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Overview

DELTA-SVD is a containerised diffusion-MRI pipeline that turns preprocessed diffusion-weighted images into diffusion metrics designed for longitudinal tracking of change in cerebral small vessel disease (cSVD). It fits the diffusion (bi)-tensor, projects the resulting maps onto a white matter skeleton (TBSS-style), applies a custom mask and reports summary endpoints per timepoint and per region.

For a longitudinal run it builds a within-subject template so that the skeleton and the skeleton-derveid metrics are directly comparable across timepoints, rather than re-deriving them independently at each visit.

Pipeline at a glance

Preprocessed DWI (per timepoint) → tensor fit → white-matter skeleton projection → endpoints table + QC report

  • Input — one preprocessed 4D DWI per timepoint, with its gradient table and a brain mask.
  • Processing — diffusion-tensor fitting, then skeletonisation and masking; longitudinal runs first build a within-subject template so timepoints share one skeleton.
  • Output — a metrics table (delta-svd_results.csv) and an HTML quality-control report.

Typical input

Each timepoint is a preprocessed 4D DWI plus its b-values, b-vectors, and a DWI-space brain mask. DELTA-SVD does not preprocess the data itself. See Data requirements for acquisition guidance and the expected preprocessing.

Usage in a nutshell

DELTA-SVD runs as a container; you pass the pipeline's arguments after the image name:

apptainer run delta-svd.sif --dwi <image> --id <subject>

Pass a single DWI for a cross-sectional run, or several (one per timepoint) to trigger longitudinal processing. Full options, mask handling, and cross-subject aggregation are in Usage.

Outputs

  • delta-svd_results.csv — the metrics table, reporting three validated endpoints per timepoint and per region:
    • MSMD — mean skeletonised mean diffusivity; the recommended primary endpoint for most datasets.
    • PSMD — peak width of skeletonised mean diffusivity; an established marker of white-matter damage in cSVD.
    • MSFW — mean skeletonised free water.
  • delta-svd_qc.html — a quality-control report with the skeleton and masks overlaid on the data.

For guidance on which endpoint to report, see the FAQ; for the full output detail and QC levels, see Usage.