Configure mkanalysis-sess
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The first step in the first-level analysis is to configure analyses and contrasts. This step describes what preprocessing stages should have been run as well as the parameters needed to construct a design matrix (no data are analyzed yet). This is done with mkanalysis-sess.
A good way to make it clear how you are configuring your analysis is to declare important parameters as shell environment variables, and then use them when calling mkanalysis-sess:
SMOOTHING=6; REFEVENTDUR=2.0; TR=2.0; NCONDITIONS=6; SURFACE=self; HEMIS=( lh rh ); PARFILE=booth.par;
for hemi in "${HEMIS[@]}" do mkanalysis-sess \ -fsd bold \ -surface ${SURFACE} ${hemi} \ -fwhm ${SMOOTHING} \ -event-related \ -paradigm ${PARFILE} \ -nconditions ${NCONDITIONS} \ -timewindow 24 -spmhrf 2 \ -polyfit 2 \ -mcextreg \ -TR ${TR} \ -refeventdur ${REFEVENTDUR} -per-run -force done
The above code could be saved as a script in your ~/bin directory (e.g., mkanalysis.sh) and modified as required for different datasets or parametric choices.