⬇️ Installation and Import

nidataset is available on PyPI and needs Python 3.9 or newer:

pip install nidataset

and is imported as:

import nidataset as nid

Optional extras

Extra	Install	Enables
yaml	pip install "nidataset[yaml]"	YAML configs for nii run and niqc --config. JSON configs work without it.
dev	pip install -e ".[dev]" (from a clone)	pytest, pytest-cov, ruff for development.

The full dependency list lives in pyproject.toml.

External tools

• FSL — only for skull stripping (skull_CTA, pipeline op skull_strip). Install it from the FSL website and make sure bet and fslmaths are on PATH; run from a terminal that sources FSL’s profile.
• Registration templates — register_CTA needs a template brain and brain mask. FSL ships MNI152 templates in $FSLDIR/data/standard/ (e.g. MNI152_T1_1mm_brain.nii.gz and MNI152_T1_1mm_brain_mask.nii.gz).

Command-line tools

Installing the package also installs two commands:

• nii — quick edits and pipelines (docs).
• niqc — quality control (docs).