6a. Overlaying Common Space Tmaps onto Reference Image

  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 result map you wish to overlay (this map must be already saved in reference space).
  4. On the BrainRegister menu bar choose (Help | T-distribution Table).  A new window called Critical Points of the T-distribution will appear.
  5. On the new Critical Points of the T-distribution window enter the degrees of freedom for your chosen result map.  Also, enter the desired t-tailed pvalue.  Use the following formulas to deterrmine your degrees of freedom.
    • Single group composite:  df=#Subj-1
      • Difference between two groups of subjects:  df=(#SubjGrp1+#SubjGrp2)-2
  6. On the Critical Points of the T-distribution window click the "P(2t)->T" button.  This will calculate the T-value needed (shown in green box) for your degrees of freedom and chosen p-value.
  7. On the BrainRegister menu bar choose (Registration | Functional Overlay).  A new Registration/Overlay Tool window will appear.  
  8. On the new Registration/Overlay Tool window enter the t-value displayed on the Critical Points of the T-distribution window.
  9. On the Registration/Overlay Tool window click "Create Overlay".
  10. There are several options the user can manipulate to display different results other than the threshold.  See Figure 6a image II.
    1. Overlay Type (shown in red box):  Positive, Negative or Both.  This toggle button changes what values of the image are displayed.
    2. Colormap (shown in green box):  F1, F2, F4.  This toggle button changes which colormap is used to display the results.  The user can change the default colormap by going back to the BioImage Suite main window and choose Preferences (as seen in Figure 1).  A new BioSuite User Preference window will appear and the user can choose the desired default colormap.  Then choose Save to save your default preferences.
    3. Clustering (shown in purple box):  This slide bar can generate a cluster size and the displayed image will contain only clusters that are greater than the chosen cluster size.
Figure 6a1

Methods used to overlay a result map in reference space onto the reference anatomical image.

Figure 6a2

Methods used to overlay a result map in reference space onto the reference anatomical image.