Differences between revisions 2 and 3
Deletions are marked like this. Additions are marked like this.
Line 32: Line 32:
|| -nosumconds || don't sum conditions (for f-test) || || -nosumconds || don't sum conditions (for f-test) || Specifies that the conditions be tested separately ||

Index TableOfContents

Name

mkcontrast-sess - creates a contrast matrix that is then used as input to test hypotheses.

Synopsis

mkcontrast-sess

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

volume1

description

volume2

description

Description

This program 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

command foo -i f -o out

description

Example 2

command foo -i f -o out -f fvalue

description

Bugs

None

See Also

["othercommand1"], ["othercommand2"]

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

JaneSmith

mkcontrast-sess (last edited 2008-04-29 11:46:14 by localhost)