PSMD (Peak width of Skeletonized Mean Diffusivity)

PSMD is a robust, fully-automated and easy-to-implement marker for cerebral small vessel disease based on diffusion tensor imaging, white matter tract skeletonization (as implemented in FSL-TBSS) and histogram analysis.

Caution

PSMD is NOT a medical device and for academic research use only. Do not use PSMD for diagnosis, prognosis, monitoring or any other clinical routine use. Any application in clinical routine is forbidden by law, e.g. by Medical Device Regulation article 5 in the EU.

Usage

As of version 1.9.0, the preferred way of using PSMD is a pre-built container image, which can be used with Docker, Apptainer, and compatible container platforms.

The usage is simple. For more detailed information on usage, including FAQ, please visit the PSMD Wiki.

Using Apptainer:

# 1. Pull the container image and save as .sif file 
apptainer build psmd.sif docker://ghcr.io/miac-research/psmd:latest

# See available command line options:
apptainer run psmd.sif -h

Using Docker:

# 1. Pull the container image into your local registry
docker pull ghcr.io/miac-research/psmd:latest
docker tag ghcr.io/miac-research/psmd:latest psmd:latest

# For advanced usage, see available command line options:
docker run --rm psmd:latest -h

Local installation (not recommended): Alternatively, you can download the PSMD script from the releases page and run it in your local environment with all requried dependencies installed.

Version history

Starting with version 1.6, all development is done in this GitHub repository. See the releases page for the version history and the packages page for available pre-built container images.

Note

For a new project, take the latest release. It is best practice to stick with one release version or – even better – the same container image throughout a project.

License

The PSMD script itself is published under the BSD 3-clause license. Please see the LICENSE file provided in this repository.

Important

Please note that an FSL license is required to run PSMD, regardless of whether you are using the container or a local installation.

Support

The PSMD project was initiated at the Institue for Stroke and Dementia Research (ISD), Munich, Germany, with funding support by the LMU FöFoLe program (grant 808), the Else Kröner-Fresenius-Stiftung (EKFS, grant 2014_A200), and the Vascular Dementia Research Foundation.

The ongoing development of PSMD is supported by Medical Image Analysis Center (MIAC AG), Basel, Switzerland.