5e. More Advanced Technique when Registrations are not Accurate

Sometimes if an image is quite rotated from the target, the automatic registration will not be accurate. The user can manipulate the transform image to approximate the target image using a Manual Transformation Control box. This approximation can then be used as an input starting point for the registration.

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 | Transformation). A new Registration/OverlayTool window will appear.
6. Under the Transformation block Click Manual. A separate Manual Transformation Control window will appear.
7. On the Manual Transformation Control window, with all values set to zero, click the Set&Apply button. This will center both images. Check the crosshairs in one window to see how different they are on the other.
8. Manually input shifts and rotations into the Manual Transformation Control window and click Set&Apply button to manipulate Transform window image. Repeat until the image in the Transform window approximates the image in the Reference window.
9. On the BrainRegister menu bar, choose (Registration | Linear Registration). A new Registration/OverlayTool window will appear.
10. Click Use Current Transform for Initialization, the box will turn red.
11. 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.
12. While the registration is running a PXTkConsole window will appear showing the status of the registration.
13. 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.
14. 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).
15. 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