A contrast file was created next, used to indicate which cortical thickness comparisons the Randomise program would make between the TBI and OI groups.  In this contrast matrix, left and right columns again respectfully represented TBI and OI groups.  Each row represented a comparison to be made in the program.  Comparisons indicated by the first two lines of the matrix included where cortical thickness is greater for TBI patients as compared to OI patients, and vice versa.  The final two lines indicated that analyses would be run of mean cortical thickness for TBI and OI groups, irrespective of comparisons.  This matrix was included in a text file in vi editor, and again the file was subsequently converted to a matrix file through the Text2Vest program.