## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting '''Index''' <> = Name = mkcontrast-sess - creates a contrast matrix that is then used as input to test hypotheses. = Synopsis = mkcontrast-sess -contrast -analysis [options] = Arguments = == Positional Arguments == None == Required Flagged Arguments == None == Optional Flagged Arguments == || -analysis analysisname (or use -an) || name of session-level functional analysis || Name of the analysis to create the contrast for. The analysis must have been defined by mkanalysis-sess. Also, selxavg-sess must have been run at least once. || || -contrast contrastname (or use -co) || contrast name || The name of the contrast. This name is then used in later programs (eg, stxgrinder-sess). mkcontrast-sess will create a matlab file in the study analysis directory. This file will be called contrastname.mat. When stxgrinder-sess is run, it will create a subdirectory called contrastname under the analysis directory for each sessions. || || -a a1 <-a a2 ...> || positive contrast conditions || These specify which conditions to use in the contrast, where 1, a2, c1, c2, etc, are the condition numbers as found in the paradigm file. The -a conditions will be weighted positively. The -c conditions will be weighted negatively. Eg, -a 2 -c 1 -c 3 will weight conditions 1 and 3 by -0.5 and condition 2 by +1. || || -c c1 <-c c2 ...> || negative contrast conditions || These specify which conditions to use in the contrast, where 1, a2, c1, c2, etc, are the condition numbers as found in the paradigm file. The -a conditions will be weighted positively. The -c conditions will be weighted negatively. Eg, -a 2 -c 1 -c 3 will weight conditions 1 and 3 by -0.5 and condition 2 by +1. || || -nosumconds || don't sum conditions (for f-test) || Specifies that the conditions be tested separately || || -ircorr nircorr || correlate with gamma function || || -deltarange dmin dmax || range of delta for gamma function || || -taurange tmin tmax || range of tau for gamma function || || -umask umask || set unix file permission mask || || -scriptonly || don't run, just generate a script || || -version || print version and exit || || -help || === For FIR Designs === || -setwdelay || prompt for setting of delay weights || For FIR designs, allows the user to set the weight for each post-stimulus delay. When the program runs, it will prompt the user to enter the weights (eg, if there are 10 points in the FIR, the the user will enter a list of 10 numbers). If you do not want to include a point, set its weight to 0. Eg, if thre are 10 points, but you only want to consider points 3-7, then enter 0 0 1 1 1 1 1 0 0 0. These weights are applied on a condition-by-condition basis. See also -sumdelays. || || -sumdelays || sum weighted delays || For FIR designs, sum the points inside the FIR window so that each condition is represented by a single number (ie, the sum). If delay weights have been specified (see -setwdelay), then the weighted sum is computed. || || -rmprestim || subtract prestimulus baseline || For FIR designs, compute a contrast such that the average hemodynamicresponse prior to simulus onset is subtracted from the hemodynamic response waveform. This is good for removing baseline shifts. || = Outputs = || ?? || ?? || = Description = [[mkcontrast-sess]]creates a contrast matrix that is then used as input to test hypotheses. The actual voxel-by-voxel statistical test is performed by [[stxgrinder-sess]]. = Examples = == Example 1 == ?? == Example 2 == ?? = Bugs = ?? = See Also = [[stxgrinder-sess]] = Links = FreeSurfer, FsFast = Methods Description = {{{ description description }}} = References = [[References/Lastname###]] = Reporting Bugs = Report bugs to = Author/s = DougGreve