Qc-meg

coglib/meeg/README.md

@@ -19,6 +19,10 @@ The environments are tailored for Linux and the HPC, so some things might break
 To run the analysis described below on the sample data, make sure to change the bids root path in /meeg/config/config.py:
 *$ROOT/sample_data/bids*
 
+### Running 3rd level quality checks:
+In the command line, enter:
+sbatch --array=<subjectID> srun_qc.sh <SA/SB> V1
+
 ### Running preprocessing:
 In the command line, enter:
 ```

coglib/meeg/qc/P00_bids_conversion.py

@@ -6,13 +6,6 @@
 
 https://mne.tools/mne-bids/stable/index.html
 
-Questions/Issues:
-    - what to write in the participants and dataset_description metadata
-    files?
-    - what session ID should we give to the anat scan (e.g., v0, v2, mri)?
-    - for visit 2, what to count the replay runs? Continue the count from
-    where it was left from the VG (run 4) or restart from run 1?
-
 Notes:
     - the conversion must be done after reading the events. Here, the event 
     list includes all the triggers/events

coglib/meeg/qc/P00_run_qc.py

@@ -37,46 +37,4 @@
         has_eeg = True
 
 
-# # =============================================================================
-# # DEFINE PREPROCESSING STEPS
-# # =============================================================================
-
-# def pre_step1():
-#     P01_maxwell_filtering.run_maxwell_filter(subject_id, 
-#                                              visit_id)
-#     if has_eeg:
-#         P02_find_bad_eeg.find_bad_eeg(subject_id, 
-#                                       visit_id, 
-#                                       has_eeg)
-#     P03_artifact_annotation.artifact_annotation(subject_id, 
-#                                                 visit_id, 
-#                                                 has_eeg, 
-#                                                 # threshold_muscle,
-#                                                 )
-#     P04_extract_events.run_events(subject_id, 
-#                                   visit_id)
-#     P05_run_ica.run_ica(subject_id, 
-#                         visit_id, 
-#                         has_eeg)
-
-# def pre_step2(
-#               # meg_ica_eog=opt.mICA_eog, meg_ica_ecg=opt.mICA_ecg,
-#               # eeg_ica_eog=opt.eICA_eog, eeg_ica_ecg=opt.eICA_ecg,
-#               ):
-#     P06_apply_ica.apply_ica(subject_id, 
-#                             visit_id, 
-#                             has_eeg)
-
-#     P07_make_epochs.run_epochs(subject_id, 
-#                             visit_id, 
-#                             has_eeg)
-
-
-# =============================================================================
-# RUN
-# =============================================================================
-# if opt.step == '1':
-#     pre_step1()
-# elif opt.step == '2':
-#     pre_step2()
 QC_processing.run_qc_processing(subject_id, visit_id, has_eeg)