Overview
MNE-BIDS-Pipeline processes your data in a sequential manner, i.e., one step at a time. The next step is only run after the previous steps have been successfully completed. There are, of course, exceptions; for example, if you chose not to apply ICA, the respective steps will simply be omitted and we'll directly move to the subsequent steps. The following flow chart aims to give you a brief overview of which steps are included in the pipeline, in which order they are run, and how we group them together.
Info
All intermediate results are saved to disk for later inspection, and an extensive report is generated.
Info
Analyses are conducted on individual (per-subject) as well as group level.
Filesystem initialization and dataset inspection¶
flowchart TD
A1[initialize the target directories] --> A2[locate empty-room recordings]
Preprocessing¶
flowchart TD
B1[Noisy & flat channel detection] --> B2[Maxwell filter]
B2 --> B3[Frequency filter]
B3 --> B4[Epoch creation]
B4 --> B5[SSP or ICA fitting]
B5 --> B6[Artifact removal via SSP or ICA]
B6 --> B7[Amplitude-based epoch rejection]
Sensor-space processing¶
flowchart TD
C1[ERP / ERF calculation] --> C2[MVPA: full epochs]
C2 --> C3[MVPA: time-by-time decoding]
C3 --> C4[Time-frequency decomposition]
C4 --> C5[MVPA: CSP]
C5 --> C6[Noise covariance estimation]
C6 --> C7[Grand average]
Source-space processing¶
flowchart TD
D1[BEM surface creation] --> D2[BEM solution]
D2 --> D3[Source space creation]
D3 --> D4[Forward model creation]
D4 --> D5[Inverse solution]
D5 --> D6[Grand average]