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.

BIDScoin tutorial

  1. Data preparation. Activate the bidscoin environment and create a tutorial playground folder in your home directory by executing these bash commands (users from outside the DCCN may have to adapt the first two commands to their environment):
$ module add bidscoin                # Load the DCCN bidscoin module with the PATH settings and Anaconda environment
$ source activate /opt/bidscoin      # Activate the python virtual environment with the BIDScoin python packages
$ bidscoin --download .              # Download the tutorial data (use a "." for the current folder or adapt it to your needs)
$ cd bidscointutorial                # Go to the downloaded data (or provide the path to the subfolders when calling the bidscoin tools)

The new bidscointutorial folder contains a raw source-data folder and a bids_ref reference BIDS folder, i.e. the intended end product of this tutorial. In the raw folder you will find these DICOM series (aka “runs”):

001-localizer_32ch-head                  A localizer scan that is not scientifically relevant and can be left out of the BIDS dataset
002-AAHead_Scout_32ch-head               A localizer scan that is not scientifically relevant and can be left out of the BIDS dataset
007-t1_mprage_sag_ipat2_1p0iso           An anatomical T1-weighted scan
047-cmrr_2p4iso_mb8_TR0700_SBRef         A single-band reference scan of the subsequent multi-band functional MRI scan
048-cmrr_2p4iso_mb8_TR0700               A multi-band functional MRI scan
049-field_map_2p4iso                     The fieldmap magnitude images of the first and second echo. Set as "magnitude1", bidscoiner will recognize the format. This fieldmap is intended for the previous functional MRI scan
050-field_map_2p4iso                     The fieldmap phase difference image of the first and second echo
059-cmrr_2p5iso_mb3me3_TR1500_SBRef      A single-band reference scan of the subsequent multi-echo functional MRI scan
060-cmrr_2p5iso_mb3me3_TR1500            A multi-band multi-echo functional MRI scan
061-field_map_2p5iso                     Idem, the fieldmap magnitude images of the first and second echo, intended for the previous functional MRI scan
062-field_map_2p5iso                     Idem, the fieldmap phase difference image of the first and second echo

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

  • Are the DICOM files for all the bids/sub-* folders organised in series-subfolders (e.g. sub-001/ses-01/003-T1MPRAGE/0001.dcm etc)? Use dicomsort if this is not the case (hint: it’s not the case). A help text for all BIDScoin tools is available by running the tool with the -h flag (e.g. rawmapper -h)
  • 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. Now we can make a study bidsmap, i.e. the mapping from DICOM source-files to BIDS target-files. To that end, scan all folders in the raw data collection by running the bidsmapper command:
$ bidsmapper raw bids
  • In the GUI that appears, edit the task and acquisition labels of the functional scans into something more readable, e.g. task-Reward for the acq-mb8 scans and “task-Stop” for the acq-mb3me3 scans. Also make the name of the T1 scan more user friendly, e.g. by naming the aquisition label simply acq-mprage.
  • Add a search pattern to the IntendedFor field such that the first fieldmap will select your Reward runs and the second fieldmap your Stop runs (see the bidseditor fieldmap notes for more details)
  • Since for this dataset we only have one session per subject, remove the session label (and note how the output names simplify, omitting the session subfolders and labels)
  • When all done, go to the Options tab and change the dcm2niix settings to get non-zipped nifti output data (i.e. *.nii instead of *.nii.gz). Test the tool to see if it can run and, as a final step, save your bidsmap. You can always go back later to change any of your edits by running the bidseditor command line tool directly. Try that.
  1. BIDS coining. The next step, converting the source data into a BIDS collection, is very simple to do (and can be repeated whenever new data has come in). To do this run the bidscoiner command-line tool (note that the input is the same as for the bidsmapper):
$ bidscoiner raw bids
  • Check your bids/code/bidscoin/bidscoiner.log (the complete terminal output) and bids/code/bidscoin/bidscoiner.errors (the summary that is also printed at the end) files for any errors or warnings. You shouldn’t have any :-)
  • Compare the results in your bids/sub-* subject folders with the in bids_ref reference result. Are the file and foldernames the same (don’t worry about the multi-echo images and the extra_data images, they are combined/generated as described below)? 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.
  1. Finishing up. Now that you have converted the data to BIDS, you still need to do some manual work to make it fully ready for data analysis and sharing
  • Combine the echos using the echocombine tool, such that the individual echo images are replaced by the echo-combined image
  • Deface the anatomical scans using the echocombine tool. This will take a while, but will obviously not work well for our phantom dataset. Therefore store the ‘defaced’ output in the derivatives folder (instead of e.g. overwriting the existing images)
  • 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?