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PSMD Download

Disclaimer and License

The script and accompanying data are provided under the revised BSD (3-clause) license (for details see license file in the download package). The use of the script and/or data needs to be acknowledged through proper citation (see below).


For the PSMD pipeline, cite the main PSMD paper:

Baykara E, Gesierich B, Adam R, Tuladhar AM, Biesbroek JM, Koek HL, Ropele S, Jouvent E, Alzheimer's Disease Neuroimaging Initiative (ADNI), Chabriat H, Ertl-Wagner B, Ewers M, Schmidt R, de Leeuw FE, Biessels GJ, Dichgans M, Duering M. A novel imaging marker for small vessel disease based on skeletonization of white matter tracts and diffusion histograms. Annals of Neurology 2016 80(4):581-92 DOI:10.1002/ana.24758

For FSL-TBSS: Follow the guidelines provided at the TBSS page!

Example text for the methods section:

Peak width of skeletonized mean diffusivity (PSMD) was calculated with the PSMD tool provided at [PSMD citation]. The calculation comprises two steps: Skeletonization of DTI data and histogram analysis. First, DTI data were skeletonized using the Tract-Based Spatial Statistics procedure (TBSS), part of the Functional Magnetic Resonance Imaging of the Brain (FMRIB) Software Library (FSL) [FSL citations] and the FMRIB 1mm FA template (thresholded at an FA value of 0.2). MD images were projected onto the skeleton, using the FA derived projection parameters. In order to avoid contamination of the skeleton through CSF partial volume effects, the MD skeletons were further masked with a standard skeleton thresholded at an FA value of 0.3 and a custom mask provided with the PSMD tool in order to exclude regions adjacent to the ventricles, such as the fornix. Finally, PSMD was calculated as the difference between the 95th and 5th percentiles of the MD voxel values within the skeleton.


PSMD is available through its development repository at GitHub. To download a specific version, please head directly to the Releases page of the repository.


Please read the license file in the download package! Please note that PSMD is not a medical device and for research use only. Any clinical use is forbidden.


Last update: 2021-03-12