MNE-BIDS-Pipeline 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 or SSP, the spatial filtering steps will simply be omitted and we'll directly move to the subsequent steps. See the flowchart below for a visualization of the steps, or check out the list of processing steps for more information.
All intermediate results are saved to disk for later inspection, and an extensive report is generated. Analyses are conducted on individual (per-subject) as well as group level.
Caching¶
MNE-BIDS-Pipeline offers automated caching of intermediate results. This means that
running mne_bids_pipeline config.py once will generate all outputs, and running it
again will only re-run the steps that need rerunning based on:
- Changes to files on disk (e.g., updates to
bids_rootfiles), and - Changes to
config.py
This is particularly useful when you are developing your pipeline, as you can quickly iterate over changes to your pipeline without having to re-run the entire pipeline every time -- only the steps that need to be re-run will be executed.
Flowchart¶
For more detailed information on each step, please refer to the detailed list of processing steps.
Filesystem initialization and dataset inspection
Preprocessing
Sensor-space analysis
Source-space analysis
FreeSurfer-related processing