The purpose of the BIDS Study Design Spreadsheet is to help you prepare for BIDS curation. The Study Design is based on the ReproIn naming protocol that is the basis of our ReproIn project curation template. After reviewing the Study Design Spreadsheet you will have a better understanding of:
- The acquisition names used for the ReproIn naming protocol and what part of the BIDS specification they are associated with
- What type of information you should know about your acquisitions before starting BIDS curation, including which part of the BIDS specification the acquisitions are association with
The BIDS Study Design spreadsheet
Columns of the spreadsheet are:
- Project Curation Template Rule ID: name of the "rule" that the acquisition file matches
- Acquisition Label: Flywheel acquisition name which is derived from the SeriesDescription DICOM tag
- File Name: name of the file generated by dcm2niix from the original DICOM series
- File Type: nifti, dicom, tsv, etc.
- BIDS path/name: final BIDS folder and file name that should be generated for this acquisition file
- Count: number of times this acquisition file should be found for each subject (can be a range)
- BIDS Specification Link: URL to the section of the official BIDS Specification that describes this type of acquisition
- Notes: any comments, questions, etc.
How to use the spreadsheet
Use the acquisition labels in the spreadsheet as examples of how to set them at the scanner console if you are acquiring new data. For data already in Flywheel, use the bids-pre-curate gear to change existing acquisition labels match the labels in the Study Design. In both of these cases, the ReproIn template should just work when running the BIDS curation gear.
The spreadsheet will also help you plan out how you may need to expand the standard ReproIn template if needed.
Expanding the spreadsheet
Describing your data using the BIDS Study Design Spreadsheet is the best way to start thinking about editing the ReproIn Template. For example, if there is a type of acquisition that is not yet in our Study Design, a new rule can be added to the project curation template to follow the BIDS Specification. In the Study Design you would create a new row with this new rule name and the rest of the columns should be filled out, including the link to the relevant BIDS Specification.
If you want to use your existing acquisition labels instead of following the ReproIn standard, you would add a new column to specify these labels. The project curation template will need to be modified so that the existing rules can recognize the new labels.
The above modifications to the spreadsheet, adding a row or adding a column, and the accompanying modifications of the project curation template, can be done with assistance from Flywheel, or Flywheel can be contracted to do the work.
Click to go to the BIDS Study Design.xlsx