Difference between revisions of "Projects:RegistrationLibrary:RegLib C17"
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=== Modules === | === Modules === | ||
| − | *[ | + | *[https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] |
| − | *for mask generation: ''Draw'' tool in the [ | + | *for mask generation: ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor] and/or [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation], |
=== Keywords === | === Keywords === | ||
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=== Procedures=== | === Procedures=== | ||
*'''Phase 1''': obtain masks for kidney ROI | *'''Phase 1''': obtain masks for kidney ROI | ||
| − | #Use the ''Draw'' tool in the [ | + | #Use the ''Draw'' tool in the [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor] and/or use the [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 Fast-Marching Segmentation] module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd" |
| − | #See the [ | + | #See the [https://www.slicer.org/wiki/Slicer_3.6:Training tutorials] for the Editor and and segmentation methods for details on how to obtain an efficient segmentation. |
*'''Phase 2''': obtain initial manual alignment | *'''Phase 2''': obtain initial manual alignment | ||
| − | **Details in the [ | + | **Details in the [https://www.slicer.org/wiki/Slicer3.6:Training manual registration tutorial] and also in the [https://www.slicer.org/wiki/Slicer-3-6-FAQ#How_do_I_initialize.2Falign_images_with_very_different_orientations_and_no_overlap.3F Slicer FAQ] |
| − | #go to the [ | + | #go to the [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module] |
#right click on the "Scene" mode and select ''Insert New Transform''. In the MRML edit field below, rename it to "Xf0_manual" or similar | #right click on the "Scene" mode and select ''Insert New Transform''. In the MRML edit field below, rename it to "Xf0_manual" or similar | ||
#In the ''Data'' module, drag the "MRI" image volume inside the"Xf0_manual" node | #In the ''Data'' module, drag the "MRI" image volume inside the"Xf0_manual" node | ||
#Select the views so that the MR and CT volumes are displayed in the slice views | #Select the views so that the MR and CT volumes are displayed in the slice views | ||
| − | #Go to the [ | + | #Go to the [https://www.slicer.org/wiki/Modules:Transforms-Documentation-3.6 Transforms module] and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time |
*'''Phase 3''': automated rigid/affine alignment | *'''Phase 3''': automated rigid/affine alignment | ||
| − | #Go to the [ | + | #Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] module |
##select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below: | ##select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below: | ||
##fixed image: "Probe1CT", moving image: "MRI" | ##fixed image: "Probe1CT", moving image: "MRI" | ||
| Line 67: | Line 67: | ||
##Mask Processing: check ''ROI'' box, ''Input Fixed Mask'' select CT segmentation created in Phase 1 above. For ''Input Moving Mask'' select MRI segmentation created in Phase 1 above. | ##Mask Processing: check ''ROI'' box, ''Input Fixed Mask'' select CT segmentation created in Phase 1 above. For ''Input Moving Mask'' select MRI segmentation created in Phase 1 above. | ||
##Click Apply | ##Click Apply | ||
| − | #return to the [ | + | #return to the [https://www.slicer.org/wiki/Modules:Data-Documentation-3.6 Data module] and drag the MRI inside/outside the different registration transforms to compare the alignment |
#to obtain a resampled volume: move MRI inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name. | #to obtain a resampled volume: move MRI inside Xform of choice and then right-click on the volume and select ''Harden Transforms''. Save MRI under new name. | ||
Latest revision as of 17:36, 10 July 2017
Home < Projects:RegistrationLibrary:RegLib C17Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory
Contents
v3.6.3 
Slicer Registration Library Case #17: Kidney pre-op MR to intra-op CT
Input
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|
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| fixed image/target: intra-operative CT | moving image: per-operative MRI |
Modules
- BRAINSfit
- for mask generation: Draw tool in the Editor and/or Fast-Marching Segmentation,
Keywords
CT, MRI, abdominal, image-guided therapy, IGT, tumor ablation
Input Data
- fixed: intra-operative CT, oblique, 0.58 x 0.58 x 3 mm voxel size, dimensions 512 x 512 x 20
- moving: opre-operative MRI lique, 1.2 x 1.2 x 4 mm voxel size, dimensions 320 x 240 x 64
Download
- Data
- Presets
Registration Challenges
- intra-operative CT is acquired with limited FOV and very oblique position
- intra-operative CT contains artifacts from surgical needles
- both datasets have strong voxel anisotropy
- the region of interest (kidney) is small compared to the FOV, i.e. there is substantial "distracting" image content
Key Strategies
- manual alignment to obtain initial pose
- rough segmentation of both kidneys to mask "distracting" image content
- gradual increase in registration DOF.
Procedures
- Phase 1: obtain masks for kidney ROI
- Use the Draw tool in the Editor and/or use the Fast-Marching Segmentation module to obtain segmentations of the kidney in both CT and MR image. In the example dataset, you can find those segementations as files "Probe1CT_seg.nrrd" and "MRl_seg.nrrd"
- See the tutorials for the Editor and and segmentation methods for details on how to obtain an efficient segmentation.
- Phase 2: obtain initial manual alignment
- Details in the manual registration tutorial and also in the Slicer FAQ
- go to the Data module
- right click on the "Scene" mode and select Insert New Transform. In the MRML edit field below, rename it to "Xf0_manual" or similar
- In the Data module, drag the "MRI" image volume inside the"Xf0_manual" node
- Select the views so that the MR and CT volumes are displayed in the slice views
- Go to the Transforms module and adjust the translation and rotation sliders to adjust the current position. To get a finer degree of control, enter smaller numbers for the translation limits and enter rotation angles numerically in increments of a few degrees at a time
- Phase 3: automated rigid/affine alignment
- Go to the BRAINSfit module
- select Presets "Xf1_Rigid" or "Xf2_Affine" or set the parameters as given below:
- fixed image: "Probe1CT", moving image: "MRI"
- Initialize with previous transform: select "Xf0_manual" from Phase 1 above
- Initialize Transform Mode: leave at default = OFF
- check Include Rigid registration Phase box. For affine also check ScaleVersor3D and Affine
- Output: under Slicer Linear Transform, select new and rename to "Xf1_Rigid" or "Xf2_Affine" or similar
- Registration Parameters: set "Number of Samples" to 100,000 at least
- Mask Processing: check ROI box, Input Fixed Mask select CT segmentation created in Phase 1 above. For Input Moving Mask select MRI segmentation created in Phase 1 above.
- Click Apply
- return to the Data module and drag the MRI inside/outside the different registration transforms to compare the alignment
- to obtain a resampled volume: move MRI inside Xform of choice and then right-click on the volume and select Harden Transforms. Save MRI under new name.
Registration Results
original unregistered
after manual initial alignment
after rigid registration
after affine registration
