VoxelDesk

VoxelDesk is a library of Python tools, designed to work with magnetic resonance imaging (MRI) data. It is aimed at users who provide image processing in a clinical setting. Some of its key features are listed below:

• Functionality for organizing DICOM files across multiple patients, studies, series, etc.

• DICOM anonymization tools

• Conversion between DICOM and NIFTI file formats

• Streamlined pre-processing of raw diffusion-weighted MRI data, to facilitate tractography.

VoxelDesk utilizes a number of third-party applications and open-source code, which we would like to acknowledge below:

• The dicomsort project

• Chris Roden’s dcm2niix

• Oxford FMRIB Software Library FSL

• MRtrix3

• The pydicom python tools

• The deid anonymization tools

Warning

VoxelDesk software is not classified as a medical device, and is issued with no guarantees or warranty. It is intended for research purposes only.

Table of Contents

Installation

• Installing the dependencies
• Installing voxelDesk
• Creating the conda virtual environment
• Setting the environment variables and file permissions

Configuration

• Setting the configuration parameters

DICOM Sorting and NIFTI Conversion

• vxdSort.py

DICOM Tools

• vxd_make_dicom.py
• vxd_summarize_dcminfo.py

NIFTI Tools

• vxd_make_nii_rgb.py
• vxd_make_nii_rgb_fusion.py
• vxd_tidy.py

Diffusion Pre-Processing

• vxd_diff_preproc.py