A growing number of researchers are adopting the BIDS standard for their data. Flywheel has many tools to support curating data into this standard. In order to make this curation process as automated as possible, the metadata describing the data needs to be as complete as possible. The best way to accomplish this is to name the Acquisitions on the scanner with the desired BIDS naming convention.
As a default, Flywheel uses the SeriesDescription DICOM field to set the Flywheel Acquisition Label. The BIDS Curate gear will rely on the Flywheel Classifications to determine which BIDS data type the file is in. The Flywheel BIDS Curate Gear then uses the Acquisition Label to manipulate the file metadata so that it can be viewed and exported in BIDS format.
For more information on the BIDS specification for MRI data, see the BIDS documentation.
The BIDS specification has several templates for the different data types. In these templates, the fields in [ ] are optional, everything else is mandatory.
For example for anatomy imaging data:
sub-<label>/[ses-<label>/]
anat/
sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
Here's the Functional template as another example.
sub-<label>/[ses-<label>/]
func/
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
Not all acquisitions that are acquired during a session are relevant to the BIDS standard. One example would be localizer scans. If there is no rule in the project curation template that matches an acquisition, it will not be included in the BIDS formatted data. If there is a rule that matches a an acquisition and that acquisition should not be included in the BIDS formatted data (for example a scan repeated due to subject motion), it can be ignored by appending
_ignore-BIDS
at the end of their acquisition label. Note that this functionality is implemented in the curation template. The default curation template does this for acquisitions, sessions, and subjects.
For a complete description of how to name acquisitions, please see "Flywheel + BIDS: how to start" and "BIDS Study Design Spreadsheet".