Documentation:Nightly:Registration:RegistrationLibrary:RegLib C02

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Slicer Registration Library Case #2: Multi contrast MRI + segmentation labelmap

Input

this is the fixed MRI reference image. All images are aligned into this space		this is the moving image, to be aligned with the reference on the left	this is a segmentation labelmap in the same space as the moving image. To be registered also
fixed image 1/target MRI T1		moving image 2a MRI FLAIR	moving image 2b segmentation labelmap

Objective / Background

Goal is to align the FLAIR image and its segmentation labelmap with the structural reference T1 scan.

Modules used

• General Registration (BRAINS)

Download (from NAMIC MIDAS)

Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself.

• RegLib_C02.mrb: input data only, use this to run the tutorial from the start (Slicer mrb file. 19 MB).
• RegLib_C02_full.mrb: includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 30 MB).

Keywords

MRI, brain, head, intra-subject, labelmap

Video Screencasts

1. Movie/screencast showing registration for Case #02

Procedure

1. Compute Registration: open the General Registration (BRAINS) module
   1. Input Images: Fixed Image Volume: T1
   2. 'Input Images: Moving Image Volume: FLAIR
   3. Output Settings:
      1. Slicer Linear Transform (create new transform, rename to: "Xf1_Affine")
      2. Output Image Volume none. No resampling required for linear transforms
   4. Registration Phases: select/check Rigid , Rigid+Scale, Affine
   5. Main Parameters:
      1. increase Number Of Samples to 200,000
   6. Leave all other settings at default
   7. click: Apply; runtime < 1 min.
2. Align LabelmapI: We have now computed the registration transform. To reorient both FLAIR and its label map, we place both volumes inside the transform.
   1. 1. Place "T1" in the background and "FLAIR" in the foreground. Select "LesionSeg" as the labelmap to display.
   2. Go to the Data module
      1. the "FLAIR" image should already be placed within the transform "Xf1_Affine", that was done by the registration module. If not, left click on the "FLAIR" node and drag it onto the "Xf1_Affine" node. You will see a "+" sign appear indicating that the image is placed within the transform.
      2. Do the same for the "LesionSeg" node, i.e. drag it into the "Xf1_Affine" transform.

Registration Results

	baseline & T2 before registration (click to enlarge)
	baseline to T2 after affine+nonrigid alignment (click to enlarge)