Configure mkanalysis-sess

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 ${REFEVENTDUR} \
 -analysis booth500.sm${SMOOTHING}.${hemi} \
 -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.

This step creates analysis directories in your $SUBJECTS_DIR containing single files that contain all the information needed for the next step.