Documentation:Nightly:Registration:RegistrationLibrary:RegLib C01

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Slicer Registration Library Case #1: Follow-up MRI of Brain Tumor

Input

fixed image		moving image

Objective / Background

Goal is to align the follow-up image with the reference/baseline scan to assess changes.

Modules used

• General Registration (BRAINS)

Download (from NAMIC MIDAS)

• RegLib_C03.mrb: includes raw data + all solutions and intermediate files (Slicer mrb file. 13 MB).

Keywords

MRI, brain, head, intra-subject, meningioma

Video Screencasts

1. Movie/screencast showing generating a registration mask to exclude the tumor
2. Movie/screencast showing rigid and affine registration

Procedure

1. Rigid Registration: open the General Registration (BRAINS) module
   1. Input Images: Fixed Image Volume: MRMeningioma_1
   2. 'Input Images: Moving Image Volume: MRMeningioma_2
   3. Output Settings:
      1. Slicer Linear Transform (create new transform, rename to: "Xf1_Rigid")
      2. Output Image Volume none
   4. Registration Phases: select/check Rigid
   5. Initialization Phases: none
   6. Main Parameters:
   7. Leave all other settings at default
   8. click: Apply; runtime < 10 sec
2. Building Registration Masks: We have now generate two masks that exclude the tumor region from contributing to the registration.
   1. open the Editor module
   2. As Master Volume, select the MR_1_baseline image
   3. click on the threshold tool and lower the threshold until the entire volume is selected (about a threshold of 5). Then click Apply.
   4. select the Brush tool. Increase the radius so that the brush completely covers the tumor (about 18mm).
   5. set the paint color to 0 (background).
   6. place the brush on an axial slice over the tumor. Use a left click to paint and the arrow keys to switch to the next slice. Repeat for all slices showing the tumor.
   7. save the mask as "MR_1_baseline_mask.nrrd"
   8. Now we generate a mask for MR_2. We can repeat the above or we can generate a mask by sending the first one through the rigid transform we already computed. We need two masks, because the two images do not have the same resolution and FOV.
   9. Go to the BRAINSResample module
3. Affine registration: We have now increase the DOF to 12 in the form of an affine transform that also corrects scale and allows shear.

Registration Results

	baseline and follow-up before registration (click to enlarge)
300px	after rigid alignment. Note the residual shape differences (click to enlarge)
	after affine registration (click to enlarge)

Discussion: Key Strategies

• The affine registration seeks to address residual distortions that are typical for longitudinal MRI. However to prevent the tumor (and putative tumor change) from affecting the registration, we mask out the tumor so that it does not contribute to the registration. The assumption is thus that aside from the tumor we expect the two serial scans to be matching exactly, i.e. any differences in size or shape is considered an artifact we wish to remove by registration.