dl-task-contrast-prediction

Referenced Work

Soren J. Madsen, Young-Eun Lee, Lucina Q. Uddin, Jeannette A. Mumford, Deanna M. Barch, Damien A. Fair, Ian H. Gotlib, Russell A. Poldrack, Amy Kuceyeski, Manish Saggar. Predicting Task Activation Maps from Resting-State Functional Connectivity using Deep Learning [bioarXiv]

Overview

This project contains the source code for several models to be used in predicting task activation maps from resting-state fMRI data. BrainSurfCNN is a surface-based convolutional neural network implemented by Ngo et al., 2022 and published in NeuroImage. BrainSERF makes incremental changes to this model to include Squeeze-Excitation attention and modified activation functions. BrainSurfGCN uses a graph convolution approach instead of surface-based convolution.

Note: Much of the work in this code has been adapted from BrainSurfCNN which is adapted from UGSCNN.

1. data folder contains the surface mesh templates, medial-wall mask and subject IDs from the Human Connectome Project (HCP) S1200 used in our experiments.
2. model folder contains BrainSurfCNN, BrainSERF, and BrainSurfGCN source code.
3. preprocess folder contains functions needed for preprocessing the surface data.
4. utils folder contains utility functions to run the experiment and perform some portions post-hoc evaluation.
5. train folder contains training functions to train each stage of the model (MSE or fine-tuning) and save the model parameters.
6. test folder contains functions to test the trained models and save the predictions.
7. posthoc_analysis folder contains Jupyter notebooks for computing model metrics and creating figures used in the paper. Please note: in order to recreate figures, it may require some playing around with the plotting parameters especially for the figures that are plotted on brains.

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Getting Started

1. Set up your environment with the packages in requirements.txt in Python 3.9:

2. Download HCP Workbench https://www.humanconnectome.org/software/get-connectome-workbench for data preprocessing.

3. Download HCP S1200 and HCP Retest dataset https://db.humanconnectome.org/, which are used in our experiments.

4. HCP1200 Parcellation+Timeseries+Netmats (PTN) https://db.humanconnectome.org/data/projects/HCP_1200 data are also needed for computing the resting-state fingerprints.

5. Run data preprocessing with the scripts under preprocess folder.

6. Run training and prediction with the scripts under the train and predict folders. Note: each script is designed to work with one type of model rather than that being an input argument.

Example Usage:

PROJECT_DIR=/home/users/sjmadsen/dl-task-contrast-prediction

NUM_ICS=100
NUM_SAMPLES=8
NUM_VAL_SUBJ=5

RSFC_DIR=/path/to/rsfc_data
CONTRASTS_DIR=/path/to/joint_contrasts
SUBJ_LIST_FILE=/path/to/HCP_train_val_subj_ids.csv
MESH_TEMPLATES_DIR=/path/to/fs_LR_mesh_templates
MESH_PATH=$MESH_TEMPLATES_DIR/icosphere_2.pkl
OUTPUTS_DIR=/where/to/store/the/model.pth

python3 -u train_gnn.py \
       --gpus 0 \
       --ver gnn_mse_larger \
       --n_samples_per_subj $NUM_SAMPLES\
       --loss mse \
       --subj_list $SUBJ_LIST_FILE \
       --rsfc_dir $RSFC_DIR \
       --contrast_dir $CONTRASTS_DIR \
       --mesh_dir $MESH_PATH \
       --save_dir $OUTPUTS_DIR \
       --n_val_subj $NUM_VAL_SUBJ \
       --n_channels_per_hemi $NUM_ICS

Note: BrainSurfGCN's --mesh_dir argument requires a path to the icosphere_2.pkl file whereas BrainSurfCNN and BrainSERF require the entire directory of fs_LR_mesh_templates/ for the model parameters.

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Having Issues?

Email Soren Madsen at soren dot j dot madsen at gmail dot com.