Inputs

BIDS input directory

The BIDS (Brain Imaging Data Structure) input directory is a standardized way to organize and describe neuroimaging and behavioral data. The nf-pediatric pipeline expects the input data to be organized in the BIDS format. Good resources to convert your raw DICOMs files in a BIDS structure include dcm2bids and/or heudiconv. It is recommended that users validate their BIDS layout using the official bids-validator tool docker image or the web-based version.

Directory Structure

The most basic BIDS directory should have a similar structure (note that sessions folder are optional but recommended):

• Directorybids_directory

  • dataset_description.json
  • participants.tsv
  • Directorysub-01

    • Directoryses-01

      • Directoryanat

        • sub-01_ses-01_T1w.nii.gz
        • sub-01_ses-01_T1w.json
        • sub-01_ses-01_T2w.nii.gz
        • sub-01_ses-01_T2w.json
      • Directorydwi

        • sub-01_ses-01_dwi.nii.gz
        • sub-01_ses-01_dwi.json
        • sub-01_ses-01_dwi.bval
        • sub-01_ses-01_dwi.bvec
      • Directoryfmap

        • sub-01_ses-01_epi.nii.gz
        • sub-01_ses-01_epi.json

Required Files

• dataset_description.json: A JSON file describing the dataset.
• participants.tsv: A TSV file listing the participants and their metadata. nf-pediatric requires the participants’ age to be supplied within this file, using age as the column name. If not available, the pipeline will return an error at runtime.

Important!

The age can be specified using either post conceptual age (only recommended for infant data, for participants > 44 weeks post-conceptual age, users should supply age in years) or years. If multiple session are available for a single subject, each session needs to be entered in different rows.

participants.tsv example

participant_id	session_id	age
sub-test1	ses-baseline	42
sub-test1	ses-time1	4
sub-test2		8
…	…	…

Column separator

In order for nf-pediatric to properly read the participants.tsv file, columns need to be tab-separated. If the pipeline returns an error regarding age not being correctly entered, this should be the first validation step to take (e.g., ensure a single tab is separating each of your columns).

Mandatory files per subject:

• sub-<participant_id>/: A directory for each participant containing their data.
  • anat/: A directory containing anatomical MRI data (e.g., T1w, T2w). If both are available, the optimal one will be selected and both will be coregistered.
    • T1w is mandatory for participants >= 3 months old.
    • T2w is mandatory for participants < 3 months old (only for the segmentation profile, otherwise a T1w will also work).
  • dwi/: A directory containing diffusion-weighted imaging data (e.g., DWI, bval, bvec). Acquisition with both direction DWI data are also supported (e.g. AP/PA). Specify them according to the BIDS guidelines
  • fmap/: A directory containing field map data (optional but recommended for distortion correction).