In this brief guide I'll describe how to prepare your neuroimaging data for the NDA submission with minimal fuss.
Minimal required data
NDA requires each study to collect and share some small subset of values for all subjects and scans:
- Name, surname, date of birth, and place of birth. This data will not be share with the NDA, but is required to generate unique IDs for your subjects. Those IDs are used by NDA to link participants across studies. Therefore you should collect this data and keep it in a safe place linked to the IDs you use internally. You will use this data during the submission process to generate NDA compatible IDs.
- Age (in months at the time of scan) and sex (male or female). Those are minimal required demographic information you will need to collect.
- Repetition time, echo time, flip angle, scanner manufacturer, model, and field strength, date of acqusition for all of your neuroimaging files (T1s, fMRI, DWI etc.)
- bvec and bval files if you include diffusion files.
- Slice timing if your dataset includes fMRI data.
For organizing your data after acquisition I recommend using the Brain Imaging Data Structure (BIDS). It's an intuitive file organization scheme that will make it easier to analyze your data later due to growing set of tools that use it (such as mriqc, FMRIPREP or AA). Use can use tools like dcm2niix (to convert from DICOM to NIFTI and extract metadata) and/or heudiconv (batch processing and sorting DICOMs from many scans). Data required by NDA can be included in your BIDS dataset in the following places:
- Age and sex can be included as columns in the participants.tsv file. If your data comes from a longitudinal study you can include age and sex in the _session.tsv files (one per subject) to specify the values for each session independently.
- If you use dcm2niix you should have almost all of the required metadata values and extra files (bval and bvec). Double check scanner model, field strength and flip angle.
- Finally date of acquisition can be inserted as the acq_time column in the _scans.tsv files.
When the data acquisition is completed and the validator passes all of the checks it is a good habit to make the folder with the dataset read only. This will prevent from any accidental deletion or modification of the data down the road.
Submission to NDA
- Use the GUID Tool to generate GUIDs for each of your subject. This will require providing name, date of birth and place of birth and will result in a file mapping from the IDs you use internally to GUIDs. Make sure you keep this data safe – it includes personal information!
- Create NDA submission package using the BIDS2NDA tool. This command line tool take three arguments: your BIDS dataset, GUID mapping file and the folder where NDA submission package will be stored.
- Submit the data using NDA Validation and Submission tool. If the BIDS2NDA tool worked correctly NDA Validator should not return any errors and you should be able to submit your dataset without problems.