Brainstripping in MEDx

Procedure for brainstripping in MEDx
  1. If the machine you are on does not have medx installed, telnet to a machine that has medx installed on it (in CABI, this is either kryten or zaphod).
  2. Type medx in the command line to start medx.
  3. Accept the agreement message and select "new folder" under "file".
  4. Select "open image" under "image" to choose an image you want to work on.
  5. Select the header file for the image to be used, or choose another format and choose your formatting options if the image is not in .img/.hdr format.
  6. Under "display" choose "display range". Move the display slider so that you can see the brain easily (we use 150 as the standard).
  7. Under "view" choose the "orthogonal view". This will give you 3 views of the brain (Sagittal, Coronal, and Axial).
  8. Click the hammer icon to open the toolbox. Using the ellipsoidal tool, capture the brain in all three views so that the most non-brain matter possible is outside of the ellipse without having any brain tissue outside of the ellipse. Scan through the frames of the profile to make sure no brain material is outside the ellipse.
  9. Under "Graphic", select "Graphic Region", then "Erase outside region" to remove any material outside of the ellipse. (You can also press Esc,g,o.)
  10. Use the ellipsoidal tool to capture as much of the orbital tissue (eyes) as possible without capturing any brain material inside the ellipse.
  11. Under "Graphic" select "Graphic Region", then "Erase Inside region" to remove the orbital tissue. (You can also press Esc,g,O.)
  12. In the toolbox select "FSL" then "Structural Analysis", then "Brain Extraction Tool (BET)". Under advanced options set the threshold to 4.0 and select "OK". (Running FSL may change your display range so reset it if necessary.)
  13. Switch display to "lightbox" view.
  14. Under "image", select "flip volume", choose "Up and Down".
  15. Change dimensionality to 2d by clicking the box in the top left corner from "3d" to "2d" (not "2d all"). Use the pencil tool to capture any non-brain material frame by frame. Open the original image in art2 for reference.
  16. Under "graphic" choose "graphic region", and then choose "erase inside region" (or Esc, g, O.)
  17. Make sure to return your image to "3d" mode before saving.