The goal of the second brain extraction process is to be more accurate around the brain and remove the meninges and any remaining skull.
- Choose (File | Load), then
- Choose [filename]_stripped.hdr and click Open
- 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.
- Change Fractional Intensity Threshold to 0.4 or 0.3 and the Gradient Threshold to 0.2
- Click Execute Brain Extraction Tool. BioImageSuite will automatically save second stripped brain as [filename]_stripped_stripped.hdr.
- Click Display under Brain/Skull Overlay to check if any brain is erroneously included or excluded.
- Examine outline of stripping as stated in 4a, step 7.