CLI Overview¶

csttool is invoked as a single binary with a family of subcommands. Each subcommand corresponds to one stage of the corticospinal-tract analysis pipeline (or to orchestration of all stages). The entry point is defined in src/csttool/cli/__init__.py and dispatched via argparse.

csttool <command> [options]
csttool <command> --help

Commands at a glance¶

The commands fall into four functional groups.

Environment & data preparation¶

Command	Purpose
`check`	Verify the Python environment and required dependencies.
`check-dataset`	Assess DWI acquisition quality and recommend processing options.
`fetch-data`	Download FSL-licensed atlases (FMRIB58_FA, Harvard-Oxford).
`import`	Convert DICOM to NIfTI or validate an existing NIfTI dataset.

Processing stages¶

Command	Purpose
`preprocess`	Denoise, unring, motion-correct and brain-mask the DWI series.
`track`	Whole-brain deterministic tractography with the CSA-ODF model.
`extract`	Atlas-based ROI filtering to isolate the bilateral CST.
`metrics`	Compute scalar metrics, tract profiles and a PDF/HTML report.
`validate`	Compare extracted bundles against reference tractograms.

Orchestration¶

Command	Purpose
`run`	Execute the full pipeline (check → import → preprocess → track → extract → metrics) for one subject.
`batch`	Run the pipeline over many subjects via manifest or BIDS auto-discovery.

Typical workflows¶

Single subject, end-to-end

csttool fetch-data --accept-fsl-license
csttool run --dicom /data/raw/sub-001 --out ./derivatives \
    --denoise-method patch2self --perform-motion-correction --generate-pdf

Stage-by-stage (interactive debugging)

csttool import     --dicom /data/raw/sub-001 --out ./work --subject-id sub-001
csttool preprocess --nifti ./work/sub-001/dwi/sub-001_dwi.nii.gz --out ./work/sub-001/preproc
csttool track      --nifti ./work/sub-001/preproc/dti_preproc.nii.gz --out ./work/sub-001/tracking
csttool extract    --tractogram ./work/sub-001/tracking/whole_brain.trk \
                   --fa ./work/sub-001/tracking/dti_FA.nii.gz \
                   --out ./work/sub-001/extract
csttool metrics    --cst-left ./work/sub-001/extract/cst_left.trk \
                   --cst-right ./work/sub-001/extract/cst_right.trk \
                   --fa ./work/sub-001/tracking/dti_FA.nii.gz \
                   --out ./work/sub-001/metrics --generate-pdf

Batch over a BIDS dataset

csttool batch --bids-dir /data/bids --out ./derivatives --bids-out --generate-pdf

Global conventions¶

Paths: every --* option that names a file accepts an absolute or relative path; output directories are created on demand.
Verbosity: most commands accept --verbose and --quiet (the latter overrides).
Determinism: tracking is seeded with --rng-seed (default 42); pass --random to disable seeding.
BIDS output: run and batch accept --bids-out to emit a BIDS-Derivatives layout.

See Parameters for a single-page reference of every flag.