Work With Different Data Formats¶
csttool accepts two input types: DICOM directories and 4D NIfTI files with separate gradient sidecars. This page covers conversion, naming conventions, and the FOV check that catches most "extraction failed" errors before they happen.
DICOM → NIfTI¶
csttool import wraps dcm2niix and produces a BIDS-style output.
If the DICOM directory contains multiple diffusion series, specify one:
Use --scan-only to see what would be converted without writing anything:
Gradient sidecar naming¶
csttool auto-discovers .bval/.bvec files that share the stem of the DWI NIfTI. Both BIDS-style and dcm2niix-style names are recognised:
| DWI file | Accepted gradient files |
|---|---|
sub-001_dwi.nii.gz |
sub-001_dwi.bval + sub-001_dwi.bvec |
sub-001_dwi.nii.gz |
sub-001_dwi.bvals + sub-001_dwi.bvecs |
If your sidecars live elsewhere, pass them explicitly to check-dataset (the other commands derive everything from import's output):
FOV and resolution¶
Atlas-based CST extraction registers a template (FMRIB58_FA) into your subject's space, then projects motor-cortex and brainstem ROIs. If your acquisition does not include both endpoints in the field of view, extraction will succeed but produce empty or truncated bundles.
Whole-brain FOV is required
The DWI volume must cover from the vertex down to the caudal medulla (foramen magnum). Acquisitions clipped at the supratentorial level will silently produce bilateral CSTs that stop at the level of the cropping plane.
Use csttool check-dataset --dwi raw_dwi.nii.gz for a coverage diagnostic before launching the pipeline. See the check-dataset reference for the full report.
Voxel size¶
Default tracking parameters assume voxels in the 1.5–2.5 mm isotropic range. If your data is highly anisotropic, reslice during preprocessing: