5a. Co-Register 2D Conventional Thick Slice Anatomicals to Individual 3D

  1. Choose brainregister from the BioImageSuite main menu. Three windows will appear:  a transform viewer, a reference window 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 | Linear Registration).  A new Registration/OverlayTool window will appear.
  6. In the new Registration/OverlayTool window click Rigid. This will compute a Linear Registration between the two loaded images.  If the Auto Save Results box is red, BioImageSuite will automatically save the resulting .matr transformation file in the current working directory.
  7. While the registration is running a PXTkConsole window will appear showing the status of the registration.
  8. 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.  Click OK.
  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).  Three examples are shown - the gyral patterns should match on both images.
    • Superior Frontal Gyrus
    • Supramarginal Gyrus
    • Middle Occipital Gyrus
  10. In a unix window rename the newly generated .matr file to [studynum]_2Dto3D.matr
    • ex:  %  mv  tr3567_3D_stripped.hdr_tr3567_PIname_stack3d_S003.matr   tr3567_2Dto3D.matr