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; #FWHM smoothing kernel; rule of thumb is 2 x VoxelSize
REFEVENTDUR=0.8; #How long are the events?
TR=2.0; #What is the TR
NCONDITIONS=3; #How many conditions in the par files
SURFACE=self; #generally valid options are 'self' or 'fsaverage'
HEMIS=( lh rh ); #for automatically looping over both hemispheres
PARFILE=LDT.par; #What's the name of the .par files in your bold/ directories?
SKIPS=4; #If you wish to drop the first n volumes, set to some value other than 0
ANROOT="LDT.sm" #base name for the analysis directories

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} \
 -nskip ${SKIPS} \
 -refeventdur ${REFEVENTDUR} \
 -analysis ${ANROOT}${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.