Nipype — Neuroimaging Workflow Engine
Python dataflow engine that wraps FSL, SPM, FreeSurfer, ANTs, and AFNI into reproducible neuroimaging pipelines.
Nipype — Neuroimaging Workflow Engine
Nipype is a neuroimaging workflow framework that provides uniform Python interfaces to dozens of tools — FSL, SPM, FreeSurfer, ANTs, AFNI, MRtrix, Camino — and chains them into reproducible dataflow pipelines with parallel execution and smart caching.
Key features
- 500+ interface wrappers covering every major neuroimaging toolbox
- DAG-based workflow with conditional re-execution (only re-runs changed nodes)
- MultiProc, SGE, SLURM, PBS, and AWS Batch execution plugins
- Generates provenance records and dot-graph visualizations
- Underlies fMRIPrep, dMRIPrep, and HALFpipe
Quick start
pip install nipype
from nipype import Workflow, Node
from nipype.interfaces.fsl import BET, MCFLIRT
skull_strip = Node(BET(in_file="bold.nii"), name="skull_strip")
mc = Node(MCFLIRT(), name="motion_correct")
wf = Workflow(name="preproc", base_dir="/tmp")
wf.connect(skull_strip, "out_file", mc, "in_file")
wf.run()
npx ai-supply add nipype-neuroimaging-workflows
Curated mirror of the open-source Nipype (Apache-2.0). Get it from the source.
Compromise signals — malicious or tampered code (leaked secrets, backdoors, a dropped executable) — reduce the score, and known dependency CVEs carry a bounded penalty (they warrant review but never QUARANTINE — update the dependency to clear). Other dangerous-by-capability traits are risk surface, expected for some capabilities. Every finding is mapped to its OWASP control below.
Findings mapped to the OWASP Top 10 for LLM Applications (2025) and the OWASP Machine Learning Security Top 10. Expand any flagged control for the exact findings — compromise reduces the score; expected/risk-surface do not, except a known CVE, which carries a small bounded penalty (high/critical → Review).
The same gate an agent runs before installing (POST /api/v1/trust/nipype-neuroimaging-workflows/check). Click a policy:
Consume Nipype — Neuroimaging Workflow Engine programmatically. Authenticate with an API key or session — see Authorize an agent.
# Agents: CHECK BEFORE YOU INSTALL (no auth) — score, grade, level, capability manifest
curl https://ai-supply.store/api/v1/trust/nipype-neuroimaging-workflows
# Gate against your org policy (returns { pass, violations })
curl -X POST https://ai-supply.store/api/v1/trust/nipype-neuroimaging-workflows/check \
-H "Content-Type: application/json" \
-d '{"minGrade":"B","denyPermissions":["shell"],"denyUnknownEgress":true}'
# CLI
npx ai-supply add nipype-neuroimaging-workflows
# REST (install → download)
curl -X POST https://ai-supply.store/api/v1/listings/nipype-neuroimaging-workflows/install \
-H "Authorization: Bearer $AIM_KEY"
# MCP tool
install_listing({ "slug": "nipype-neuroimaging-workflows" })OpenAPI spec →Curated mirror — latest upstream source. See the repository for tagged releases.