DCE-Utilities

This repository contains functionality for transforming dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) series, including:

1. Conversion of DCE MRI dicom series to NIfTI format.

2. Conversion of 3D DCE MRI in NIfTI format to 4D (spatial dims + time dim) DCE MRI in NIfTI format.

3. Calculation of DCE parameter maps using 4D DCE data^{1 2}: initial slope, maximum enhancement, time-to-maximum enhancement, and final slope.

If you use this repository, please cite the following publication:

Mehta, P., Antonelli, M., Ahmed, H.U., Emberton, M., Punwani, S., Ourselin, S. Computer-aided diagnosis of prostate cancer using multiparametric MRI and clinical features: A patient-level classification framework. Medical Image Analysis 2021, 73, 102153, doi:10.1016/j.media.2021.102153.

Installation instructions

1. Clone/download repository.

2. Change directory into repository.

3. Install:

   pip install .
   

How to use it

• Function imports.

• Command line:

  • Dicom to NIfTI format conversion:

     dce_dicom2nifti_convert --input_dir .\sample_data\0_sample_dce_dicom --output_dir .\sample_data\1_dce_nifti_3d
    

  • 3D to 4D:

     dce_nifti4d --input_dir .\sample_data\1_dce_nifti_3d --output_dir .\sample_data\2_dce_nifti_4d
    

  • Parameter maps:

     dce_parameter_maps --input_dir_or_path .\sample_data\2_dce_nifti_4d  --output_dir .\sample_data\3_dce_parameter_maps --temporal_resolution 3.5 --window_size 5 --onset_time_constraint 1 --final_slope_time 1 
    

References

¹ Zelhof, B.; Lowry, M.; Rodrigues, G.; Kraus, S.; Turnbull, L. Description of magnetic resonance imaging-derived enhancement variables in pathologically confirmed prostate cancer and normal peripheral zone regions. BJU International. 2009, 104, 621–627.

² Kubassova, O.A.; Boyle, R.D.; Radjenovic, A. Quantitative Analysis of Dynamic Contrast-Enhanced MRI Datasets of the Metacarpophalangeal Joints. Academic Radiology. 2007, 14, 1189–1200.