MRI BIDS and OSF
BIDS
Brain Imaging Data Structure (more information here).
Validating BIDS dataset
With docker, you can run this line in the terminal:
$ docker run -ti --rm -v [path_to_your_toplevel_bids_directory]:/data:ro bids/validator /data
Common issues:
- files don’t follow BIDS naming conventions (more info about filenames here)
- events.tsv files are missing
- participants.tsv is missing
- participants.json file is missing or does not describe all variables from the tsv file
- datasset_description is missing or there is no name of the dataset or author names in it.
- readme file is missing or too short
- …
OSF
Upload your dataset to OSF using osfclient (user’s guide here). This is a useful python-based package to uploading data in bulk to OSF, especially because you cannot upload folders to OSF projects via browser.
Installation: $ pip3 install osfclient
Upload a file to an OSF project
$ osf -p <projectid> -u yourOSFacount@example.com upload local/file.txt remote/path.txt ### Upload a folder (recursively) to an OSF project $ osf -p <projectid> -u yourOSFacount@example.com upload -r local/folder remote/path
Set your OSF acctount password
Set a password so you don’t have to enter it each time you upload data
$ export OSF_PASSWORD=yourpassword