FM-APP Model Doc

Overview

FM-APP is a multi-stage framework for phenotype prediction via fMRI to sMRI knowledge transfer.

• Paper: He Z, Li W, Liu Y, et al. FM-APP, IEEE TMI, 2024, 44(10): 4010-4022
• Official code: https://github.com/ZhibinHe/FM-APP
• Primary input: fMRI ROI connectivity features
• Additional input: sMRI ROI structural features (required in Stage 2)
• Primary output: multi-phenotype prediction and zero-shot phenotype reconstruction

In NeuroClaw, this is model-level guidance. Upstream preparation should be delegated to:

• fmri-skill for fMRI preprocessing and ROI extraction
• smri-skill for structural ROI feature extraction
• hcpya-skill if HCP Young Adult download/orchestration is needed

Research use only.

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Quick Start (From git clone)

1) Clone repository

git clone https://github.com/ZhibinHe/FM-APP.git
cd FM-APP

2) Create environment and install dependencies

python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

If using GPU, install CUDA-compatible PyTorch and graph-related packages first.

3) Prepare required data

Before training, ensure these are ready:

• fMRI ROI/connectivity features from fmri-skill
• sMRI ROI structural features from smri-skill (for Stage 2)
• phenotype CSV files and text feature tensors in data/

4) Run staged pipeline

# Stage 0: data preparation (example scripts)
python 00-create-folder_hcp_4fmri.py
python 01-fetch_data_hcp_4fmri.py
python 02-process_data_hcp_4fmri.py

# Stage 1: fMRI model training
python 101-main_stage1_fmri_HCP.py

# Stage 2: fMRI-T1w alignment
python 102-main_stage2_fmri_t1w_HCP.py

# Stage 3: decoder and zero-shot inference
python 103-main_stage3_t1w_HCP.py

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Pipeline Definition

Stage	Script pattern	Purpose	Core output
Stage 0	00-*, 01-*, 02-*	Data folder setup, ROI connectivity extraction, HDF5 packaging	raw/*.h5, processed inputs
Stage 1	101-main_stage1_fmri_HCP.py	fMRI feature extraction and phenotype regression	model/stage1_*.pth, model/stage1_dataset_*.pt
Stage 2	102-main_stage2_fmri_t1w_HCP.py	fMRI-T1w feature alignment (Sinkhorn-RPM)	model/stage2_*.pth
Stage 3	103-main_stage3_t1w_HCP.py	masked decoder training and zero-shot phenotype inference	stage-3 checkpoints and inference outputs

Run order must be: Stage 0 -> Stage 1 -> Stage 2 -> Stage 3.

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Stage Inputs and Outputs

Stage 0 (Data Preparation)

Required inputs:

• subject lists and dataset files (HCP/HCPA)
• phenotype CSV files under data/
• pre-encoded text feature tensors (*.pt)

Main outputs:

• per-subject connectivity features (corr/pcorr)
• HDF5 packaged samples for model training

Stage 1 (fMRI Training)

Required inputs:

• Stage 0 packaged features
• phenotype text features

Main outputs:

• best checkpoint: model/stage1_fmri_best_*.pth
• stage1 feature package: model/stage1_dataset_*.pt

Stage 2 (fMRI-sMRI Alignment)

Required inputs:

• frozen Stage 1 model/features
• sMRI ROI features (e.g., 333x9 per subject)

Main outputs:

• best checkpoint: model/stage2_fmri_to_t1w_best_*.pth

Stage 3 (Decoder and Zero-shot)

Required inputs:

• Stage 1 fused features and regression weights
• masks / phenotype supervision setup

Main outputs:

• decoder checkpoints
• reconstructed masked phenotype representations

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Typical Configuration Notes

• Atlas: Gordon333 (333 ROIs)
• Stage 1 typical settings: Adam, lr=0.0005, batch size=8, long-epoch training
• Stage 2 includes Sinkhorn matching; runtime is usually higher than Stage 1
• Stage 3 supports zero-shot phenotype inference using masked reconstruction

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Recommended Directory Layout

FM-APP/
  data/
    HCP_train_phenotype.csv
    HCP_test_phenotype.csv
    HCP_all_phenotype.csv
    HCPA_train_phenotype.csv
    HCPA_test_phenotype.csv
    phenotype_text_feature_tr.pt
    phenotype_text_feature_te.pt
    HCPA_phenotype_text_feature_tr.pt
    HCPA_phenotype_text_feature_te.pt
  raw/
    *.h5
  model/
    stage1_*.pth
    stage2_*.pth
    stage1_dataset_*.pt
  net/
  imports/
  loss_function/
  util/
  requirements.txt

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NeuroClaw Delegation Rules

• fMRI preprocessing and ROI extraction: fmri-skill
• sMRI feature extraction: smri-skill
• HCP data orchestration: hcpya-skill (or hcpa-skill / hcpd-skill / hcpep-skill for other HCP variants)
• dependency management: dependency-planner + conda-env-manager
• command execution: claw-shell

No execution before explicit plan confirmation.

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Limitations and Notes

• CUDA-capable GPU is strongly recommended for training.
• Stage 2 depends on valid Stage 1 artifacts and sMRI features.
• Stage 3 depends on stage1_dataset_*.pt and proper masking setup.
• Keep train/val/test split strict to avoid leakage.
• Verify phenotype column counts and subject ID alignment before Stage 1.

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Reference

• He Z, Li W, Liu Y, et al. FM-APP: Foundation model for any phenotype prediction via fMRI to sMRI knowledge transfer. IEEE Transactions on Medical Imaging, 2024, 44(10): 4010-4022.
• Official repository: https://github.com/ZhibinHe/FM-APP
• NeuroSTORM HCP download scripts: https://github.com/CUHK-AIM-Group/NeuroSTORM/tree/main/scripts/dataset_download

Created At: 2026-03-28 20:03 HKT Last Updated At: 2026-03-28 20:03 HKT Author: chengwang96