Difference between revisions of "Projects:RegistrationLibrary:RegLib C47"
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− | ==<small> | + | == <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br> Slicer Registration Library Case #47: Liver Tumor Cryoablation == |
=== Input === | === Input === | ||
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
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=== Slicer4 Modules used === | === Slicer4 Modules used === | ||
− | * | + | *[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]''' |
===Objective / Background === | ===Objective / Background === | ||
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*large differences in FOV | *large differences in FOV | ||
*strong differences in image contrast between MRI & CT | *strong differences in image contrast between MRI & CT | ||
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*we have strongly anisotropic voxel sizes with much less through-plane resolution | *we have strongly anisotropic voxel sizes with much less through-plane resolution | ||
− | + | *[[Projects:RegistrationLibrary:RegLib_C47 there is a related example for pre-operative contrast CT to MRI here]] | |
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− | * | ||
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=== Procedures === | === Procedures === | ||
− | *'''Phase I: | + | *'''Phase I: MR-CTpre registration''' |
− | # | + | #Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT. |
− | # | + | #open [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''' module |
− | ## | + | ##''Input Images'' |
− | ##create new | + | ###''Fixed Image Volume'': CT_intraop |
− | ## | + | ###''Moving Image Volume'': MRI_preop |
− | # | + | ##''Output Settings'': |
− | # | + | ###''Slicer BSpline Transform'' none |
− | # | + | ###''Slicer Linear Transform'' (create new transform, rename to: "Xf1_MRI-CT_Affine") |
− | # | + | ###''Output Image Volume'' none |
− | + | ##''Registration Phases'': select/check ''Rigid'' , ''Rigid+Scale'', ''Affine'' | |
− | # | + | ##Leave all other settings at default |
− | ## | + | ##click: ''Apply'' |
− | ## | + | #switch to the [http://www.slicer.org/slicerWiki/index.php/Modules:Data Data module] |
− | # | + | ##click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above |
− | + | ##this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration | |
− | + | *'''Phase II: nonrigid registration''' | |
− | ## | + | #open [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]'''module |
− | ### | + | ##''Input Images'' |
− | ### | + | ###''Fixed Image Volume'': CT_intraop |
− | ##Output Settings: | + | ###''Moving Image Volume'': MRI_preop |
− | ### | + | ##''Output Settings'': |
− | ### | + | ###''Slicer BSpline Transform'' (create new transform, rename to: "Xf2_MRI-CT_BSpline") |
− | + | ###''Slicer Linear Transform'' none | |
− | + | ###''Output Image Volume'' create new volume, rename to "MRI_Xf2" | |
− | ## | + | ##''Initialization'' |
− | + | ##''Initialization transform'': select "" created in phase 1 above | |
− | + | ##'''Initialize Transform Mode'': Off | |
− | ## | + | ##''Registration Phases'': select/check ''BSpline'' only |
− | + | ##''Main Parameters'' | |
− | + | ##''Number Of Samples'': 200,000 | |
− | ## | + | ## ''B-Spline Grid Size'': 7,7,5 |
− | ## | ||
− | ## | ||
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##Leave all other settings at default | ##Leave all other settings at default | ||
− | ##click: | + | ##click: ''Apply'' |
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=== Registration Results=== | === Registration Results=== | ||
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
− | |[[Image: | + | |[[Image:RegLib_C47_unregistered.gif|300px|left|unregistered MRI & CT]] |
|unregistered MRI & CT | |unregistered MRI & CT | ||
|- | |- | ||
− | |[[Image: | + | |[[Image:RegLib_C47_Affine.gif|300px|left|after linear (affine) registration]] |
− | + | |after linear (affine) registration | |
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− | |affine | ||
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− | |[[Image: | + | |[[Image:RegLib_C47_BSPline.gif|300px|left|after nonrigid registration]] |
− | |nonrigid | + | |after nonrigid registration |
|- | |- | ||
− | |[[Image: | + | |[[Image:RegLib_C47_registered_kidney.gif|300px|left|comparing kidney alignment at different registration stages]] |
− | | | + | |comparing kidney alignment at different registration stages |
|} | |} | ||
===Download === | ===Download === | ||
− | + | *[[Media:RegLib_C47_Data.zip|'''download input image data''' <small> (Input Data, NRRD images, zip file 42 MB) </small>]] | |
− | *[[Media: | ||
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=== Acknowledgments === | === Acknowledgments === | ||
Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case. | Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case. |
Revision as of 20:46, 9 May 2012
Home < Projects:RegistrationLibrary:RegLib C47Back to ARRA main page
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Contents
updated for v4.1
Slicer Registration Library Case #47: Liver Tumor Cryoablation
Input
fixed image/target | moving image |
Slicer4 Modules used
Objective / Background
We seek to align a pre-operative MRI with the intra-operative CT for surgical guidance.
Keywords
MRI, CT, IGT, intra-operative, liver, cryoablation, change detection, non-rigid registration
Input Data
- reference/fixed : pr-op CT, 0.95 x 0.95 x 5 mm voxel size
- moving: intra-op MRI, 0.78 x 0.78 x 2.5 mm axial,
Discussion: Registration Challenges
- large differences in FOV
- strong differences in image contrast between MRI & CT
- we have strongly anisotropic voxel sizes with much less through-plane resolution
- Projects:RegistrationLibrary:RegLib_C47 there is a related example for pre-operative contrast CT to MRI here
Procedures
- Phase I: MR-CTpre registration
- Following the concept of manual registration, we create an initial transform that roughly aligns the MR to the pre-op CT.
- open General Registraion (BRAINS) module
- Input Images
- Fixed Image Volume: CT_intraop
- Moving Image Volume: MRI_preop
- Output Settings:
- Slicer BSpline Transform none
- Slicer Linear Transform (create new transform, rename to: "Xf1_MRI-CT_Affine")
- Output Image Volume none
- Registration Phases: select/check Rigid , Rigid+Scale, Affine
- Leave all other settings at default
- click: Apply
- Input Images
- switch to the Data module
- click on the "MRI_intra" node, and drag it onto the transform node "Xf1_MRI-CT_Affine" created above
- this should yield a rough alignment as shown in the result section below. We will use this to initialize a more refined nonrigid registration
- Phase II: nonrigid registration
- open General Registraion (BRAINS)module
- Input Images
- Fixed Image Volume: CT_intraop
- Moving Image Volume: MRI_preop
- Output Settings:
- Slicer BSpline Transform (create new transform, rename to: "Xf2_MRI-CT_BSpline")
- Slicer Linear Transform none
- Output Image Volume create new volume, rename to "MRI_Xf2"
- Initialization
- Initialization transform: select "" created in phase 1 above
- 'Initialize Transform Mode: Off
- Registration Phases: select/check BSpline only
- Main Parameters
- Number Of Samples: 200,000
- B-Spline Grid Size: 7,7,5
- Leave all other settings at default
- click: Apply
- Input Images
Registration Results
unregistered MRI & CT | |
after linear (affine) registration | |
after nonrigid registration | |
comparing kidney alignment at different registration stages |
Download
Acknowledgments
Thanks to Dr.Stuart Silverman and Dr. Nobuhiko Hata for sharing this case.