A Modality-agnostic Multi-task Foundation Model for Human Brain Imaging

Peirong Liu^1,2, Oula Puonti², Xiaoling Hu², Karthik Gopinath², Annabel Sorby-Adams², Daniel C. Alexander³, Juan Eugenio Iglesias^2,3,4

¹Johns Hopkins University
²Harvard Medical School and Massachusetts General Hospital
³University College London
⁴Massachusetts Institute of Technology

This is the official repository for our preprint: A Modality-agnostic Multi-task Foundation Model for Human Brain Imaging [arXiv]
More detailed and organized instructions are coming soon...

Environment

Training and evaluation environment: Python 3.11.4, PyTorch 2.0.1, CUDA 12.2. Run the following command to install required packages.

conda create -n pre python=3.11
conda activate pre

git clone https://github.com/jhuldr/BrainFM
cd /path/to/brainfm
pip install -r requirements.txt 

Downloads

The pre-trained model weight is available on OneDrive. After downloading, please put them under ckp/.

Demo

cd scripts 
python demo_test.py

Generator

cd scripts 
python demo_generator.py

Generator setups

Setups are in cfgs/generator, default setups are in default.yaml. A customized setup example can be found in train/brain_id.yaml, where several Brain-ID-specific setups are added. During Config reading/implementation, customized yaml will overwrite default.yaml if they have the same keys.

dataset_setups: information for all datasets, in Generator/constants.py
augmentation_funcs: augmentation functions and steps, in Generator/constants.py
processing_funcs: image processing functions for each modality/task, in Generator/constants.py

dataset_names: dataset name list, paths setups in Generator/constants.py
mix_synth_prob: if the input mode is synthesizing, then probability for blending synth with real images
dataset_option: generator types, could be BaseGen or customized generator
task: switch on/off individual training tasks

Base generator module

cd Generator
python datasets.py

The dataset paths setups are in constants.py. In datasets.py, different datasets been used are fomulated as a list of dataset names.

A customized data generator module example can be found in datasets.py -- BrainIDGen.

Refer to "getitem" function. Specifically, it includes:
(1) read original input: could be either generation labels or real images;
(2) generate augmentation setups and deformation fields;
(3) read target(s) according to the assigned tasks -- here I seperate the processing functions for each item/modality, in case we want different processing steps for them;
(4) augment input sample: either synthesized or real image input.

(Some of the functions are leaved blank for now.)

Trainer

cd scripts 
python train.py

Citation

@article{Liu_2025_BrainFM,
    author    = {Liu, Peirong and Puonti, Oula and Hu, Xiaoling and Gopinath, Karthik and Sorby-Adams, Annabel and Alexander, Daniel C. and Iglesias, Juan E.},
    title     = {A Modality-agnostic Multi-task Foundation Model for Human Brain Imaging},
    booktitle = {arXiv preprint arXiv:2509.00549},
    year      = {2025},
}