4a. First Brain Extraction

The goal of the first brain extraction process is to remove most of the skull/throat/neck without loosing any brain tissue. This extraction will not be extremely accurate and may include more skull than desired in order to keep all of the brain tissue. The remainder of the skull can be removed in the second brain extraction.

1. Choose (Segmentation | Brain Extraction Tool)
2. Put crosshairs in center of brain above corpus callosum along the midline
3. Click use current crosshairs (make the box to the left, red in color)
4. Set Fractional Intensity Threshold to 0.6 and the Gradient Threshold to 0.0
5. Click execute brain extraction tool - BioImageSuite will automatically save new stripped brain as [filename]_stripped.hdr
6. Click Display Under Brain/Skull Overlay to check if any tissue is erroneously included or excluded
7. Examine outline of stripping by clicking and holding the left mouse button and dragging it back and forth over one view space (coronal) while watching the other (sagittal).

• If part of the brain is excluded: Decrease Fractional Intensity Threshold (in increments of 0.1 or 0.5) and repeat steps 2-7.
• If too much skull/throat/neck is included: Increase Fraction Intensity Threshold (in increments of 0.1 or 0.5) and repeat steps 2-7.