**Canny Parameters**The canny parameters given here are the same as in the Edge Tool. Hysteresis thresholding is part of the Canny algorithm, whereby first the edges with an intensity gradient above a low threshold are identified; then linked edge strings that are entirely below an upper threshold are eliminated.**Sigma**The parameter of the gaussian convolution profile used to smooth the image prior to the gradient calculation. It essentially selects the scale of the edge detector.**Precision**The ratio of the smallest stored value of the gaussian convolution profile with respect to the largest. Lower values give increased precision, larger convolution masks and increased computation time.**Lower Thresh**The lower threshold (see above).**Upper Thresh**The upper threshold (see above).**Length Thresh**A lower threshold on the length of connected edge strings, where strings shorter than this value are eliminated.

**Skull Segmentation Parameters****Skull Seg**The skull segmentation process involves a couple of erosion/dilation operations, the first of which requires user-defined thresholding to ensure that the white matter of the brain is not removed too. This value should be between 3.0 and 4.0, if it is set outside this range, the value used will be 3.05.

**Cortical Thickness Parameters****Grey/White Midpoint**The average of the mean tissue values for the grey and white matter.**Grey Mean**The grey matter mean tissue value.**Search extent**The maximum search extent when finding the opposing grey/white matter boundary. The maximum search extent for finding a grey matter/CSF boundary is half of this. The default value is 20mm. This parameter is also used when performing the bootstrapped grey matter offset calculation, when a value of approximately 2mm is sufficient.**Edge limit**When applying the Median Filter to the thickness values at each position on the GM/WM boundary edge string, this value is the maximum difference allowed between the central edge position value and the median of the five currently being windowed.**Fraction**The fractional volume on the GM volume probability maps at which a transition from GM to another tissue takes place. It is assumed to be 0.5.