Research Protocols

Brain Masking (Manual)

  1. The raw resliced file is displayed to create the brain mask
  2. Display case#_reslice_raw.mnc (-label case#_reslice_mask.mnc if you have used BSE)
  3. Once display opens up, there should be an image of a brain that is orangeish
  4. Type the following commands:
  5. “F”- to open the segmentation menu
  6. “Y”-to establish the threshold
  7. “Avg 2_3 max”-to define the threshold. The first value comes from the average of the CSF and gray tags picked. Get this value by fetching the tags over to the PC, and then use Excel to get the averages. The second value is the maximum from the contrast bar on the left; its usually a good idea to overestimate the max value. Using these numbers for the threshold will allow you to use the raw image to create the brain mask instead of the segmented image.
  8. “D”-to change the pain label
  9. “4”-the new paint label (this is the color of the mask/label) – This option allows you to pick different colors for different ROI’s and basically create different masks for each ROI by distinguisihing between the paint label colors.
  10. The raw resliced image will be altered as follows:
  11. “Space bar”-to go to the main menu
  12. The new image should be very dark, and have a red-orange tint to it.”Space bar”-to go to the main menu
  13. “D”-to go to the color menu
  14. “D”-to set the new color as gray
  15. Pull the bottom line of the color scale down to zero (0) until the image can be clearly viewed.
  16. “C”-to change the label opacity
  17. “0.2”-the label opacity (This opacity should be low so that the raw file can be seen underneath. Sometimes it is hard to distinguish between brain and non-brain, so the opacity can be lowered to better view the raw file, and to make it more transparent).
  18. The brain mask can now be created. To get to the segmentation menu, type:
  19. “Space bar”-to go to the main menu
  20. “F”-to go the segmentation menu
  21. All the work will be done in the coronal plane, so pull the axis down so that the coronal view is at a comfortable size. To navigate between slides, use the “+” and “-” keys. The whole idea of the brain mask is to fill in all that is brain, and exclude all that is not. Often times that which is brain is touching that which is not.
  22. To fill in only the brain, paint (using the right mouse button) the portion of the brain touching non-brain . When you fill in the rest of the brain (by moving the mouse on to the brain and then pressing “E”), the regions you have already painted will serve as a limit to how far the filling will go.
  23. Check Reference for Figure
  24. Note: Be careful when you paint the brain regions touching non-brain. If you miss even one pixel, the entire slide gets painted. Press 7 to undo and fill the pixels.
  25. This process continues for each slice of the image. Different regions of the brain have different areas that need to be avoided. In the most posterior regions, watch out for the dura mater in between the two hemispheres.
  26. The next non-brain tissue to avoid is the transverse and sigmoid sinus separating the cerebrum from the cerebellum. After these, watch out for the meninges and superior sagittal sinus in between the two hemispheres. These will continue throughout the entire brain
  27. Check Figure for Reference
  28. When the brain stem appears, only paint in the part that is above the most posterior portion, bottom, of the cerebellum.
  29. The brain stem will disappear with the pons leaving last. Everything in between the temporal lobes, from the pons forward, is non-brain, and so it is removed. Sometimes the border between the temporal lobes and the non-brain is very hard to distinguish. One of the more difficult things to distinguish in the tempseg view is the optic nerve crossing. The optic nerves emerge along side of the temporal lobes, and then pass up into the gap between the temporal lobes and the insula. Use the raw image, in particular, to make sure these aren’t included in the brain mask.
  30. The final region to watch out for is in the most anterior portion of the brain. Like the most posterior region, the dura will be in between the two hemispheres. When you are finished, save the brain mask. To do this, type:
  31. “Space bar”- to go to the main menu
  32. “T”- to enter the file menu
  33. “W”- to save the label (brain mask) as a mnc
  34. case#_reslice_mask_2mm.mnc