Brainmarks

Brainmarks is an open evaluation suite for fMRI foundation models.

Installation

pip install brainmarks
# or
uv add brainmarks

Model wrappers for third-party encoders are optional extras:

pip install "brainmarks[brain-jepa,brainlm,swift,brainharmonix,brain-semantoks,neurostorm]"

To install the latest development version from GitHub:

pip install "brainmarks @ git+https://github.com/MedARC-AI/brainmarks"

From source:

git clone https://github.com/MedARC-AI/brainmarks
cd brainmarks
uv sync --python 3.11

Usage

Brainmarks has two main evaluation modes.

Probe — trains a frozen-backbone classifier head (linear, attention, or MLP):

python -m brainmarks.main_probe <model> <representation> <classifier> <dataset>
# e.g.
python -m brainmarks.main_probe brainlm_vitmae_111m patch attn nsd_cococlip

Logistic — extracts embeddings once and fits a logistic regression:

python -m brainmarks.main_logistic <model> <representation> <dataset>
# e.g.
python -m brainmarks.main_logistic brainlm_vitmae_111m patch aabc_sex

representation selects which embedding type the model exposes to the head: cls, reg (registers), or patch. Pass --help to either command to see the full list of available models and datasets. Use --config to pass a YAML config file and --overrides key=value for per-run overrides.

# e.g.
python -m brainmarks.main_logistic \
  brainlm_vitmae_111m \
  patch \
  aabc_sex \
  --overrides \
  batch_size=16 \
  num_workers=4 \
  device=cpu

All available options are documented in the default configs: default_probe.yaml, default_logistic.yaml.

Datasets

Benchmark datasets are distributed in Huggingface Arrow format hosted in the MedARC R2 bucket. To request access, fill out this form.

Once you have credentials, configure them as environment variables:

export AWS_ACCESS_KEY_ID=...
export AWS_SECRET_ACCESS_KEY=...
export AWS_ENDPOINT_URL_S3=...   # Cloudflare R2 endpoint

Datasets are downloaded automatically on first use and saved in the Huggingface dataset cache.

Adding a model

Brainmarks uses namespace package plugin discovery. To add a model from your own repo without modifying this one:

0. Install brainmarks as a dependency in your project environment.

1. Create a brainmarks namespace package in your repo:

   mkdir -p my_repo/src/brainmarks/models

2. Copy src/brainmarks/models/template.py as a starting point and implement ModelWrapper, ModelTransform, and a @register_model constructor.

3. Validate with the smoke test:

   python -m brainmarks.models.test_models my_model

See template.py for more details.

Adding a dataset

Adding a dataset involves two parts: curation scripts that preprocess raw data into Arrow shards, and a loader module that registers the dataset with Brainmarks.

Curation scripts live in datasets/, one subdirectory per source dataset. See datasets/HCP-YA/ for a reference example — it contains metadata, preprocessing scripts, and a README describing the raw data layout and curation steps.

Loader modules live in src/brainmarks/datasets/. Each module defines one or more functions decorated with @register_dataset that load Arrow shards (local or from S3) into an HFDataset. See src/brainmarks/datasets/hcpya.py as a reference.

Dataset loader modules are discovered via the same namespace package plugin mechanism as models, so they can live in an external repo.

Support

For help with any issues, reach out to us on MedARC Discord in the #neuro-fm channel.

Citation

@article{lane2025scaling,
  title   = {Scaling Vision Transformers for Functional {MRI} with Flat Maps},
  author  = {Lane, Connor and Tripathy, Mihir and Murali, Leema Krishna and
             Grandhi, Ratna Sagari and Yang, Shamus Sim Zi and Gijsen, Sam and
             Das, Debojyoti and Ram, Manish and Singh, Utkarsh Kumar and
             Villanueva, Cesar Kadir Torrico and Wei, Yuxiang and Beddow, Will and
             Cort\'{e}s, Gianfranco and Cho, Suin and Kaplan, Daniel Z. and
             Warner, Benjamin and Abraham, Tanishq Mathew and Scotti, Paul S.},
  journal = {arXiv preprint arXiv:2510.13768},
  year    = {2025},
  url     = {https://arxiv.org/abs/2510.13768}
}