web-neuroimaging

name	web-neuroimaging
description	Web research for neuroimaging documentation, SimpleITK, nibabel, napari, BIDS specs, and neuroscience methods. TRIGGER when user asks to look up docs, find API references, or research neuroimaging methods.
user-invocable	false

Web Research for Neuroimaging

Priority Documentation Sources

Domain	URL	Use For
SimpleITK	simpleitk.readthedocs.io	Registration, filters, transforms
SimpleITK examples	simpleitk.org/SimpleITK-Notebooks	Jupyter notebooks with full pipelines
nibabel	nipy.org/nibabel	NIfTI I/O, affines, orientation
napari	napari.org/stable	Viewer API, layers, events
BIDS	bids-specification.readthedocs.io	Data format, iEEG extension
PySide6/Qt	doc.qt.io/qtforpython-6	Widget API, signals/slots
NumPy	numpy.org/doc/stable	Array operations
SciPy	docs.scipy.org/doc/scipy	Signal processing, ndimage

Search Strategy

1. Official docs first — use WebFetch on the URLs above
2. GitHub repos — SimpleITK/SimpleITK, nipy/nibabel, napari/napari
3. NeuroStars (neurostars.org) — neuroimaging-specific Q&A forum
4. PubMed/Scholar — methodology references, validation studies
5. Stack Overflow — general Python/Qt issues

Common Lookups

SimpleITK Registration

• Registration method API: simpleitk.readthedocs.io/en/master/link_Registration_docs.html
• Transform types: Euler3D, Affine, BSpline, Displacement
• Metrics: MattesMutualInformation, Correlation, MeanSquares
• Optimizers: GradientDescentLineSearch, LBFGSB, ConjugateGradient

nibabel

• Affine handling: nipy.org/nibabel/coordinate_systems.html
• Image types: Nifti1Image, Nifti2Image, MGHImage
• Orientation codes: RAS, LAS, LPI, etc.

BIDS-iEEG Extension

• Electrode files: *_electrodes.tsv with x,y,z,size,type columns
• Coordinate systems: *_coordsystem.json specifying space (T1w, MNI152NLin2009aSym, etc.)
• Channel files: *_channels.tsv with name,type,units,sampling_frequency

napari

• Layer types: Image, Points, Shapes, Labels, Surface, Tracks, Vectors
• Events: dims.events.current_step, mouse_drag_callbacks, mouse_move_callbacks
• Rendering: mip, attenuated_mip, minip, translucent, iso

Version-Specific Notes

• SimpleITK v2.x changed API significantly from v1.x — always check version
• napari 0.5→0.6 had breaking changes in viewer embedding
• PySide6 6.5+ required for latest Qt features
• nibabel 5.0 deprecated some older image classes

When Reporting

• Include direct URLs to relevant doc pages
• Provide minimal code examples
• Note any version-specific behavior
• Flag deprecated APIs