README.md

metadata

tags:
  - neuroscience
  - connectomics
  - timeseries
  - matlab
  - functional-connectivity

PPMI Connectivity Graphs — HF Staging (Derivatives)

This dataset ships ready-to-use functional brain connectivity graphs derived from the PPMI cohort in a BIDS-ish derivatives layout. For each subject and parcellation, we include:

• ROI time-series (*_desc-timeseries_parc-<name>.mat)
• Pearson correlation connectivity matrix (*_desc-correlation_matrix_parc-<name>.mat)
• JSON sidecars with summary fields (nodes, measure, symmetric/weighted flags)

Contents

data/
parc-<schema>/
sub-<id>/
sub-<id>\_desc-timeseries\_parc-<schema>.mat
sub-<id>\_desc-correlation\_matrix\_parc-<schema>.mat
\*.json
manifests/
manifest.jsonl                # one JSON object per raw file (sha256, bytes, target\_rel)
participants.tsv
phenotype/                      # subject-level variables (if present)
metadata/
raw/                          # resources & summaries used to build the set
artifacts/                    # inventory, checks, B5 manifest & reports
provenance/                   # author notes, dataset summaries, exclusions

Quick start (Python)

from huggingface_hub import snapshot_download
from pathlib import Path
from scipy.io import loadmat

root = Path(snapshot_download(repo_id="<org>/<dataset>", repo_type="dataset", revision="<tag>"))
pid, parc = "sub-prodromal75492", "ward100"
ts = loadmat(root / f"data/parc-{parc}/{pid}/{pid}_desc-timeseries_parc-{parc}.mat")
cm = loadmat(root / f"data/parc-{parc}/{pid}/{pid}_desc-correlation_matrix_parc-{parc}.mat")

# common variable names (fallback-friendly)
X = next((ts.get(k) for k in ["features_timeseries","timeseries","X"] if k in ts), None)   # (nodes × time)
A = next((cm.get(k) for k in ["correlation_matrix","corr","A"] if k in cm), None)          # (nodes × nodes)
print("Timeseries:", None if X is None else X.shape, "  Connectivity:", None if A is None else A.shape)

Use with datasets (viewer‑ready, no scripts)

Note: modern datasets (>= 3.x) does not execute local Python dataset scripts. Use data_files= with Parquet/JSONL as shown below.

You can explore a tiny, fast preview split directly via the datasets library. The preview embeds a small 8×8 top‑left slice of the correlation matrix so the Hugging Face viewer renders rows/columns quickly. Paths to the full on‑disk arrays are included for downstream loading.

from datasets import load_dataset

# Root-level Viewer splits (recommended on the Hub):
#   train.parquet — tiny preview with embedded 8×8 matrices
#   validation.parquet — metadata-only dev slice

ds = load_dataset("pakkinlau/multi-modal-derived-brain-network", data_files="train.parquet", split="train")
row = ds[0]
print(row["parcellation"], row["subject"])      # e.g., 'AAL116', 'sub-control3351'
print(row["corr_shape"], row["ts_shape"])      # e.g., [116, 116], [116]
corr8 = row["correlation_matrix"]               # 8×8 nested list (for display)

# Light dev slice (metadata+paths only). Stream to avoid downloads in CI.
dev = load_dataset("pakkinlau/multi-modal-derived-brain-network", data_files="validation.parquet", split="train", streaming=True)
for ex in dev.take(3):
    _ = (ex["parcellation"], ex["subject"], ex["corr_path"])  # no embedded arrays

You can also use the manifest entrypoints under manifests/:

from datasets import load_dataset

preview = load_dataset("pakkinlau/multi-modal-derived-brain-network", data_files="manifests/preview.parquet", split="train")
dev = load_dataset("pakkinlau/multi-modal-derived-brain-network", data_files="manifests/dev.parquet", split="train", streaming=True)

To access the full arrays, load from the returned corr_path / ts_path using SciPy or mat73 with variable name fallbacks:

from pathlib import Path
from scipy.io import loadmat

root = Path(ds.cache_files[0]["filename"]).parents[2]  # dataset snapshot root (one way to locate)
row = ds[0]
cm = loadmat(root / row["corr_path"])                  # correlation matrix (.mat)
ts = loadmat(root / row["ts_path"])                    # timeseries (.mat)
A = next((cm.get(k) for k in ["correlation_matrix","corr","A"] if k in cm), None)
X = next((ts.get(k) for k in ["features_timeseries","timeseries","X"] if k in ts), None)

Preview vs. dev vs. full

• preview: tiny split meant for the HF viewer, includes 8×8 correlation_matrix as a nested list plus shapes and file paths (see manifests/preview.parquet).
• dev: small metadata‑only slice across 1–2 parcellations; yields parcellation, subject, shapes, and file paths (see manifests/dev.parquet).
• full arrays: kept in‑repo under data/ and referenced by the manifests; load them locally using the variable fallbacks above.

If you use our main analysis repo, you can also load pairs via its adapters (if installed):

from brain_graph.data import hf_pair  # provided by the main repo
# hf_pair(parcellation, subject, root=Path(...)) returns (timeseries, correlation) arrays
X, A = hf_pair("AAL116", "sub-control3351", root=Path("/path/to/local/snapshot"))

Parcellations

• AAL116 — 116 ROIs
• harvard48 — 48 ROIs
• kmeans100 — 100 ROIs
• schaefer100 — 100 ROIs
• ward100 — 100 ROIs

File layout

data/
  parc-<parc>/
    sub-<id>/
      <id>_desc-timeseries_parc-<parc>.mat
      <id>_desc-correlation_matrix_parc-<parc>.mat
      *.json   # sidecars
manifests/
  manifest.jsonl         # machine inventory (sha256, bytes, target_rel per file)
  preview.jsonl          # tiny viewer split (subject+paths+8x8)
  preview.parquet        # Parquet version (fast viewer)
  dev.jsonl              # optional light split (metadata+paths only)
  dev.parquet            # Parquet version (fast viewer)

Data files

• Root (used by the Viewer):
  • train.parquet — tiny viewer‑ready preview with embedded 8×8 correlation matrices
  • validation.parquet — dev metadata‑only slice (no embedded arrays)
• Manifests (secondary entrypoints):
  • manifests/preview.parquet — same content as train.parquet (if duplicated)
  • manifests/dev.parquet — same as validation.parquet (if duplicated)

Integrity & Checksums

Rows in the preview/dev manifests include *_sha256 and *_bytes for both corr_path and ts_path, derived from manifests/manifest.jsonl. You can verify a local copy by recomputing SHA‑256 and matching the values.

Example (verify a correlation .mat):

import hashlib
from pathlib import Path

def sha256(path: Path, buf=131072):
    h = hashlib.sha256()
    with open(path, 'rb') as f:
        while True:
            b = f.read(buf)
            if not b:
                break
            h.update(b)
    return h.hexdigest()

# compare with row['corr_sha256']

Scripts (optional)

• scripts/enrich_manifests.py: Enrich preview/dev JSONL with shapes (from sidecars), embedded 8×8 tiles (from preview/), and checksums (from manifests/manifest.jsonl).
• scripts/jsonl_to_parquet.py: Convert any JSONL to Parquet with a stable schema.
• scripts/scan_to_manifest.py: Scan data/ to produce a metadata-only JSONL (parcellation, subject, shapes, paths, checksums). Useful for making new dev slices.
• scripts/make_preview.py: Generate 8×8 correlation previews from .mat files for rows in a manifest. Requires SciPy or mat73 locally.

Cohort & Metadata

• participants.tsv (+ optional participants.json)
• phenotype/ (subject-level variables)
• metadata/raw/, metadata/artifacts/, metadata/provenance/ (provenance, inventories, checks)
• JSON sidecars colocated with .mat under data/
• Parquet mirrors (optional, if you add them later)

Integrity

• A machine manifest lives at manifests/manifest.jsonl (one JSON object per raw file) with SHA-256 and byte size.
• You can re-compute and verify locally if needed.

License

• Data (everything under data/, participants.tsv, phenotype/, and metadata tables): CC BY-NC-SA 4.0.
• Docs & examples (this README, helper scripts): Apache-2.0. See LICENSE for details.

How to cite

See CITATION.cff. Please also acknowledge PPMI and the original derivative providers.

Changelog

• v1.0.0 — Initial HF release: multi-schema connectivity with cohort tables & provenance.