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Bad Baby reanalysis

This repo is for reanalysis of the "Bad Baby" data, using the MNE-BIDS-Pipeline.

Notes on data sources and data munging

  • local folder /media/<REDACTED>/Untitled contains badbaby data with prebad files defined and many missing emptyroom files tracked down. This is our starting point, rsync'd to ./local-data.

  • server folder /mnt/brainstudio/badbaby/ has lots of anomalies / redundancies. It gets rsync'd to ./server-data.

  • file and folder naming anomalies and known-bad-file exclusions are handled by prep-dataset/select-files-from-*.py

Data prep

There is a Makefile in the prep-dataset folder. make all will:

  1. rsync data from local and remote sources.
  2. sort through the copied file trees, generate a mapping from filenames we want to keep to new file locations (correcting folder- or file-names along the way), and make a hardlink to each "kept" file at the new location.
  3. write summaries of how much data we have for each subject/session.
  4. generate logs / lists of missing or unexpected files.

Converting to BIDS

The script prep-dataset/bidsify.py will convert the dataset to BIDS format in folder bids-data. It also checks/validates the events found in the FIF files against the TAB files from the stimulus presentation script (enabled in the bidsify.py script via a boolean flag verify_events_against_tab_files). Any failures to match up events from the FIF and TAB files will be flagged in prep-dataset/qc/log-of-scoring-issues.txt.

TODOS

  • coreg
  • add the MRIs to bidsify.py (or write a separate script to add them to the bids tree?)
  • setup MNE-BIDS-pipeline to do the preprocessing