Extract NIMH Data Archive compatible metadata from Brain Imaging Data Structure (BIDS) compatible MR or EEG datasets. Adapted and extended from https://github.com/bids-standard/bids2nda to also:
- zip and include stimulus files referenced in events.tsv files
- populate experiment ID column using a BIDS taskname to NDA experiment ID mapping text file
pip install https://github.com/brown-bnc/bids2nda/archive/master.zip
usage for MR data: mr_bids2nda [-h] [-e EXPID_MAPPING] [--lookup_csv LOOKUP_CSV] [--lookup_fields LOOKUP_FIELDS [LOOKUP_FIELDS ...]] BIDS_DIRECTORY GUID_MAPPING OUTPUT_DIRECTORY
usage for EEG data: eeg_bids2nda [-h] [-e EXPID_MAPPING] [--lookup_csv LOOKUP_CSV] [--lookup_fields LOOKUP_FIELDS [LOOKUP_FIELDS ...]] BIDS_DIRECTORY GUID_MAPPING OUTPUT_DIRECTORY
BIDS to NDA converter.
positional arguments:
BIDS_DIRECTORY Location of the root of your BIDS compatible directory
GUID_MAPPING Path to a text file with participant_id to GUID mapping. You will need to use the GUID Tool (https://ndar.nih.gov/contribute.html) to generate GUIDs for
your participants.
OUTPUT_DIRECTORY Directory where NDA files will be stored
options:
-h, --help show this help message and exit
-e EXPID_MAPPING, --expid_mapping EXPID_MAPPING
Path to a text file with experiment name to NDA experiment ID mapping.
-b BIRTHDATE, --birthdates BIRTHDATE
Path to a text file with BIDS subject ID to birthdate (MM/DD/YYYY) mappings. i.e. 101 - 05/24/1990
If provided, this will be used to calculate participant age at the time of each session, which is required by NDA.
Otherwise, approximate age in months will be calculated from the participants.tsv file.
Because birthdate is personally identifiable information, it will not be included in the output csv file or zipfiles.
Delete this mapping file after running the converter.
--lookup_csv LOOKUP_CSV
Path to a csv with data we need for the image03.csv, i.e. ndar_subject01.csv
--lookup_fields LOOKUP_FIELDS [LOOKUP_FIELDS ...]
List of column names to grab from the lookup csv. i.e. --lookup_fields interview_age sex
This is the file format produced by the GUID Tool, one line per subject in the format:
<participant_id> - <GUID>
This is a text file with one line per task present in the dataset in the format:
<BIDS task name> - <NDA experiment ID number>
The BIDS task name should match the value associated with the "task-" key in the .nii filename.
The NDA experiment ID number(s) are received from NDA after setting the study up through the NDA website here.
This is a text file, with one line per subject in the format:
<participant_id> - MM/DD/YYYY
This can be any csv file, including something like the ndar_subject01.csv, with data you want to use to populate the image03.csv file.
This is useful in cases where the BIDS-derived data is missing or incorrect, such as the calculation of interview_age in months, which is only approximated based on age in years from the BIDS data.
If you pass a lookup csv, you need to specify which columns you want to use to populate the image03.csv. The column names must match, so if you're trying to populate the interview_age column in the image03.csv, your lookup csv must have a column with the same name.
You can pass more than one value, separated by spaces, like: --lookup_fields interview_age gender
See /examples