Difference between revisions of "Projects:RegistrationLibrary:RegLib C37"
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=== Input === | === Input === | ||
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
− | |[[Image:RegLib_C37_Thumb1.png| | + | |[[Image:RegLib_C37_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]] |
− | |[[Image: | + | |[[Image:RegArrow_NonRigid.png|100px|lleft]] |
− | |[[Image:RegLib_C37_Thumb2.png| | + | |[[Image:RegLib_C37_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]] |
|- | |- | ||
|fixed image/target | |fixed image/target | ||
Line 17: | Line 17: | ||
=== Modules === | === Modules === | ||
'''Slicer 3.6.1''' recommended modules: | '''Slicer 3.6.1''' recommended modules: | ||
− | *[ | + | *[https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit] |
− | *[ | + | *[https://www.slicer.org/wiki/Modules:SkullStripperModule Skull-Stripper Module] |
===Objective / Background === | ===Objective / Background === | ||
Line 28: | Line 28: | ||
*reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal | *reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal | ||
*moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal | *moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal | ||
+ | |||
+ | === Overall Strategy === | ||
+ | :#run rigid/affine registration (BRAINSfit) with "CenterOfHeadAlign" initialization | ||
+ | :#run 7x7x7 nonrigid regista=ration (BRAINSfit BSpline) using the above affine as input | ||
+ | :#alternative: run skull stripper module on both images to generate masks for the nonrigid registration | ||
+ | |||
+ | === Procedures === | ||
+ | *'''Phase I: Register Rigid/Affine''' | ||
+ | #open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2 | ||
+ | ##Registration Phases: | ||
+ | ###select/check ''Include Affine registration phase'' | ||
+ | ###for affine also select/check ''Include Scale Versor 3D'' and ''Include Affine'' registration phase'' | ||
+ | ##Registration Parameters: increase ''Number Of Samples'' to 200,000 | ||
+ | ###select a new transform "Linear Transform", rename to "Xf1_affine" | ||
+ | ##Leave all other settings at default | ||
+ | *'''Phase II: [optional]: generate skull mask | ||
+ | #open ''Skull Stripper for Structural MRI'' Module (Extension module) | ||
+ | #increase ''Iterations" to 200 and ''Subdivisions'' to 12 | ||
+ | #both results will have to be edited manually using the Editor module. | ||
+ | *'''Phase III: Register BSpline''' | ||
+ | #open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf3 or _Xf4 | ||
+ | ##select a new volume "Output Image Volume'', rename to "DTI_base_Xf1" | ||
+ | ##Registration Parameters: increase ''Number Of Samples'' to 200,000 | ||
+ | ##Registration Parameters: set ''Number Of Grid Subdivisions'' to 7x7x7 | ||
+ | ##Leave all other settings at default | ||
+ | ##if using masks, set the ''Mask Processing Mode'' to "ROI" and select the two labelmaps generated in phase II as Input Masks | ||
=== Registration Results=== | === Registration Results=== | ||
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0" | ||
− | |[[Image:RegLib_C37_unreg. | + | |[[Image:RegLib_C37_unreg.png|400px|center|unregistered]] |
+ | |original unregistered | ||
+ | |- | ||
|[[Image:RegLib_C37_Xf1.gif|400px|center|rigid]] | |[[Image:RegLib_C37_Xf1.gif|400px|center|rigid]] | ||
|[[Image:RegLib_C37_Xf2.gif|400px|center|affine]] | |[[Image:RegLib_C37_Xf2.gif|400px|center|affine]] | ||
+ | |- | ||
+ | |rigid registered | ||
+ | |affine registered | ||
+ | |- | ||
|[[Image:RegLib_C37_Xf3.gif|400px|center|BSpline (7x7x7) unmasked]] | |[[Image:RegLib_C37_Xf3.gif|400px|center|BSpline (7x7x7) unmasked]] | ||
|[[Image:RegLib_C37_Xf4.gif|400px|center|BSpline (7x7x7) masked]] | |[[Image:RegLib_C37_Xf4.gif|400px|center|BSpline (7x7x7) masked]] | ||
|- | |- | ||
− | |||
− | |||
− | |||
|nonrigid registered (7x7x7 BSpline unmasked) | |nonrigid registered (7x7x7 BSpline unmasked) | ||
− | |nonrigid registered (7x7x7 BSpline masked) | + | |nonrigid registered (7x7x7 BSpline '''masked''') |
|} | |} | ||
===Download === | ===Download === | ||
− | *Data | + | *Data |
− | ** | + | **[[Media:RegLib_C37_Data.zip |'''RegLib_C37_Data''' , image data, resets & solution transforms <small> (NRRD files, zip file 41 MB) </small>]]''' |
− | *Presets: | + | *Presets |
− | [[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]] | + | **[[Media:RegLib_C37_Presets.mrml|'''RegLib_C37_Presets''' Presets for BRAINSFIT registration <small> (.mrml file 12 kB) </small>]]''' |
− | + | **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]] | |
+ | |||
+ | |||
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comment | comment | ||
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Latest revision as of 18:07, 10 July 2017
Home < Projects:RegistrationLibrary:RegLib C37Back to ARRA main page
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Contents
v3.6.1 Slicer Registration Library Case #37:
Intra-subject Brain MRI: T1 Tumor Growth / Resection Assessment
Input
fixed image/target | moving image |
Modules
Slicer 3.6.1 recommended modules:
Objective / Background
This is a typical case of change assessment.
Keywords
MRI, brain, head, intra-subject, T1, tumor, change assessment
Input Data
- reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal
- moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x176 ,sagittal
Overall Strategy
- run rigid/affine registration (BRAINSfit) with "CenterOfHeadAlign" initialization
- run 7x7x7 nonrigid regista=ration (BRAINSfit BSpline) using the above affine as input
- alternative: run skull stripper module on both images to generate masks for the nonrigid registration
Procedures
- Phase I: Register Rigid/Affine
- open Registration : BrainsFit module (presets: BRAINSfit_Xf1 or _Xf2
- Registration Phases:
- select/check Include Affine registration phase
- for affine also select/check Include Scale Versor 3D and Include Affine registration phase
- Registration Parameters: increase Number Of Samples to 200,000
- select a new transform "Linear Transform", rename to "Xf1_affine"
- Leave all other settings at default
- Registration Phases:
- Phase II: [optional]: generate skull mask
- open Skull Stripper for Structural MRI Module (Extension module)
- increase Iterations" to 200 and Subdivisions to 12
- both results will have to be edited manually using the Editor module.
- Phase III: Register BSpline
- open Registration : BrainsFit module (presets: BRAINSfit_Xf3 or _Xf4
- select a new volume "Output Image Volume, rename to "DTI_base_Xf1"
- Registration Parameters: increase Number Of Samples to 200,000
- Registration Parameters: set Number Of Grid Subdivisions to 7x7x7
- Leave all other settings at default
- if using masks, set the Mask Processing Mode to "ROI" and select the two labelmaps generated in phase II as Input Masks
Registration Results
original unregistered | |
rigid registered | affine registered |
nonrigid registered (7x7x7 BSpline unmasked) | nonrigid registered (7x7x7 BSpline masked) |
Download
- Data
- Presets