This column lists the core metadata files and imaging modality folders defined by the BIDS standard. In the screenshot above, the items listed below do not have ‘toggles’ but rather check boxes:

• participants.tsv (Tabular)
  Lists all participants along with optional metadata such as sex, handedness, and age.

• dataset_description.json (JSON)
  Required in every BIDS dataset. Contains critical metadata: study name, version, authors, funding sources, and references.

• sessions.tsv (Tabular)
  Provides session-level information for multi-session studies, including visit labels, dates, and site locations.

• scans.tsv (Tabular)
  Includes file-specific metadata for each imaging scan—e.g., acquisition time and run number.

• beh/ (Directory)
  Stores behavioral task outputs such as events and response data, typically linked to fMRI tasks.

These metadata files serve as the scaffolding for navigating and parsing the BIDS directory structure. They are essential for aligning sessions with scan files and associating imaging data with subject metadata.

Raw Imaging Modalities (Toggles)

Below the files, you see a list of toggle switches labeled:

• anat (anatomical)

• beh (behavioral)

• dwi (diffusion)

• fmap (field maps)

• func (functional MRI)

• mrs (magnetic resonance spectroscopy)

What happens when you toggle these on?

Each toggle enables viewing and selecting corresponding imaging folders under the BIDS /sub-<ID>/ses-<ID>/ hierarchy:

• Anatomical Data (/anat/)‍

• Includes: T1w, T2w, rec-NORM, rec-NORMALIZED, acq-MPRAGE, acq-SPGR, acq-NORM

• Diffusion Data (/dwi/)

• Includes: dwi, dir-AP, dir-PA, acq-64dirPA, acq-64dirAP

• Functional Data (/func/)

• Includes: task-FEED, task-REST, _events.tsv, _physio.json

• Field Maps (/fmap/)

• Includes: acq-FUNC, dir-PA, dir-AP, _epi.nii.gz

• Behavioral Data (/beh/)

• Includes: blocklog.tsv, events.tsv, tap.tsv, tap.json

• MRS Data (/mrs/)

• Includes: HERCULES_SHORTTE, sub-*/mrs/HERCULES_SHORTTE

Each scan has associated.nii.gz files and .json sidecars for acquisition metadata.

This directory contains derived neuroimaging and behavioral data outputs generated through standardized and study-specific preprocessing pipelines. These derivatives serve as precomputed resources for analysis, quality control, and visualization. Some folders follow the BIDS Derivatives specification, while others use internally defined conventions.

Folder Structure

Each derivative folder is organized by participant (sub-<ID>) and session (ses-<ID>), and may contain:

• Processed NIfTI images

• Surface reconstructions

• Confound regressors

• Motion parameters

• Quality metrics

• Tabular summaries

• JSON metadata (dataset_description.json)

Included Pipelines

ABCD Derivatives

• freesurfer/
  Performs cortical surface reconstruction and volumetric segmentation.
  Includes subfolders like surf, mri, label, stats, etc.

• mmps_mproc/
  ABCD-specific pipeline for structural, diffusion, and functional data preprocessing.

• dataset_description.json
  Contains metadata for each pipeline output, adhering to BIDS-derivative guidelines.

HBCD Pipelines

• freesurfer/
  Standard surface-based morphometry.

• qsiprep/, qsirecon/
  Handles diffusion MRI preprocessing and reconstruction using models from DIPY, DSI Studio, and TORTOISE.

• xcp_d/
  Post-fMRIPrep BOLD timeseries processing including nuisance regression and filtering.

• mriqc/
  Automates image quality metrics generation.

• qmriqpostproc/, symri/
  Supports quantitative MRI postprocessing.

• osprey/, nibabies/, mcribs/
  Provides pipelines for infant-optimized processing and spectroscopy.

• hbcd_motion/, madel/, bibsnet/
  Includes motion quantification and infant segmentation tools.

• qsigc_*, qsirecon-*, TORTOISE_*
  Specialized pipelines for dMRI modeling and reconstructions.

• dataset_description.json
  Present in top-level derivative folders for documentation purposes.

Metadata Files

Each pipeline directory typically includes:

• dataset_description.json: Describes the derivative dataset origin and tool versions

• *.tsv: Tabular summaries or metrics per participant/region

• *.json: Metadata describing acquisition, processing parameters, or QC outcomes

Notes and Best Practices

• Not all derivative folders are fully BIDS-compliant; check the dataset_description.json for versioning and schema.

• Some outputs may include additional quality-control images, masks, or intermediate files not suitable for direct statistical analysis.

• When using derived data in publications, cite the appropriate software (e.g., FreeSurfer, FMRIPrep, QSIPrep) and study Date Use Certification (DUC) guidelines.

This section lists additional source-level metadata not embedded in the raw folders. These help with study-level quality control or linking files to scan procedures.

Examples:

• fasttrack_mri_qc.csv
  Captures imaging quality control flags and metrics across sessions.

• scans.tsv / scans.json
  Documents the scans that were executed, including timing information and file-level annotations.

• sessions.tsv / sessions.json
  Provides details about study visits, such as scanning site, scanner used, and visit date.

• dataset_description.json
  Reiterated here for clarity—offers an overview of the entire study including its structure and metadata.