Masking the Brain

When you have outlined the brain in every image slice, you may want to remove all the extra-cerebral tissue from the image. This is useful, for example:

  • If you want to see the brain intensity histogram so that you can decide what type of histogram to fit when finding the Brain Parenchymal Fraction.
  • If you want to use the resulting brain/CSF only image as a mask for another image.

Note: if you have previously created the brain outline, and saved the ROIs to disk, you can simply reload them from disk at this stage, without redefining them.

To remove the extra-cerebral tissue, simply click on the mask_brain_button button. This process will take a few moments, as each slice is processed. During the procedure, you will be prevented from changing any of the ROIs or adding new ones.