Projects:ARRA:SlicerReg

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Aim

3D Slicer provides access to powerful registration tools. Based on our experience with clinician scientist through the Harvard Catalyst, the current interface and documentation are not suitable for that audience. We propose to address this critical shortcoming through a number of measures listed below. If successful, this will open access to powerful technologies for data fusion and analysis of progression of disease to a new class of clinical users.

Research Plan

The registration modules in 3Dslicer are built in ITK and are controlled by complex sets of command-line parameters that are not easily accessible to non-experts. How the parameters interact and how they should be adjusted based on image characteristics, such as tissue contrast, field of view, voxel anisotropy, initial misalignment, differential bias etc. are poorly explored and not documented. To make the tool-set accessible to the clinical end-user we propose to support/enhance the existing tool with:

• introductory documentation to the principles and pitfalls of 3D registration, global guidelines for the choice of registration method and parameters.
• tutorials for image registration (rigid, affine, non-rigid)
• explain strategies to choose and vary parameters (DOF, cost function, search range, masking, choice of reference scan, scale space approaches)
• explain methods to measure and visualize registration quality/success
• develop parameter space exploration methods/tools
• build and publish a library of use-case scenarios (same subject & contrast, different contrast, different subject, different modality)

Key Personnel

• Dominik Meier, Ph.D., 81%, 9-17-2009 through 9-16-2011

Progress

• 2011/09/09: new case 17: kidney MR-CT , new case 20: whole body PET-CT , new case 21: knee MRI
• 2011/09/02: new case 09: fMRI to anatomical ref , batch processing for in-vitro spine registration: scripting for Matlab & Windows OS
• 2011/08/26: new case 12: liver MR-CT ; testing of Registration example case for Slicer4 presentation at RSNA; new case 07: prostate MRI
• 2011/08/19: new case 44: CT human pelvis ; testing of Registration modules for Slicer4; new case 43: CT vetebra surface registration
• 2011/08/12: testing of Registration modules for Slicer4; in-vitro spine registration: surface-to-surface registration & batch pipeline
• 2011/08/05: new case 42: serial pediatric MRI in Autism
• 2011/07/27: new case 46: lung 2D MRI nonrigid
• 2011/07/01: new case 41: mouse brain MRI nonrigid, prelim. Slicer4 testing/updates of Registration protocols
• 2011/06/24: NA-MIC 2011 All-Hands Meeting
• 2011/06/17: registration basics tutorial, BRAINSfitIGT, MouseMRI Brain Registration
• 2011/06/10: liver-CT registration, AHM tutorial prep., IGT registration
• 2011/06/03: applying non-rigid registration transform to fiducials, FAQ updates
• 2011/05/27: Prostate multichannel registration: parameter testing, in-vitro spine registration,
• 2011/05/20: FAQ updates, in-vitro spine registration, Slicer in NCIGT registration, Prostate multichannel registration:fiducial-based parameter testing
• 2011/05/13: registration for EM segmenter:comparison with CMTK, FAQ updates, in-vitro spine registration
• 2011/05/06: Prostate multichannel registration, DTI registration, registration parameter search for EM segmenter, FAQ updates
• 2011/04/22: Prostate multichannel registration, Registration Library update to Slicer version 3.6.3
• 2011/04/15: Registration Library update to Slicer version 3.6.3 ,Creation & visualization of deformation fields
• 2011/04/08: registration parameter search for EM segmenter, Registration FAQ extensions, New Registration library category: auxiliary data: A01-A04: grid images to evaluate nonrigid registration
• 2011/04/01: new case 39: in vitro thoracic vertebrae CT,new case 40: micro CT structural analysis
• 2011/03/25: new case 28: in vitro spine CT, FAQ updates
• 2011/03/18: user support & updates/fixes to tutorial for atlas merging, spine CT registration , CMTK module
• 2011/03/11: new case 37:brain tumor MRI
• 2011/03/04: new case 35:mouse MRI, cardiac MRI registration, new case 36: CT in head & neck cancer
• 2011/02/25: NA-MIC registration retreat
• 2011/02/18: cardiac MRI registration
• 2011/02/11 : EMAtlas registration: large-scale parameter study (linux cluster) CMTK+BRAINSfit, cardiac MRI registration for AF treatment assessment
• 2011/02/04 : user support Atlas registration: parameter study on BSpline inter-subject matching guided by labelmap : CMTK, cardiac MRI registration for AF treatment assessment
• 2011/01/28 : user support mouse MRI: increase automation, user support Atlas registration: parameter study on BSpline inter-subject matching guided by labelmap overlap analysis
• 2011/01/21 : Benchmarking, DTI module development
• 2011/01/14 : participation 2011_Winter_Project_Week
• 2011/01/07 : preparation AHM 2010: Python scripted module, testing of registration dataset & demo for Demo Breakout Session
• 2010/12/24 : preparation AHM 2010: DTI registration module: install developer package & libraries
• 2010/12/17 : preparation AHM 2010
• 2010/12/10 : new case 34: mouse MRI , User FAQ:moved, edited and expanded , new case 31: TBI
• 2010/12/03 : new case 33: multispectral MRI (surg.planning) incl. FLAIR,T1Gd and DWI- DTI-T1
• 2010/11/26 : Slicer Registration FAQ ]; DTI registration support
• 2010/11/19 : new Slicer Registration FAQ; new case 32: inverse DTI-T1, joint histogram experiments on Effects of Anisotropy and Bias Field Study;
• 2010/11/12 : 3.6.1 updates for Case 19 MRA and Case 16: manual registration; user support for TBI;
• 2010/11/05 : user support for TBI;
• 2010/10/29 : 3.6.1 updates for Case 14 PET-MRI; Case 15 AC-PC;
• 2010/10/22 : Effects of Anisotropy and Bias Field Study;
• 2010/10/15 : 3.6.1 update for Case 10 (inter-subj. MRI probabilistic tissue atlas); Effects of Anisotropy and Bias Field Study; New Case 18 (Serial MRI in Ageing),
• 2010/10/08 : 3.6.1 update for Case 08 (Breast MRI); Effects of Anisotropy and Bias Field Study
• 2010/10/01 : new Case 30 (DTI), 3.6.1: update for Case 06 (Breast MRI),
• 2010/09/24 : 3.6.1: update for Case 27 (DTI), Case 05 (Knee)
• 2010/09/17 : 3.6.1: update for Case 04 (MS), Case 03 (DTI)
• 2010/09/10 : DTI resampling issue, tutorial for Case 29 (DTI)
• 2010/09/03 : update registration case library for Slicer 3.6.1: Case 29 (DTI), method for combining affine+nonrigid transforms
• 2010/08/27 : update registration case library for Slicer 3.6.1: Case 01
• 2010/08/20 : update registration case library for Slicer 3.6: Case 02
• 2010/07/16 : user assistance with in-vitro spine CT registration ; speed benchmarking; MICCAI Registration Challenge: Methods Paper Revision
• 2010/07/09 : DTI resampling, ; updating library for new registration options available in Slicer 3.6;
• 2010/07/09 : MICCAI Registration Challenge: Report Paper
• 2010/07/02 : registration speed benchmarking, Library Case #19 (multi-contrast inter-subject MRI)
• 2010/06/25 : attending the NA-MIC 2010 Summer All Hands Meeting, Boston
• 2010/06/18 : MICCAI-EMPIRE10 (Lung registration) Method 2: DemonsWarp, concatenating 3D deformation fields,
• 2010/06/11 : MICCAI MICCAI-EMPIRE10 (Lung registration) Method 1: BSpline, debugging issues with loading 3D deformation fields, Slicer3.6 New Features Overview
• 2010/06/04 : MICCAI-EMPIRE10 (Lung registration): Cluster Batch Processing, new sortable library case table
• 2010/05/28 : MICCAI-EMPIRE10 (Lung registration) , new library case naming scheme , new sortable library case table
• 2010/05/21 : Library Case #27, Update Registration + Resampling Decision Matrix, User support Animal MRI, Registration Documentation updates for Slicer v3.6
• 2010/05/14 : Library Case #10, Mori Atlas registration, User support DTI, Registration Documentation updates for Slicer v3.6
• 2010/05/07 : Resampling Feature Matrix, Mori Atlas registration
• 2010/04/30 : User support prostate IGT, Registration Feature Matrix, Mouse tumor serial MRI registration, Mori Atlas registration
• 2010/04/23 : Slicer 3.6 documentation page, Library advertisement page, anonymization instructions, Registration portal: select by category, IGT example case
• 2010/04/16 : reformat Slicer registration portal page & links, complete Case #8 (BSpline Resampling), Library Case #16 (manual registration)
• 2010/04/09 : Library Case #15 (Brain AC-PC alignment), user support for IGT registration
• 2010/04/02 : Library Case #14 (Brain PET-MRI), Deformable B-spline registration: resampling issues
• 2010/03/26 : Library Case #5 (Knee MRI), NITRC advertisement, Deformable B-spline registration: resampling & concatenating transform, User support for PET-MRI registration
• 2010/03/19 : Library Case #8 (PET-CT), Module testing: Demons non-rigid registration, Library Case #5 (Knee MRI)
• 2010/03/12 : NCIGT 2010 attendance, Library Case #12 & 13 (Liver tumor, offline), building separate Wiki page with full library case list, Module testing: AC-PC alignment, Demons non-rigid registration
• 2010/03/05 : Revision webpages (Slicer registration portal page, Library layout & call for data), Registration Basics Tutorial, NCIGT Registration Breakout session preparation, Edits on Library Case #11 (Brain Atlas), new Library Case #12 (offline, Liver Tumor)
• 2010/02/25 : Registration Library Case #06: Breast Cancer non-rigid registration, revision Slicer registration portal page, NCIGT Registration Breakout session preparation
• 2010/02/18 : Slicer Tutorial for surface-based registration, downloadable case file inventory on NA-MIC Wiki and mirrored on MIDAS server, registration parameter presets manual, registration parameters listed explicitly on Case Library Wiki,
• 2010/02/12 : Atlas co-registration (inter-subject thalamic nuclei); user assistance with 1) non-rigid registration of probabilistic atlas data for EM segmentation and 2) non-rigid registration of MRI data in schizophrenia.
• 2010/02/05 : Case Library extension (DTI, fMRI, knee), fiducial based registration example, DTI non-rigid registration methodology
• 2010/01/29 : Slicer3 Manual Registration Tutorial, User support for nonrigid liver registration, DTI registration case example
• 2010/01/22 : Slicer Wiki registration pages, NA-MIC wiki registration pages (new registration portal page & new library portal page), user assistance with registration for EM segmenter
• 2010/01/08 : AHM 2010 in Salt Lake City; discussion with registration users & developers, collecting library case examples
• 2010/01/01 : AHM 2010 preparation
• 2009/12/18 : Case Library revisions, Extension of Case 02, result evaluation and visualization, fiducial based registration
• 2009/12/11 : GUI design specifications (modules & parameters), user support (atlas registration), registration basics tutorial, result evaluation and visualization, AHM preparation.
• 2009/12/04 : test of new multiresolution scheme, extended registration case library (case 02), prototypes for new registration result visualization (true color & animated gifs)
• 2009/11/27 : parameter exploration scheme, GUI organization and concepts, updated registration case library (case 01), video tutorial
• 2009/11/20 : reorganized documentation WIKI, Testing of new multi-resolution algorithm: apply parameter exploration scheme to compare robustness with existing algorithm; download and organize further library cases (MIDAS inter-subject, MS intra-subject, brain MRI with strong voxel size differences, BIRN dataset ELUDE on serial MRI in depression)
• 2009/11/13 : Discussed multi-resolution/multi DOF scheme w. developers and built mock-up GUI and recursive scheme, prepared AHM2010 project page, user assistance with breast MRI registration, documentation Wiki: reference manual, updated "Call for Datasets", new "Notes for Developers".
• 2009/11/06 : implemented batch registration and parameter variation on linux cluster. Processing of parameter exploration and validation sets for intra-subject brain registration.
• 2009/10/30 : User assistance with PET-MR registration; User consulting with MR-intraoperativeCT registration; building example use case #1; compiled working list for developer/GUI efforts
• 2009/10/23 : Began expanding a single case to full coverage (data, registration, documentation, tutorial) . Explored Video Tutorial capabilities, example demo video on the Wiki. Drafted posting call for datasets. Clarified IRB issues re. data anonymization. Discussed GUI concepts w. developer team.
• 2009/10/16: Prioritized the first 10 cases to prepare for publication. Candidates: 6 brain and 4 non-brain cases. Downloaded, organized and reformatted image data for fMRI+DTI cases. Discussed GUI structure and modularization, concatenation of transforms, recursive multiresolution concepts. Direct user & developer assistance with DTI tensor resampling problem. Discussion and planning for obtaining abdominal datasets.
• 2009/10/09: Collect first inventory of datasets used thus far for training & testing. Collect links to further datasets. Set up the Documentation Wiki. Provided direct user assistance (DTI to baseline).
• 2009/10/02 : Prepared use-case hierarchy structure used to catalog the collection of registration example scenarios. Discuss GUI concepts with developer team.

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• ongoing efforts are documented here : Projects:RegistrationDocumentation