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overview.txt
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Overview of the scripts in DrumsAndBrains
Legend
(D) needs Data folder
(S) run separately for all subjects (needs Subject number, see runall_ scripts)
(R) needs Result folder
(A) needs number of all subjects (21)
(C) needs condition (both/listen/silence)
a/b/... script can run in parallel (not dependent on each other)
* motor only
1a. (DSR) read_aif.py
plots: 'NeuralEntrl_Ss%02dresponse.pdf', 'SelfAssessmentAndResponseSs%02d.pdf'
data: 'behavioural_results.npz'
1b. (DSR) eeg_outlier.py
plots: 'Channel_spectra_precleaning.pdf', 'ICA_patterns.pdf',
'ICA_spectra.pdf', 'Channel_spectra_postcleaning.pdf'
data: 'ICA_result.joblib', 'artifact_segments.npy', 'clean_data.npz'
2a. (DSR) prepareFFTSSD.py
data: 'prepared_FFTSSD.npz'
2b. (DSR) read_eeg.py
plots: 'ERP_all_channels.pdf', 'ERP_CCA_channels.pdf', 'SSD_patterns.pdf',
'OszillationAmp_Performance_Listen.pdf',
'OszillationPhase_Performance_Listen.pdf',
'OszillationAmp_Performance_Silence.pdf',
'OszillationPhase_Performance_Silence.pdf'
data: 'eeg_results.npz'
2c. (DR) sourceRecon.py
plots: not stored, only plt.show()
2d. (DR) basicAnalysis_behavioral.py
plots: 'performance_background_plot.pdf', 'snare_vs_wdBlk_performance.pdf',
'NeuralEntrl_response.pdf'
2e. (DR) basicAnalysis_EEG.py
plots: 'Channel_spectra_Listening.pdf','Channel_spectra_Silence.pdf',
'Channel_spectra_Listening.pdf', 'Channel_spectra_Silence.pdf'
2f. (DR) basicAnalysis_EEGvsBehavior.py
plots: 'ListeningAmp_Performance.pdf', 'ListeningPhase_Performance.pdf',
'SilenceAmp_Performance.pdf', 'SilencePhase_Performance.pdf'
3a. (R) calcMultisubjectFFTSSD.py (uses mtCSP.py)
plots: 'FFTSSD_patterns_mtCSP.pdf'
data: 'mtCSP.npz
*3b. (DR) basicAnalysis_motor.py
plots: 'motor/BP_2000mspreresponse.pdf',
'motor/ERD_2000mspreresponse.pdf' (also for each subject),
'motor/channelSpectra0-30.pdf', 'motor/channelSpectra_ERD0-30.pdf'
data: 'motor/ERD_p', 'motor/BP.npz', 'motor/ERD.npz',
'motor/covmat.npz', 'motor/inlier.npz'
3c. PlotEvokedComponents.py
plots: 'EvokedComponent.pdf'
4a. (DRC) prepareModelData.py
data: 'snare_data_both.csv' (wdblk, listen, silence respectively)
4b. (R) bestDipoleFit.py
plots: 'BestDipoleFit_snarePaired.pdf', 'BestDipoleFit_snareSingle.pdf'
*4c. (DR) csp.py
plots: 'motor/CSP_patterns.pdf'
data: 'motor/mtCSP.npz', 'motor/ERDCSP.npz'
*4d. (DR) lda.py
data: 'motor/lda.npy'
5a. lmmelsm.R
data:
plots:
5b. (DR) SSDMusicCorr.py
plots: 'SNNR_exp.pdf'
*5c. (DR) motorPlots.py
plots: 'motor/BPLDA.pdf', 'motor/mtCSP_filter_optLam2.pdf',
'motor/mtCSP_patterns[band].pdf', 'motor/erdmtcsp_comp[band].pdf',
'motor/mtCSP[band].pdf', 'motor/patternsByTime.pdf'
*5d. (DR) prepareModelData_motor.py
data: 'snare_data_motor.csv'. 'wdBlk_data_motor.csv'
*5e. (DR) motorMusicCorr.py
plots: 'motor/motorMusicCorr_BP.pdf', 'motor/motorMusicCorr_ERD.pdf'
*6a. lmmelsm_motor.R
data: 'motor/lmmelsm_motor_snare_all0.999_0.1_12.RData',
'motor/lmmelsm_motor_wdBlk_all0.999_0.1_12.RData'
plots: 'motor/lmmelsm_motor_snare_all0.999_0.1_12',
'motor/lmmelsm_motor_wdBlk_all0.999_0.1_12',
'motor/snareAll_CI0.999',
'motor/wdBlkAll_CI0.999'
# other scripts
helper_function.py: includes some helpful functions
checksum.sh: calculate checksum
runall_*: shell scripts to run python scripts for each subject
stepdown_p.py: Calculate corrected p values
# old
temporary.py: add artifacts for subject 02 and 12 (one-time and already done)
gamlss.R: R script with design matrix, different model calculations (gamlss)
lm_tests.R: R script, contains different lm models
REWBmodel.py: older version of REWB2.py
SPoC.py: not using SPoC anymore
calcFFTSSD.py: SSD, replaced by calcMultisubjectFFTSSD.py
rCSP-tlw.py: used by calcFFTSSD, replaced by calcMultisubjectFFTSSD.py
REWB2.py: now calculating models with lmmelsm.R (made .rds and .html files)
brms.R: now calculating models with lmmelsm.R
# motor Pipeline (necessary for model)
1a. (DSR) read_aif.py
1b. (DSR) eeg_outlier.py
3b. (DR) basicAnalysis_motor.py
4c. (DR) csp.py
4d. (DR) lda.py
5c. (DR) motorPlots.py
5d. (DR) prepareModelData_motor.py
5e. (DR) motorMusicCorr.py
6a. lmmelsm_motor.R