Brain Finder Tool - Masking the Brain

Brain Finder - 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.

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