BIDS — Brain Imaging Data Structure

BIDS is the community-standard way to organize, name, and describe neuroimaging datasets. It covers MRI/fMRI, EEG, MEG, iEEG, PET, DWI, NIRS, microscopy, motion capture, and MRS. BIDS compliance unlocks the full ecosystem: bids-validator, fMRIPrep, MRIQC, pybids, MNE-BIDS, and 100+ BIDS Apps. Over 1500 public datasets on OpenNeuro use it; 3000+ papers cite it.

---

When to invoke this skill

• User asks how to structure, organize, or convert neuroimaging data
• Dataset has BIDS-like structure and you need to navigate or validate it
• User is setting up a new study and needs to know what files/folders to create
• Running /data phase: inventory, validate, or convert to BIDS
• Running /data-preprocess: loading BIDS-organized data into MNE or nibabel
• Running /data-analyze: querying the dataset with pybids or MNE-BIDS
• User mentions bids-validator errors or compliance issues

---

BIDS hierarchy at a glance

dataset/
├── dataset_description.json   ← required
├── participants.tsv            ← required
├── participants.json           ← recommended
├── README                      ← recommended
├── CHANGES                     ← recommended
├── .bidsignore                 ← optional
├── sub-<label>/
│   ├── [ses-<label>/]          ← optional; omit if single session
│   │   ├── anat/               ← T1w, T2w, FLAIR, ...
│   │   ├── func/               ← BOLD fMRI + events
│   │   ├── dwi/                ← diffusion + bval/bvec
│   │   ├── fmap/               ← field maps
│   │   ├── eeg/                ← EEG + channels + coordsystem
│   │   ├── meg/                ← MEG + channels + coordsystem
│   │   ├── ieeg/               ← iEEG + electrodes + coordsystem
│   │   ├── pet/                ← PET + blood data
│   │   ├── perf/               ← perfusion (ASL)
│   │   ├── nirs/               ← fNIRS
│   │   ├── motion/             ← motion capture
│   │   ├── mrs/                ← MR spectroscopy
│   │   └── beh/                ← behavioral-only data
│   └── scans.tsv               ← optional; lists files + acq_time
├── sourcedata/                 ← raw/pre-BIDS originals (unvalidated)
├── derivatives/                ← pipeline outputs (fMRIPrep, MNE, etc.)
└── code/                       ← analysis scripts

---

Filename entity ordering

Entities appear in this exact order — wrong order fails validation:

sub-<label>  [ses-<label>]  [task-<label>]  [acq-<label>]  [ce-<label>]
[rec-<label>]  [dir-<label>]  [run-<index>]  [echo-<index>]  [flip-<index>]
[part-<label>]  [chunk-<index>]  _<suffix>.<extension>

Examples:

sub-01_T1w.nii.gz
sub-01_ses-01_task-rest_bold.nii.gz
sub-01_ses-01_task-faces_run-1_bold.nii.gz
sub-01_task-rest_acq-multiband_bold.json
sub-01_dir-AP_epi.nii.gz
sub-01_ses-01_task-rest_eeg.edf
sub-01_ses-01_task-auditory_meg.fif

Rules: alphanumeric + hyphens + underscores only; no spaces; each entity once per filename; case-sensitive; suffix always last before extension.

---

Required top-level files

dataset_description.json (required)

{
  "Name": "My Study",
  "BIDSVersion": "1.11.1",
  "DatasetType": "raw",
  "License": "CC-BY-4.0",
  "Authors": [{"name": "Jane Doe", "email": "jane@example.com"}],
  "Acknowledgements": "Funded by ...",
  "HowToAcknowledge": "Please cite: ...",
  "Funding": [{"Funder": "NIH", "Grant": "R01DA123456"}],
  "EthicsApprovals": [{"Name": "IRB", "Reference": "IRB00012345"}],
  "ReferencesAndLinks": ["https://doi.org/10.1038/..."]
}

For derivatives, add:

{
  "DatasetType": "derivative",
  "GeneratedBy": [{"Name": "fMRIPrep", "Version": "22.1.1",
                   "CodeURL": "https://github.com/nipreps/fmriprep"}],
  "SourceDatasets": [{"URL": "ds004157", "Version": "1.0.0"}]
}

participants.tsv (required)

participant_id  age sex group   handedness
sub-01  25  M   control R
sub-02  28  F   patient L

participants.json (recommended)

{
  "age": {"Description": "Age in years", "Units": "years"},
  "sex": {"Description": "Biological sex", "Levels": {"M": "male", "F": "female"}},
  "group": {"Description": "Group", "Levels": {"control": "Healthy control", "patient": "Patient"}}
}

---

Key metadata rules by modality

Modality	Required in JSON sidecar
func BOLD	TaskName, RepetitionTime
EEG	SamplingFrequency, PowerLineFrequency
MEG	SamplingFrequency
iEEG	SamplingFrequency, PowerLineFrequency
DWI	(needs .bval and .bvec files, not just JSON)
PET	Manufacturer, BodyPart, TracerName, InjectedRadioactivity

For full field lists → references/metadata.md

---

BIDS validation

# CLI (Node.js)
npm install -g bids-validator
bids-validator /path/to/dataset

# Web tool
# https://bids-standard.github.io/bids-validator/

# Python
pip install bids-validator
python -m bids_validator /path/to/dataset

Suppress known non-issues with .bidsignore:

*_physio.tsv.gz      # custom physio format
sourcedata/          # always excluded
tmp_*/               # temp folders

For validator error codes and fixes → references/tools.md

---

Loading BIDS in Python

from bids import BIDSLayout

layout = BIDSLayout('/path/to/dataset')
print(layout.get_subjects())          # ['01', '02', ...]
print(layout.get_tasks())             # ['rest', 'nback']

# Get all BOLD files
bold = layout.get(suffix='bold', extension='nii.gz', return_type='file')

# Get metadata
meta = layout.get_metadata('sub-01_task-rest_bold.nii.gz')
print(meta['RepetitionTime'])

For MNE-BIDS (EEG/MEG) → references/tools.md For pybids full API → references/tools.md For complete example datasets → references/examples.md

---

Derivatives

Preprocessed outputs live in derivatives/<pipeline>/: - Use space-MNI152NLin2009cAsym entity for normalized images - Use res-<label> for resampled resolution - derivatives/ needs its own dataset_description.json with DatasetType: derivative

Full derivatives structure → references/structure.md

---

BIDS in neuroflow phases

/data phase

1. Inventory the data directory — identify modalities, subjects, sessions
2. Validate with bids-validator or manual check against this skill
3. Convert if needed: raw → BIDS using mne_bids.write_raw_bids() (EEG/MEG) or dcm2niix + renaming (MRI)
4. Save data-inventory.md to .neuroflow/data/ noting BIDS compliance status

/data-preprocess phase

• Load BIDS data: BIDSLayout + layout.get() or mne_bids.read_raw_bids()
• Pull sidecar metadata: sampling rate, task name, events from events.tsv
• Save preprocessed outputs to derivatives/<pipeline>/ with correct dataset_description.json

/data-analyze phase

• Query dataset structure with pybids before loading data
• Match analysis design to BIDS metadata (task labels, run indices, subject groups from participants.tsv)
• Store analysis outputs in derivatives/analysis/ or project results/

---

Reference files in this skill

File	Contents
references/structure.md	Full folder hierarchy per modality, all required/optional files, entity table
references/metadata.md	JSON sidecar fields for MRI/EEG/MEG/iEEG/PET, events.tsv, scans.tsv
references/tools.md	bids-validator, pybids, MNE-BIDS, fMRIPrep, MRIQC — install + usage
references/examples.md	Complete example dataset trees + Python code snippets

Read the relevant reference file when you need: - All required/optional files for a specific modality → structure.md - Which JSON fields to put in a sidecar → metadata.md - How to use a specific BIDS tool → tools.md - A full working example to base conversion code on → examples.md

---

Quick troubleshooting

Symptom	Likely cause	Fix
Validator: "Not a valid BIDS filename"	Entity order wrong or unknown suffix	Check entity order (sub, ses, task, acq, run…); verify suffix against spec
Validator: "IntendedFor missing file"	JSON references non-existent image	Check path; must be relative from dataset root
Validator: "Missing required file"	dataset_description.json or participants.tsv absent	Create the file
Validator: "JSON_KEY_RECOMMENDED"	Sidecar missing recommended field	Add field or use .bidsignore for now
pybids: empty layout	Wrong root path or missing dataset_description.json	Check path; ensure root-level JSON exists
MNE-BIDS: wrong channel types	channels.tsv type column incorrect	Fix: EEG, EOG, ECG, EMG, STIM, MISC, etc.

For more validator error codes → references/tools.md