OpenNeuroPET Tools¶
The OpenNeuroPET assistant provides tools for documentation retrieval and GitHub knowledge search. It covers the OpenNeuroPET ecosystem of open and reproducible tools for Positron Emission Tomography (PET) imaging: PET2BIDS (converts Digital Imaging and Communications in Medicine (DICOM) and Emission Computed Axial Tomography (ECAT) scanner files to BIDS), petprep (a BIDS App for preprocessing), bloodstream (blood data analysis), petfit (kinetic modeling), and PetSurfer.
Overview¶
| Tool | Type | Description |
|---|---|---|
retrieve_openneuropet_docs | Document retrieval | Fetch OpenNeuroPET, petprep, and petfit documentation |
search_openneuropet_discussions | Knowledge search | Search GitHub issues and PRs |
list_openneuropet_recent | Knowledge search | List recent GitHub activity |
OpenNeuroPET has no citations, docstrings, or mailman configuration, so it does not get search_openneuropet_papers, search_openneuropet_code_docs, or search_openneuropet_faq.
Document Retrieval¶
retrieve_openneuropet_docs¶
Fetches documentation from 23 configured sources across the OpenNeuroPET tool ecosystem.
Preloaded docs (embedded in system prompt):
- Getting Started (overview of OpenNeuroPET tools)
On-demand docs (22): organized by tool:
- petprep (6): overview, installation, usage, workflows (motion correction, partial volume correction, spatial normalization), outputs, FAQ
- petfit (14): overview, installation, quick start, usage guide, region definition, plasma input modeling, reference tissue modeling, supported models, reports, outputs, folder structure, Docker usage, Apptainer usage, R API reference
- PetSurfer (1): wiki (partial volume correction and kinetic modeling using FreeSurfer)
- BIDS (1): the PET extension to the Brain Imaging Data Structure (BIDS) specification
Knowledge Search Tools¶
These tools search the OpenNeuroPET community's synced knowledge database.
search_openneuropet_discussions¶
Search GitHub issues and PRs across the OpenNeuroPET repositories.
Parameters:
| Parameter | Type | Default | Description |
|---|---|---|---|
query | str | required | Search query |
include_issues | bool | True | Include issues in results |
include_prs | bool | True | Include pull requests |
limit | int | 5 | Maximum results |
Tracked repositories:
openneuropet/openneuropet.github.ioopenneuropet/PET2BIDSnipreps/petprepmathesong/bloodstreammathesong/petfit
list_openneuropet_recent¶
List recent GitHub activity ordered by creation date.
Parameters:
| Parameter | Type | Default | Description |
|---|---|---|---|
item_type | str | "all" | Filter: "all", "issue", or "pr" |
repo | str \| None | None | Filter by repository |
status | str \| None | None | Filter: "open" or "closed" |
limit | int | 10 | Maximum results |
Sync Schedule¶
| Source | Schedule | Notes |
|---|---|---|
| GitHub | Daily, 2:00 UTC | Issues and PRs from 5 repositories |
See Knowledge Sync for CLI commands and setup instructions.