Demo and tutorial

BIDS introduction and BIDScoin demo

A good starting point to learn more about BIDS and BIDScoin is to watch this presentation from the OpenMR Benelux 2020 meeting (slides). The first 14 minutes Robert Oostenveld provides a general overview of the BIDS standard, after which Marcel Zwiers presents the design of BIDScoin and demonstrates hands-on how you can use it to convert a dataset to BIDS.

Hands-on tutorial

The following tutorial is specific for researchers from the DCCN and makes use of data-sets stored on its central file-system. However, it should not be difficult to use (at least part of) this tutorial for other data-sets as well.

  1. Preparation. Activate the bidscoin environment and create a tutorial playground folder in your home directory by executing these bash commands (see also module help bidscoin):
$ module add bidscoin
$ source activate /opt/bidscoin
$ cp -r /opt/bidscoin/tutorial ~

The new tutorial folder contains a raw source-data folder and a bids_ref reference BIDS folder, i.e. the end product of this tutorial.

Let’s begin with inspecting this new raw data collection:

  • Are the DICOM files for all the sub-/ses- folders organised in series-subfolders (e.g. sub-001/ses-01/003-T1MPRAGE/0001.dcm etc)? Use dicomsort if this is not the case
  • Use the rawmapper command to print out the DICOM values of the “EchoTime”, “Sex” and “AcquisitionDate” of the fMRI series in the raw folder
  1. BIDS mapping. Scan all folders in the raw data collection for unknown data by running the bidsmapper bash command:
$ bidsmapper raw bids
  • Rename the task label of the functional scans into something more readable, e.g. “Reward” and “Stop”
  • Add a search pattern to the IntendedFor field such that it will select your fMRI runs (see the bidseditor fieldmap section for more details)
  • When all done, (re)open the bidsmap.yaml file and change the options such that you will get non-zipped nifti data (i.e. *.niiinstead of *.nii.gz) in your BIDS data collection. You can use a text editor or, much better, run the bidseditor command line tool.
  1. BIDS coining. Convert your raw data collection into a BIDS collection by running the bidscoiner commandline tool (note that the input is the same as for the bidsmapper):
$ bidscoiner raw bids
  • Check your bids/code/bidscoin/bidscoiner.log and bids/code/bidscoin/bidscoiner.errors files for any errors or warnings
  • Compare the results in your bids/sub-* subject folders with the in bids_ref reference result. Are the file and foldernames the same? Also check the json sidecar files of the fieldmaps. Do they have the right “EchoTime” and “IntendedFor” fields?
  • What happens if you re-run the bidscoiner command? Are the same subjects processed again? Re-run “sub-001”.
  • Inspect the bids/participants.tsv file and decide if it is ok.
  • Update the dataset_description.json and README files in your bids folder
  • As a final step, run the bids-validator on your ~/bids_tutorial folder. Are you completely ready now to share this dataset?