Configure mkanalysis-sess: Difference between revisions
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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: | 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= | SMOOTHING=4; #FWHM smoothing kernel; rule of thumb is 2 x VoxelSize | ||
REFEVENTDUR=0.8; #How long are the events? | REFEVENTDUR=0.8; #How long are the events? | ||
TR=2.047; #What is the TR | TR=2.047; #What is the TR |
Revision as of 16:33, 5 July 2017
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=4; #FWHM smoothing kernel; rule of thumb is 2 x VoxelSize REFEVENTDUR=0.8; #How long are the events? TR=2.047; #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.