Slicer Diffusion Tensor Image Analysis Along the Perivascular Space (DTI-ALPS)

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Welcome to the Slicer Diffusion Tensor Image Analysis Along the Perivascular Space (DTI-ALPS)!

This 3D Slicer extension was designed to assist users in processing Diffusion Tensor Imaging (DTI) for the DTI-ALPS index calculation.

Output examples

The Slicer DTI-ALPS extension is a simple way to collect the DTI-ALPS index using a GUI interface. The images below represents some examples:

DTI-ALPS example

DTI-ALPS index application in evaluating Neuromyelitis optica (NMO) patients

GUI example

DTI-ALPS index GUI that simplify the image parameters and methods calculation

Modules

DTI-ALPS

This module is able to calculate the DTI-ALPS index from a standard Diffusion-Tensor (DTI) MRI image. In this case, it is needed to use the tensorial image that was already reconstructed by other toolkit. For instance, the 3D Slicer DMRI Diffusion extension can assist you to collect the DTI image for this step.

How to use this tool

The DTI-ALPS calculation can be executed, at the moment, by two forms:

  1. Using the GUI interface
  2. Using the runDTIALPS.py command-line interface (CLI)

Using the GUI interface

For the GUI option, it only requires a DTI image (using the tensorial orientation space) and two ROIs defining the Projection and Association fibers location.

Using the MNI space orientation

If you does not have a set of Projection and Association ROIs, it can be used a standard ROIs by selecting the Advanced checkbox called Input is in MNI space (2 mm resolution). By using this set the DTI-ALPS module will load at runtime a set of ROIs adopting the MNI 2mm brain template. However, the input DTI image must be at the same MNI space.

DTI resample to MNI

A handy way to resample the input DTI image to MNI space can be done by using the 3D Slicer DMRI Diffusion extension that provide a normalization and resample method to use in DTI data. See more details at the 3D Slicer DMRI documentation.

Using the CLI script

If you want to execute the DTI-ALPS rapidly, it can be done by the Python script called: runDTIALPS.py that is installed with the Slicer DTI-ALPS extension.

Before execution the runDTIALPS script

Before executing the script, make sure where is the path location that was used in the Slicer DTI-ALPS extension installation. The runDTIALPS.py script is placed inside the extension folder.

Assuming that Slicer is installed on Linux/Mac machines:

./Slicer --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd

Assuming that Slicer is installed on Windows machines:

Slicer.exe --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py dti_volume.nrrd proj-label.nrrd assoc-label.nrrd

It is also able to execute the runDTIALPS.py with some options:

  1. --MNISpace: Informs whether the input DTI image is already in the MNI space (2 mm resolution). If yes, the input Proj/Assoc paths are changed for the standard MNI labels instead.

  2. --verbose: Show more details thoughout the processing.

When to use --MNISpace option

When the --MNISpace is used, there is no need to provide the Proj/Assoc labels because the standard MNI labels are applied instead

To see more details about the options given at the runDTIALPS.py script, one may call the help details by running:

Linux/Mac:

./Slicer --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py -h

Windows:

Slicer.exe --no-main-window --no-splash --python-script /path/to/module/runDTIALPS.py -h

Tutorials

We offer simple tutorials to guide you in using the Slicer DTI-ALPS Extension. See the following tutorials below:

  • How to Calculate the DTI-ALPS Index Using the Slicer-DTI-ALPS Extension: Load DTI directly

    • In this tutorial, we guide you step-by-step through using the Slicer-DTI-ALPS extension to calculate the DTI-ALPS index. This tool is designed for use with Slicer version 5.6 or above and provides an easy-to-use way to analyze diffusion tensor imaging (DTI) data.

      What you’ll learn in this tutorial:

      ✅ How to convert FSL NIfTI data into a Slicer-compatible DWI volume.

      ✅ How to generate DTI images from your DWI data.

      ✅ How to compute the DTI-ALPS index using the Slicer-DTI-ALPS extension.

    • Youtube

  • How to Calculate the DTI-ALPS Index Using the Slicer-DTI-ALPS Extension: Slicer DWI Sample

    • In this tutorial, we guide you step-by-step through using the Slicer-DTI-ALPS extension to calculate the DTI-ALPS index. This tool is designed for use with Slicer version 5.6 or above and provides an easy-to-use way to analyze diffusion tensor imaging (DTI) data.

      What you’ll learn in this tutorial:

      ✅ Using Slicer image samples to select a DWI volume.

      ✅ Creating ROI labels with the Slicer Segmentation tool.

      ✅ Generating DTI images from DWI data.

      ✅ Calculating the DTI-ALPS index using the Slicer-DTI-ALPS extension.

    • Youtube

Cite this tool

We hope that the DTI-ALPS can be helpful for your applications. If possible, recall to cite at least one of the following publications:

  • Senra Filho, A. C. da S.; Paschoal, A. M. "DTI-ALPS index as complementary information for Neuromyelitis Optica patients: a preliminary evaluation". ISMRM & ISMRT Annual Meeting (2025). Link

License

This project is under MIT license and following details are given at the LICENSE file in the project repository.