PSMD version 1.5 (Update 2019) - What`s new?

In 2019 the PSMD tool was refined. The currently available download contains these refinements (along with the original PSMD from 2016).

New in version 1.5:

  • A refined skeleton mask (skeleton_mask_2019.nii.gz) to further improve the exclusion of areas prone to CSF contamination.
  • An additional, enhanced masking method (option -e). Intended to further improve the exclusion of problematic areas, i.e. areas with CSF contamination as well as hyperintense regions on DWI raw images (e.g. susceptibility artefacts and acute infarcts).
    There are two drawbacks when using this option: It only works when using unprocessed data as input and processing time is longer (approx. doubled).
  • The possibility to include your own lesion mask to exclude brain areas from analysis, e.g. large haemorrhages. A mask in DTI space needs to be supplied by the user (option -l mask) .
  • The possibility to output mean skeletonized mean diffusivity (MSMD) instead of PSMD (option -o). MSMD might provide more stable results in certain scenarios.
  • New naming scheme for temporary files for a better overview during troubleshooting.
  • Minor code improvements for better compatibility.

For small changes (e.g. bug fixes), please see the minor version history.


Mostly the same prerequisites as for version 1.0 apply. Please see the corresponding page. However, PSMD v 1.5 needs FSL version 6.0 and higher for some functions. If you get an error message when using an older FSL version, please consider testing FSL 6.0 or newer.


Pipeline for unprocessed DTI data:

./ [options] -d DTI_data -b bvals -r bvecs -s skeleton_mask_file

Mandatory arguments:
-d DTI_data: Raw/unprocessed DTI data, Nifti format
-b bvals: Text file containing b-values (in FSL format)
-r bvecs: Text file containing diffusion vectors (in FSL format)
-s skeleton_mask_file: Skeleton mask file, skeleton_mask_2019.nii.gz is recommended

Optional arguments:
-e b-value NEW IN VERSION 1.5: Enhanced masking of CSF and hyperintense voxels (infarcts, artefacts). Please specify the b-value of the diffusion shell used to determine the hyperintense areas (typically 1000). Only possible from unprocessed DWI data.

Pipeline for pre-processed DTI data (tensor scalar images):

./ [options] -f FA_image -m MD_image -s skeleton_mask_file

Mandatory arguments:
-f FA_image: The fractional anisotropy image, brain extracted, Nifti format
-m MD_image: The mean diffusivity image, brain extracted, Nifti format
skeleton_mask_file: Skeleton mask file, skeleton_mask_2019.nii.gz is recommended

Additional, optional arguments for both pipelines:

-o NEW IN VERSION 1.5: Output MSMD (mean skeletonized mean diffusivity) instead of PSMD
-l lesion_mask_file_ NEW IN VERSION 1.5: Custom lesion mask image (to be supplied by the user) to exclude regions from analysis
-c: Clear temporary psmdtemp folder from previous run (if present)
-q: Quiet operation No status messages are displayed, only result (either PSMD or MSMS, when using -o). E.g. useful when writing output to file
-v: Verbose operation with very detailed status and error messages
-t: Temporary files (folder psmdtemp) will not be deleted (for troubleshooting)

Type ./ -h for detailed usage information.

Minor version history

v 1.5.1 (2020-02)

  • Fixed a bug related to the parsing of options
  • Added a check for FSL version 6 when required


Last update: 2020-01-31