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EEG IP package

In developement. Not meant for reuse by external party yet. Project in constant flux!

Campaings

Campaign have four levels, and for each levels, there is a set of properties that can be modified in a factorial design. These levels are as follow:

  • Preprocessing:
    • dataset:
      • EEGIP current datasets: ['london06', 'london12', 'washington']
  • Source reconstruction:
    • con_type: ['scalp', 'sources']
    • inv_method:
      • MNE current inv_method: ['MNE', 'dSPM', 'sLORETA', 'eLORETA']
    • event_type: Depends on the dataset. See the YAML configuration file.
  • Connectivity computation:
    • method:
      • MNE current method: [ 'coh', 'cohy', 'imcoh', 'plv', 'ppc', 'pli', 'pli2_unbiased', 'wpli', 'wpli2_debiased']
    • band: User defined, in the YAM configuration file.
  • Connectivity aggregation

File

We use the following file nomenclature:

  • EEGIP recordings:
    • pattern: [DATA][PATTERN]qcr.set
    • example: /project/def-emayada/eegip/london/derivatives/lossless/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr.set
  • Preprocessed recordings:
    • pattern: [OUT][PATTERN]qcr-raw.fif
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-raw.fif
  • Epoch:
    • pattern: [OUT][PATTERN]qcr-epo.fif
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-epo.fif
  • Evoked:
    • pattern: [OUT][PATTERN]qcr-ave.fif
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-ave.fif
  • Sources:
    • pattern: [OUT][PATTERN]qcr-{event_type}-{key1=val1}-...-{keyN=valN}-{con_type}.npy
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-direct-dSPM-sources.npy
  • Labels:
    • pattern: [OUT][PATTERN]qcr-{event_type}-{key1=val1}-...-{keyN=valN}-sources-labels.npy
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-direct-dSPM-sources-labels.npy
  • Connectivity matrix:
    • pattern: [OUT][PATTERN]qcr-{fmin}-{fmax}-{event_type}-{key1=val1}-...-{keyN=valN}-{con_type}-con.csv
    • example: /project/def-emayada/oreillyc/eegip/london/sub-s601/ses-m06/eeg/sub-s601_ses-m06_eeg_qcr-100-200-direct-wpli-scalp-con.csv
  • Connectivity aggregates:
    • pattern: [OUT]/con_matrix-{con_type}-{key1=val1}-...-{keyN=valN}.pck
    • example: /project/def-emayada/oreillyc/eegip/london06/con_matrix_scalp_wpli.pck
  • BEM model:
    • pattern: [ATLAS]/...
  • Atlas parcel meshes Meshes
    • pattern: [ATLAS]/...
  • Demo files
    • pattern: [DEMO]/...
  • Slurm log files
    • pattern: [OUT_ROOT]/log/...
  • Sbatch scripts
    • pattern: [OUT_ROOT]/slurm/...