src/BrainIAC/timetostroke/README.md

Time to Stroke Prediction

Overview

We present the time to stroke prediction training and inference code for BrainIAC as a downstream task. The pipeline is trained and infered on T1 scans, with MAE as evaluation metric.

Data Requirements

• Input: T1-weighted MR scans
• Format: NIFTI (.nii.gz)
• Preprocessing: Bias field corrected, registered to standard space, skull stripped, histogram normalized (optional)
• CSV Structure:

  pat_id,scandate,label
  subject001,20240101,10    # time since stroke onset in days
  

refer to quickstart.ipynb to find how to preprocess data and generate csv file.

Setup

1. Configuration: change the config.yml file accordingly.

   # config.yml
   data:
     train_csv: "path/to/train.csv"
     val_csv: "path/to/val.csv"
     test_csv: "path/to/test.csv"
     root_dir: "../data/sample/processed"
     collate: 1  # single input seququece 
    
   checkpoints: "./checkpoints/stroke_model.00"     # for inference/testing 
   
   train:
    finetune: 'yes'      # yes to finetune the entire model 
    freeze: 'no'         # yes to freeze the resnet backbone 
    weights: ./checkpoints/brainiac.ckpt  # path to brainiac weights
   

2. Training:

   python -m timetostroke.train_stroke
   

3. Inference:

   python -m timetostroke.infer_stroke