bidsconv
Like putting your fMRI data into BIDS format? Like using dcm2bids to do so? Too lazy to use a for-loop to iterate through each subject and call dcm2bids? Want to automatically generate most of the metadata files for BIDS? If you're like me and answered yes to all of the above, then bidsconv is for you!
Bidsconv is a multi-subject wrapper for dcm2bids, which lets you easily convert full data sets into BIDS format. Nothing special to it other than looping over multiple subject and session directories! bidsconv will also create your participants.tsv file, as well as blank README, CHANGES and dataset_description.json files.
Installation:
You must have dcm2bids installed first. To install dcm2bids:
pip install dcm2bids
Then, install bidsconv:
git clone git@github.com:danjgale/bidsconv.git
cd bidsconv/
pip install -e .
Using bidsconv
To run:
$ bidsconv -d your-dicom-directory -o your-bids-directory \
-c your-bids-config-file.json
Where your-dicom-directory is a directory that has one sub-directory per subject, and your-bids-directory is your empty BIDS directory that you wish to create.
your-bids-config-file.json is the configuration file, and follows the exact same format as the one used by dcm2bids (see example here). Refer to dcm2bids for documentation.
If you have multiple sessions, you'll need to call bidsconv for each session with the appropriate session label:
$ bidsconv -d your-dicom-directory-ses-01 -o your-bids-directory \
-c your-bids-config-file.json -s ses-01
$ bidsconv -d your-dicom-directory-ses-02 -o your-bids-directory \
-c your-bids-config-file.json -s ses-02
The full CLI can be shown by calling bidsconv -h:
usage: bidsconv [-h] [-d dicom_dir] [-o output_dir]
[--ignore ignored_dirs [ignored_dirs ...]] [-s session]
[-c config] [--force-run-labels] [-m mapping]
optional arguments:
-h, --help show this help message and exit
-d dicom_dir The path to the directory which contains all subjects'
dicom images.
-o output_dir The path to the directory which contains all subjects'
BIDS data.
--ignore ignored_dirs [ignored_dirs ...]
Subdirectories in `-d` to ignore.
-s session Session number, e.g., 'ses-01'
-c config Configuration .json file for dcm2bids. Refer to
dcm2bids documentation for examples.
--force-run-labels Force all functional runs to have a run number. This
means that singleton runs, i.e. tasks that have only
one functional run will be labeled as `run-01`. This
is a necessary workaround for fmriprep 1.4.0 or
greater. Otherwise, singleton runs will not have a run
number/label, which is the default for dcm2bids.
-m mapping .json file containing specific mappings between input
dicom folders (keys) and subject IDs (values). Useful
for multi-session data in which different dicom
folders belong to the same subject.
Note: This package was developed for the Memory, Action, and Perception lab here at Queen's University, and works for us quite well. That said, it's not a fully-tested one-size-fits-all tool for your BIDS conversions. And it's definitely in its early stages. So, if you run into any problems please let us know by creating an issue on Github. If it's really not working, then using dcm2bids directly is probably much easier!