Difference between revisions of "Projects:RegistrationLibrary:RegLib C14"
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[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br> | [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br> | ||
| − | == | + | ==Slicer Registration Use Case Exampe #14: Intra-subject Brain PET-MRI with MRI orientation adjustment == |
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| − | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | + | {| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0" |
|[[Image:RegLib_C14_Thumb_MRI.png|100px|lleft|this is the fixed reference image. All images are aligned into this space]] | |[[Image:RegLib_C14_Thumb_MRI.png|100px|lleft|this is the fixed reference image. All images are aligned into this space]] | ||
|[[Image:Arrow_left_gray.jpg|100px|lleft]] | |[[Image:Arrow_left_gray.jpg|100px|lleft]] | ||
| + | |[[Image:RegLib_C14_Thumb_PET.png|100px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]] | ||
| + | |align="left"|LEGEND<br> | ||
[[Image:Button_red_fixed.jpg|20px|lleft]] this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br> | [[Image:Button_red_fixed.jpg|20px|lleft]] this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br> | ||
[[Image:Button_green_moving.jpg|20px|lleft]] this indicates the moving image that determines the registration transform. <br> | [[Image:Button_green_moving.jpg|20px|lleft]] this indicates the moving image that determines the registration transform. <br> | ||
|- | |- | ||
| − | | | + | |[[Image:Button_red_fixed.jpg|40px|lleft]] MRI |
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| + | |[[Image:Button_green_moving.jpg|40px|lleft]] PET | ||
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| + | |MRI: <small> coronal T1w <br>256 x 256 x 79<br>0.86 x 0.86 x 2.5 mm | ||
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| − | | | + | |PET: <small> axial, fluorodeoxyglucose<br>128 x 128 x 35<br> 4.29 x 4.29 x 4.25 mm </small> |
|} | |} | ||
| − | + | ===Objective / Background === | |
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Image fusion. | Image fusion. | ||
=== Keywords === | === Keywords === | ||
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===Input Data=== | ===Input Data=== | ||
| − | *reference/fixed : baseline MRI: 0.97 x 0.97 x 3.27 mm , PET: 4.7 x 4.7 x 3.3 mm | + | *[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : baseline MRI: 0.97 x 0.97 x 3.27 mm , PET: 4.7 x 4.7 x 3.3 mm |
| − | *moving: PET: 4.1 x 4.1 x | + | *[[Image:Button_green_moving_white.jpg|20px]] moving: PET: 4.1 x 4.1 x 5 mm |
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=== Registration Results=== | === Registration Results=== | ||
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===Download === | ===Download === | ||
| − | * | + | *'''[[Media:RegLib_C14_BrainPET-MRI.zip |download full tutorial set <small> (Data+intermediate results+presets+tutorial, zip file 17 MB) </small>]]''' |
| − | + | *'''[[Media:RegLib_C14_BrainPET-MRI_Data.zip|download example data set <small> (Data only, zip file 16 MB) </small>]]''' | |
| − | + | *'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.ppt|download step-by-step tutorial <small> (PowerPoint 1.2 MB) </small>]]''' | |
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| + | [[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]] | ||
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Revision as of 13:27, 13 October 2010
Home < Projects:RegistrationLibrary:RegLib C14Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory
Contents
Slicer Registration Use Case Exampe #14: Intra-subject Brain PET-MRI with MRI orientation adjustment
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LEGEND
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 MRI
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 PET
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| MRI: coronal T1w 256 x 256 x 79 0.86 x 0.86 x 2.5 mm |
PET: axial, fluorodeoxyglucose 128 x 128 x 35 4.29 x 4.29 x 4.25 mm |
Objective / Background
Image fusion.
Keywords
PET-MRI, brain, intra-subject, image fusion
Input Data
reference/fixed : baseline MRI: 0.97 x 0.97 x 3.27 mm , PET: 4.7 x 4.7 x 3.3 mm
moving: PET: 4.1 x 4.1 x 5 mm
Registration Results
uncorrected MRI as read from DICOM. Note that image is distorted due to incomplete header information. See the registration challenges section below.
unregistered MRI & PET images.
registered MRI & PET images.
Download
- download full tutorial set (Data+intermediate results+presets+tutorial, zip file 17 MB)
- download example data set (Data only, zip file 16 MB)
- download step-by-step tutorial (PowerPoint 1.2 MB)
Link to User Guide: How to Load/Save Registration Parameter Presets
Discussion: Registration Challenges
- the original DICOM files of the MRI have image orientation data stripped. Hence the volume does not load in correct orientation and needs to be adjusted
- the two series have different voxel sizes
- image content and resolution in PET is low
Discussion: Key Strategies
- we use the Volumes module to adjust the MRI voxel size based on the info in the DICOM header
- we use the Transforms module to reorient the MRI along the proper axes
- the aspect ratio we correct via the "Volumes" module. The correct slice thickness we obtain from the DICOM header via the browser displayed when selecting "Add Volume"
- the "Transforms" module is used to correct orientation. We enter manual rotations of 90 and 180 degrees around the LR (left-right) and IS (inferior-superior) axes, respectively
- the corrected MRI volume is resampled in the Data module via "harden transforms"
- Register Images is used to automatically align the PET with the MRI. We choose mutual information ("MI") as the criterion and a 5% sampling rate. We request an affine transform to correct for small distortion differences between the PET and the MRI
Acknowledgments
Our thanks to the University of Western Ontario for providing this example case.
