5d. Loading Registration files to Check Registrations

Figure 5d1

I. Checking 2D to 3D linear registrations

  1. Choose brainregister from the BioImageSuite main menu. Three windows will appear:  a Transform Viewer, a Reference Viewer and a BrainRegister menu bar.   In the Reference Window choose (File | Load)
  2. Choose the filename that refers to the stripped whole brain acquisition from the brain extraction steps explained above and click Open.
  3. In the Transform Window choose (File | Load)
  4. Choose the conventional 2D thick slice anatomical image and click Open
  5. On the BrainRegister menu bar, choose (Registration | Transformation).  A new Registration/OverlayTool window will appear.
  6. Under the Transformation block Click Load.
  7. Choose the linear transformation for the 2D to 3D registration (i.e. [studynumber]_2Dto3D.matr) and Click Open.
  8. Under Reslice Options Click Reslice.
  9. Check the registration by clicking around in the 2D brain image (Transfrom Viewer) and seeing if the crosshairs match the same anatomical position in the 3D brain image (Reference Viewer).
Figure 5d2

II. Checking 3D to Reference Non-Linear Registrations

  1. Choose brainregister from the BioImageSuite main menu. Three windows will appear:  a Transform Viewer, a Reference Viewer and a BrainRegister menu bar.  In the Reference Viewer choose (File | Standard Images | Colin_1mm_stripped), or the filename of your chosen reference brain.
  2. In the Transform Window choose (File | Load)
  3. Choose the filename that refers to the stripped whole brain acquisition from the brain extraction steps explained above and click Open.
  4. On the BrainRegister menu bar, choose (Registration | Transformation).  A new Registration/OverlayTool window will appear.
  5. Under the Transformation block Click Load.
  6. Choose the non-linear transformation for the 3D to reference registration (i.e. [studynumber]_3DtoRef.matr) and Click Open.
  7. Under Reslice Options Click Reslice.
  8. Check the registration by clicking around in the individual 3D brain image (Transfrom Viewer) and seeing if the crosshairs match a similar anatomical position in the 3D reference image (Reference Viewer).