The PSMD tool comprises the following:
  • PSMD shell script:
  • Custom skeleton mask: skeleton_mask.nii.gz
  • Sample dataset (2 subjects) to test the pipeline
In addition to the PSMD tool provided on this page, you will need:
  • Computer with Linux or Mac OS X.
    For Windows, a Linux virtual machine is needed, e.g. the NeuroDebian Virtual Machine.
  • An installation of the FMRIB Software Library (FSL):
    • The PSMD pipeline has been tested with FSL versions 5.0.6 and 5.0.9, but other FSL versions may also work. Go to FSL download page.
    • Be advised that the terms of the FSL license apply! The PSMD tool itself is neither part of nor affiliated with FSL.
  • Diffusion tensor imaging (DTI) data:
    • A DTI sequence with at least 20 diffusion directions and a b-value between 700 and 1200 is required. A resolution of 2 mm (isotropic) is best, but other geometries might also work.
    • The use of unprocessed data (in Nifti format) is recommended. The script will perform all pre-processing.
    • As an alternative, already processed fractional anisotropy (FA) and mean diffusivity (MD) can be used as input. However, this is not recommended, since correct pre-processing of data (especially brain extraction) is crucial. Therefore, we strongly recommend to let the script handle pre-processing!
    • DTI data should undergo quick visual inspection to exclude large artefacts. No further human intervention is required in subsequent steps.
From unprocessed DTI data:
./ -d DTI_data -b bvals -r bvecs -s skeleton_mask

DTI_data: Raw/unprocessed DTI data, Nifti format
bvals: Text file containing b-values (created during DICOM conversion)
bvecs: Text file containing diffusion vectors (created during DICOM conversion)
skeleton_mask: Custom skeleton mask provided with this script
From processed DTI data:
./ -f FA_image -m MD_image -s skeleton_mask

FA_image: The fractional anisotropy image, brain extracted, Nifti format
MD_image: The mean diffusivity image, brain extracted, Nifti format
skeleton_mask: Custom skeleton mask provided with this script
Additional options:
Type ./ -h for detailed usage information.
The following steps will be performed through the PSMD tool:
  • Pre-processing of DTI data (eddy current correction, brain extraction, tensor fitting). This step is skipped when using already processed data as input.
  • Skeletonization using the FA image and the FSL-TBSS pipeline with the standard FMRIB skeleton as target.
  • Projection of MD data onto the skeleton.
  • Masking of the skeleton in order to focus the analysis on the cerebral hemispheres and to exclude areas with frequent CSF contamination.
  • Histogram analysis with calculation of peak width.
  • The entire calculation will take approx. 12 minutes on a standard desktop computer
Data from two subjects (already pre-processed) are provided for testing the pipeline at your site.
The calculated PSMD should be 0.000267824 for Subject A and 0.000894987 for Subject B.
Please note: Slight deviations might occur depending on the platform and FSL version. The results presented were obtained with FSL 5.0.9 on Mac OS X.

Simply run:
./ -f subjectA_FA.nii.gz -m subjectA_MD.nii.gz -s skeleton_mask.nii.gz
./ -f subjectB_FA.nii.gz -m subjectB_MD.nii.gz -s skeleton_mask.nii.gz