>Registration of difficult brain images is successful, body images remain challenging.
 +
<li>Registration direction has an important impact, i.e. which images are designed as fixed or moving. Symmetric or bi-directional registration is helpful.
 +
<li>Masking of problematic image regions, e.g. pathology, is an important but time-consuming pre-processing task that could be further investigated or automated. For instance, interactive masking/segmentation of pathology, linking registration and masking.
 +
</ul>
 
</div>
 
</div>
 
</div>
 
</div>
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==Delivery Mechanism==
 
==Delivery Mechanism==
 +
<b>Attention Participants:</b> Please log in and update/correct entries in the table below. For bonus points, please provide links or solutions to image registration problems on this page.<br>
 +
<table border="1">
 +
<th>Participant</th><th>Affiliation</th><th>Context</th><th>Techniques</th><th>Solutions/Links
 +
</th><tr><td>
 +
Steven Aylward</td><td>Kitware</td><td>CT, US, ressection, brain tumors, changing pathology, sliding organ</td><td>Sliding Geometry, Geometric Metamorphosis</td><td>
 +
</td><tr><td>
 +
Karl Diedrich</td><td>AZE</td><td>Rigid registration, abdomen</td><td>Multi-resolution registration</td><td>
 +
</td><tr><td>
 +
James Fishbaugh</td><td>SCI</td><td>Shape analysis and registration</td><td></td><td>
 +
</td><tr><td>
 +
Aditya Gupta</td><td>UNC</td><td>DTI, enlarged lateral ventricles</td><td></td><td>
 +
</td><tr><td>
 +
Stefan Klein</td><td>Erasmus Medical Center</td><td>General Registration</td><td></td><td>
 +
</td><tr><td>
 +
Ivan Kolesov</td><td>Georgia Tech</td><td>Articulated, point-based registration</td><td> Plastimatch, NiftyReg </td><td> [http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck Head Neck Results]
 +
</td><tr><td>
 +
Dominik Meier</td><td>BWH</td><td>General registration</td><td>Slicer: BRAINS</td><td>
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IntraOp:[[Image:IntraOp_Slicer-BRAINS_BSpline.gif|60px|lleft|IntraOp via BRAINS]]<br>
 +
TBI:[[Image:TBI_Slicer-BRAINS_BSpline.gif|60px|lleft|TBI via BRAINS]]<br>
 +
CT torso: FAILED</td><tr><td>
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Marc Modat</td><td>UCL</td><td>neuro-deg. diseases, longitudinal</td><td>NiftiReg</td><td>[https://na-mic.org/w/images/d/d5/NiftyReg_projectWeek_test.pdf Some test res]</td><tr><td>
 +
Albert Motillo</td><td>GE</td><td>Parsing CT, Detection</td><td></td><td>
 +
</td><tr><td>
 +
Simrin Nagpal</td><td>Queens University</td><td>CT/US registration</td><td></td><td>
 +
</td><tr><td>
 +
Samon Nuranian</td><td>UBC</td><td>US-guided intervension, spine</td><td></td><td>
 +
</td><tr><td>
 +
Andre Remi</td><td>UCLA</td><td>Longitudinal changes in TBI, tissue types</td><td></td><td>
 +
</td><tr><td>
 +
Peter Risholm</td><td>BWH</td><td>Brain, head and neck, radiation therapy</td><td>Probabilistic Uncertainty</td><td>
 +
</td><tr><td>
 +
Samira Sojoudi</td><td>UBC</td><td>Spine, CT/US registration</td><td></td><td>
 +
</td><tr><td>
 +
Matthew Toews</td><td>BWH</td><td>General registration</td><td>SIFT landmark correspondence</td><td>
 +
MR-brain:[[Image:mr-results-sift.gif‎|60px|lleft]]<br>
 +
CT-torso:[[Image:ct-results-sift.gif|60px|lleft]]<br>
 +
</td><tr><td>
 +
Bo Wang</td><td>Utah</td><td>TBI image segmentation</td><td></td><td>
 +
</td><tr><td>
 +
Kevin Wang</td><td>Princess Margaret Hospital</td><td>Adaptive radiation therapy, longitudinal</td><td></td><td>
 +
</td><tr><td>
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William Wells</td><td>BWH</td><td>Interventional applications</td><td>Theory: Segmentation, Registration</td><td></td>
 +
<table>
  
−
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
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== Links for Data ==
 +
* [http://www.matthewtoews.com/namic2012 Matt's initial examples]
 +
* [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable Slicer Registration Case Library]
 +
* [http://dmip1.rad.jhmi.edu/xcat/ XCAT]
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* [http://wiki.na-mic.org/Wiki/index.php/File:EnlargedLVCase_Normal.zip DTI Files Enlarged LV registration with normal control]
 +
* [http://wiki.na-mic.org/Wiki/index.php/File:Krabbe_Controls_DWI.zip DWI Files Enlarged LV registration with normal control]
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* [http://www.na-mic.org/Wiki/index.php/DBP3:UCLA#Data TBI Cases]
 +
* [http://www.nitrc.org/projects/tumorsim/ TumorSim] longitudinal data: To appear at http://midas3.kitware.com
  
−
#ITK Module
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== Links for Tools & Methods ==
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#Slicer Module
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* Sliding Geometries Registration: http://public.kitware.com/Wiki/TubeTK
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##Built-in
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* Geometric Metamorphosis: https://github.com/calaTK/calaTK
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##Extension -- commandline
 
−
##Extension -- loadable
 
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#Other (Please specify)
 
  
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==References==
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== Links for Papers ==
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
+
* Sliding Geometries
−
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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** ISBI 2011: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141338/
−
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
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** Abdominal Imaging, MICCAI, 2011: http://www.springerlink.com/content/552824638l375645/
−
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
+
* Geometric MetaMorphosis
 +
** MICCAI 2011: http://www.springerlink.com/content/7r077665012078r5/
  
 
</div>
 
</div>

Latest revision as of 18:27, 10 July 2017

Home < 2012 Summer Project Week:DifficultRegistration

Registration Result Visualization

Slicer:BRAINS
IntraOp via BRAINS
NiftyReg
IntraOp via BRAINS
SIFT Landmark
IntraOp via BRAINS IntraOp via BRAINS

Key Investigators

  • Erasmus Medical Center: Stefan Klein
  • University College London: Marc Modat
  • UNC: Aditya Gupta, Martin Styner
  • BWH: Matthew Toews, Petter Risholm, Dominik Meier, William Wells

Objective

To identify solutions to difficult image registration problems that challenge the limits of current technology. Aspects of difficulty will include:

  • inter-subject registration
  • truncation, missing tissue
  • unknown initialization
  • inter-species registration
  • articulated deformation

Approach, Plan

A set of difficult pair-wise registration problems will be considered. Participants will discuss workable solutions based on their expertise and background, and these solutions will be documented.
Registration cases can be found here.

Progress

We held a general discussion of registration challenges in the community. Results were generated for head and neck data (Ivan Kolesov), three registration approaches were evaluated on challenging head and body images: (NiftyReg - Marc Modat), (Slicer:BRAINS - Dominik Meier), (SIFT Landmarks - Matthew Toews).

  • Registration of difficult brain images is successful, body images remain challenging.
  • Registration direction has an important impact, i.e. which images are designed as fixed or moving. Symmetric or bi-directional registration is helpful.
  • Masking of problematic image regions, e.g. pathology, is an important but time-consuming pre-processing task that could be further investigated or automated. For instance, interactive masking/segmentation of pathology, linking registration and masking.

Delivery Mechanism

Attention Participants: Please log in and update/correct entries in the table below. For bonus points, please provide links or solutions to image registration problems on this page.

ParticipantAffiliationContextTechniquesSolutions/Links
Steven AylwardKitwareCT, US, ressection, brain tumors, changing pathology, sliding organSliding Geometry, Geometric Metamorphosis
Karl DiedrichAZERigid registration, abdomenMulti-resolution registration
James FishbaughSCIShape analysis and registration
Aditya GuptaUNCDTI, enlarged lateral ventricles
Stefan KleinErasmus Medical CenterGeneral Registration
Ivan KolesovGeorgia TechArticulated, point-based registration Plastimatch, NiftyReg Head Neck Results
Dominik MeierBWHGeneral registrationSlicer: BRAINS

IntraOp:IntraOp via BRAINS
TBI:TBI via BRAINS

CT torso: FAILED
Marc ModatUCLneuro-deg. diseases, longitudinalNiftiRegSome test res
Albert MotilloGEParsing CT, Detection
Simrin NagpalQueens UniversityCT/US registration
Samon NuranianUBCUS-guided intervension, spine
Andre RemiUCLALongitudinal changes in TBI, tissue types
Peter RisholmBWHBrain, head and neck, radiation therapyProbabilistic Uncertainty
Samira SojoudiUBCSpine, CT/US registration
Matthew ToewsBWHGeneral registrationSIFT landmark correspondence

MR-brain:lleft
CT-torso:lleft

Bo WangUtahTBI image segmentation
Kevin WangPrincess Margaret HospitalAdaptive radiation therapy, longitudinal
William WellsBWHInterventional applicationsTheory: Segmentation, Registration

Links for Data

Links for Tools & Methods

Links for Papers

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