08. SEEG group analysis
NOTE: These are data processing scripts based on the SEEG data collected on subject "s031" using an audio-visual stimulation paradigm. The working directory is /Users/fhlin_admin/workspace/seeg/s031/analysis.
[This script file] morphs the brain surface STC files to a template, the "fsaverage" subject in FreeSurfer. The STC files here are MNE, not noise-normalized MNE (dynamic statistical parametric maps, dSPM), for left and right hemispheres. No deep brain sources are included in these brain surface STC files. We only morph the MNE STC here because the group-level statistical inferences will be derived from the effect estimates, instead of the statistics at each individual. In this example, STC files for two conditions coded with the file name "seeg_wb_mne_091019_l_mne" and "seeg_wb_mne_091019_n_mne" will be spatially morphed from individual subjects (s041, s046, s050, s052, and s054) to a template subject ("fsaverage").
Running this script will generate new STC files with the file name in a prefix of $SUBJECT_2_fsaverage_$MNE, where $SUBJECT denotes one of the subject and $MNE denotes the file stem of the STC file.
As volumetric STC files include source estimates at both cortical and sub-cortical locations, we can use [this script file] to morph between subjects with cortical neuronal current estimates expanding cortical ribbon, instead of a thin cortical surface between, for example, gray and white matter.
[This script file] averages the MNE across subjects in the anatomical space defined by the target subject, "fsaverage" in this example. We simply calculate the Z-scores over time by first subtracting the pre-stimulus baseline average and then dividing each time point with the standard deviation within the baseline interval for each brain location. The outputs are STC files with a file name "z" appended. One STC file was created for each condition and each hemisphere.
[This script file] creates a movie for each group-level Z-score STC files. Each movie frame consists of four views (two lateral and two medial views for left and right hemispheres). To save time for movie creation, this script creates one frame from every 10 consecutive time points. Remember to set the threshold (threshold variable) to render the movie correctly. Two movies are created after running this script. Movies can be converted to dynamic GIF files as exemplified below.
[This script file] calculates the average sensitivity and SNR maps across subjects.
[This script file] displays the average sensitivity and SNR maps across subjects.