4b. Second Brain Extraction

The goal of the second brain extraction process is to be more accurate around the brain and remove the meninges and any remaining skull.

1. Choose (File | Load), then
2. Choose [filename]_stripped.hdr and click Open
3. Choose (Segmentation | Brain Extraction Tool). As above in steps 2 and 3, put the croshairs in the center of the brain and make sure that the box to the left of use current crosshairs is red.
4. Change Fractional Intensity Threshold to 0.4 or 0.3 and the Gradient Threshold to 0.2
5. Click Execute Brain Extraction Tool. BioImageSuite will automatically save second stripped brain as [filename]_stripped_stripped.hdr.
6. Click Display under Brain/Skull Overlay to check if any brain is erroneously included or excluded.
7. Examine outline of stripping as stated in 4a, step 7.