This repo is for reanalysis of the "Bad Baby" data, using the MNE-BIDS-Pipeline.
-
local folder
/media/<REDACTED>/Untitled
contains badbaby data withprebad
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
There is a Makefile
in the prep-dataset
folder. make all
will:
- rsync data from local and remote sources.
- 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.
- write summaries of how much data we have for each subject/session.
- generate logs / lists of missing or unexpected files.
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
.
- 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