5b. Co-register 4D Echoplanar Images to 2D Conventional Thick Slice Anatomicals

  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 conventional 2D thick slice anatomical image and click Open.
  3. In the Transform Window choose (File | Load)
  4. Choose the middle trial of all echoplanar image files and click Open
  5. In the Transform Window choose (Image Processing | ReOrient/Crop Image)
  6. Choose a range t that will only be one image - this will increase the registration speed.
  7. Click Crop
  8. Click Copy Results to Image
  9. There is a choice to be made as to which registration method should be used for the echoplanar to 2D registration. One can either choose to do a Linear Registration (LR), or because of the distortion found in echoplanar (i.e. functional) images once can choose to do a Linear Registration with Distortion Correction (LRDC).  Both methods are described here.  
    1. LR:  On the BrainRegister menu bar, choose (Registration | Linear Registration).
    2. LRDC:  On the BrainRegister menu bar, choose (Registration | Distortion Correction).
  10. A new Registration/OverlayTool window will apperar.  If the Auto Save Results box is red, BioImageSuite will automatically save the resulting .matr or .grd transformation file in the current working directory
    1. LR:  Click Rigid to compute the linear registration (a .matr file will be generated).
    2. LRDC: Click Compute Linear and Distortion Correction to compute the registration (a .grd file will be generated).
  11. 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.
    1. LR:  Click OK
    2. LRDC:  Click OK
  12. In a unix window, rename the newly generated registration file.  The six images at the bottom of Figure 7B were created using (Registration | Jacobian) and clicking Create. Comparing these two sets of images illustrates the difference between the two transformation methods.
    1. LR:  ex:  %  mv  tr3567_PIname_stack3d_S003.hdr_Crop_tr3567_PIname_stack4d_S708.matr   tr3567_FCTto2D.matr
    2. LRDC:  ex:  %  mv  tr3567_PIname_stack3d_S003.hdr_Crop_tr3567_PIname_stack4d_S708.grd   tr3567_FCTto2D.grd
  13. Check the registration by clicking around in the echoplanar brain image (Transfrom Viewer) and seeing if the crosshairs match the same anatomical position in the 2D anatomical image (Reference Viewer).
    1. LR:  click around on different gyri to check if gyral patterns match on both images.
    2. LRDC:  click around on different gyri to check if gyral patterns match on both images.
Figure 5b1

Methods used to Co-register a 4D echolplanar image with a 2D conventional thick slice anatomical.

Figure 5b2

Methods used to Co-register a 4D echolplanar image with a 2D conventional thick slice anatomical.

Figure 5b3

Methods used to Co-register a 4D echolplanar image with a 2D conventional thick slice anatomical.