on003380
NEMAR copy of ds003380

Corticothalamic communication under analgesia, sedation and gradual ischemia: a multimodal model of controlled gradual cerebral ischemia in pig

A multimodal neuroimaging dataset from 11 juvenile pigs examining corticothalamic communication under varying pharmacological states and controlled cerebral ischemia. Animals were monitored through sequential sedation protocols (isoflurane, fentanyl, propofol), followed by gradual ischemia episodes and recovery phases. The dataset includes both sedation-only controls and ischemia-with-recovery experimental groups, providing insights into brain function under anesthesia and ischemic stress.

EEG
Issues GitHub OpenNeuro ds003380

Download this dataset

Pick a method. Large datasets skip the zip and use the streaming methods below — all resumable. Full download guide →

  1. Download archive (.zip) — 1.5 GB

    A single zip of the published version. Best for small/medium datasets.

    Download zip

  2. NEMAR CLI recommended

    Pulls the pinned version + annexed data and resumes cleanly. Install nemar-cli → 

    nemar dataset download on003380
  3. DataLad

    Clone the dataset repo and fetch file content on demand. Docs → 

    datalad clone https://github.com/nemarDatasets/on003380 on003380
cd on003380 && datalad get .
  4. git-annex

    Plain git + git-annex against the dataset repo. Docs → 

    git clone https://github.com/nemarDatasets/on003380 on003380
cd on003380 && git annex get .
  5. Direct files (wget / curl / rclone)

    Every file with a stable, range-resumable URL from the manifest. Needs curl, jq, wget (or rclone/aria2c). Docs → 

    curl -s https://data.nemar.org/on003380/v1.0.0/manifest.json | jq -r '.[].bytes_url' > urls.txt
wget -xc -i urls.txt

Compute on this dataset

Two routes today, with a third (in-browser one-click submission) landing soon.

  1. NeuroScience Gateway (NSG) portal.

    NSG runs EEGLAB / Brainstorm / MNE pipelines on supercomputing time donated by SDSC. Create an account, point a job at this dataset's S3 prefix (s3://nemar/on003380), and submit.
    nsgportal.org →

  2. Local processing with nemar-cli.

    Pull the dataset to your machine and run any toolbox locally. Honors the published version pinning. 

    npm install -g nemar-cli
nemar dataset clone on003380
cd on003380 && nemar dataset get
  3. Just the files.

    rclone, aria2c, or any HTTPS client works against data.nemar.org/on003380/ — the manifest carries presigned S3 URLs.

Direct compute access is coming soon. One-click NSG submission from this page is scoped for a follow-up phase. Tracked on nemarOrg/website#6.

Citations

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    Files

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    Signal viewer
    How to use the data (for agentic research) license, citation, download commands, Zarr access

    What it is

    Modalities
    EEG
    Participants
    12
    Size
    1.43 GB

    License and terms

    License
    CC0
    Recommended citation
    Frasch, M. G., Walter, B., Herry, C. L., & Bauer, R. (2026). Corticothalamic communication under analgesia, sedation and gradual ischemia: a multimodal model of controlled gradual cerebral ischemia in pig (Version v1.0.0) [Data set]. NEMAR. https://doi.org/10.82901/nemar.on003380

    Where the bytes are

    Latest version (always current)
    https://data.nemar.org/on003380/latest/
    This version (v1.0.0)
    https://data.nemar.org/on003380/v1.0.0/

    How to download

    The dataset
    nemar dataset download on003380 Clones and fetches in one step. Content under stimuli/ and derivatives/ is skipped by default because those trees can be large; add --stimuli --derivatives for the whole thing.
    A subset, one step
    nemar dataset download on003380 --subjects sub-01,02 Also filters by --sessions, --tasks, --runs, --datatypes, --include and --exclude.
    A subset, step 1
    nemar dataset clone on003380 Clones git-annex pointers only; fetches no file content. Creates ./on003380.
    A subset, step 2
    cd on003380 The get command below reads the clone's annex, so it only works from inside the clone.
    A subset, step 3
    nemar dataset get <files> Pulls the files you actually need. Skips stimuli/ and derivatives/ unless the path you ask for is under one of them.
    One small file
    https://data.nemar.org/on003380/v1.0.0/participants.tsv A direct HTTPS fetch works for any single file.

    Assess fit without downloading

    Participants table
    https://data.nemar.org/on003380/v1.0.0/participants.tsv
    Dataset description
    https://data.nemar.org/on003380/v1.0.0/dataset_description.json
    Directory listing
    https://data.nemar.org/on003380/v1.0.0/?format=json
    Catalog record
    https://api.nemar.org/datasets/on003380

    Working with the Zarr copy

    1. Start at the index
    https://zarr.nemar.org/on003380/zarr/index.json The mandatory entry point. Never hardcode a bucket path.
    2. Pick a store entry
    stores[].zarr, stores[].groups[].name These two fields exist in every index format version, so a recipe that keys on them works against the whole catalog while the back conversion is still in flight.
    3. Build the store URI
    s3://nemar/on003380/zarr/{store.zarr} Derivable from the store entry alone. An index at format_version 3 or later also publishes contract_base, data_base and s3_uri; use them when they are there, never require them.
    4. Open the store anonymously
    zarr.open_group(store=..., mode="r", zarr_format=3) Anonymous FsspecStore.from_url in region us-east-2, no credentials. zarr_format=3 is required: without it zarr-python probes for Zarr v2 sidecars, and because anonymous ListBucket is denied, S3 answers a missing key with 403 rather than 404 and the open raises.
    5. Read the level-0 array
    root[store.groups[0].name]["0"] Level 0 is the full-rate signal. Never read a view/ array for inference; those exist for display.
    6. Dequantize the samples
    physical = digital * scale + offset scale and offset are attributes of the level-0 array, one entry per channel; the unit is on the group's channels attribute.
    7. Slice, don't download
    signal[0:4, 0:500] Stream a window of channels and samples; download only when you will touch most of the array.
    8. Know the HTTP contract
    index.json Only index.json is always proxied and edge-cached. A plain GET for a store object, manifest.json or events.parquet 302s to the public S3 object for non-browser clients, so follow redirects, and HEAD is never redirected.
    9. Read the attribution before reuse
    root.attrs["nemar"] The store carries its own dataset id, DOI, license, citation and source commit.
    10. Filter for pipelines
    has_zarr=1 This is the converted filter. has_zarr_verified is the stricter one, and its result set can be empty until the daily fidelity sweep reaches a dataset; verification is reported, never a precondition for serving (nemar-cli ADR 0005).