5c. Co-Register Reference 3D Brain with Individual 3D Brain

  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 aquisition from the brain extraction steps explained above and click Open.
  4. On the BrainRegister menu bar, choose (Registration | Non-Linear Registration).  A new Registration/OverlayTool window will appear.
  5. In the new Registration/OverlayTool window click "Compute Linear + Non Linear Registration". This will compute a Non-Linear Registration between the two loaded images.  If the Auto Save Results box is red, BioImageSuite will automatically save the resulting .grd transformation file in the current working directory.
  6. While the registration is running a PXTkConsole window will appear showing the status of the registration.  When the registration is complete a "For Your Information" window will appear telling you the name of the saved registration file.  If the filename already exists the window will ask if you want to overwrite the existing file.
  7. 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).
    1. Brainstem
    2. Anterior Commissure
    3. Cingulate Gyrus
  8. In a unix window, rename the newly generated .grd file to [studynum]_3DtoRef.grd
    • ex:  %  mv colin_axi_1mm_stripped_tr3567_3d_stripped.grd   tr3567_3DtoRef.grd