commands.md

High-level commans for executing analysis

Preprocessing, de-noising, and registration

Experiment 1: Task

run_fmri.py -s dots_subjects -w preproc model reg -e dots \
            -regspace epi -unsmoothed -residual -timeseries \
            -n 14

Experiment 2: Task

run_fmri.py -s sticks_subjects -w preproc model reg -e sticks \
            -regspace epi -unsmoothed -residual -timeseries \
            -n 12

Experiment 2: Rest

run_fmri.py -s sticks_subjects -w preproc model reg -e rest \
            -regspace epi -regexp sticks -unsmoothed -residual -timeseries \
            -n 12

ROI Extraction

bash run_script.sh roi_cache dots 'ifs mfc'
bash run_script.sh roi_cache sticks 'ifs mfc'
bash run_script.sh roi_cache rest 'ifs mfc'

ROI Analysis

Multivariate decoding analyses

bash run_script.sh decoding_analysis dots ifs
bash run_script.sh decoding_analysis dots mfc
bash run_script.sh decoding_analysis sticks ifs
bash run_script.sh decoding_analysis sticks mfc

Analyses of context preference spatial organization

bash run_script.sh spatial_analysis dots ifs
bash run_script.sh spatial_analysis sticks ifs

Analyses of subnetwork organization

bash run_script.sh correlation_analysis dots ifs
bash run_script.sh correlation_analysis sticks ifs
bash run_script.sh correlation_analysis rest ifs

Post-processing of individual subject results

python compile_data.py