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Changelog

Source: NEWS.md

neurosurf (development version)

Interactive report scenes

  • The bundled surfview runtime is repinned to surfviewjs 2d9f786. Report scenes gain an anatomical whole-brain layout with a data-driven overview pose, a report preset (sulcal two-tone underlay, camera-attached lighting, anti-aliased threshold isolines), overlay-aware camera framing, and fixes for self-overlap artefacts on inflated surfaces, ignored curvature restyling, and hover picks that reported a hidden hemisphere. The runtime patch is now empty: every former patch hunk is upstream.

Parcel maps

  • New publication parcel-map renderer: prepare_surface_parcels() and render_surface_parcels() rasterize a labelled surface with deferred per-pixel shading. Parcel boundaries follow smoothed label memberships, so they are smooth and antialiased rather than stair-stepped along triangle edges; the underlay combines a sulcal-depth proxy with soft Lambert lighting; filled parcels get a thin outline and the medial wall is drawn flat. surface_parcel_style() collects the settings, and surface_sulcal_proxy() estimates sulcal depth from white and inflated meshes.

Static surface figures

render_surface_rgba() and surface_figure() produce substantially better figures by default:

  • Surfaces are lit with interpolated normals (two-light Blinn-Phong with hemispheric ambient), so cortical form is visible. lighting = FALSE restores flat rendering; a named list tunes it. Overlay shading is normalized so camera-facing overlay matches the colour bar.
  • Coarse meshes are subdivided for display (subdivide = "auto") with an interpolating butterfly scheme. Original vertex values are preserved and new values are clamped to their edge’s endpoints, so no suprathreshold region appears that linear interpolation would not show.
  • Palettes span only the suprathreshold range, so the weakest displayed value is clearly coloured. New defaults suit each tail; the positive palette runs light to dark.
  • The anatomy underlay is lighter, with sulci darker than gyri. anatomy_invert = "auto" detects metrics that are larger in sulci (FreeSurfer sulc, curv) and inverts them.
  • The silhouette contour is anti-aliased, the default background is white, and the default supersampling is 3.
  • Medial views are now true camera views (the left hemisphere’s anterior pole is on the right). Previously they were mirror images.
  • surface_figure() shows dorsal and ventral views of both hemispheres in one bilateral panel beside the lateral/medial rows, adds hemisphere and view headers (labels), and draws a colour bar with only the suprathreshold segments, labelled at limits and thresholds.
  • Overlay colour stays within a few percent of its colour-bar colour at any viewing angle; lighting conveys form, the palette conveys value.
  • Bilateral dorsal and ventral panels carry anterior/posterior markers.

Templates and I/O

  • The fsaverage5 template (inflated and white surfaces, sulcal depth) is bundled: load_fsaverage("fsaverage5") and load_fsaverage_sulc(). The README and figure vignette use it instead of the legacy std.8 mesh.
  • read_surf_geometry() reads gzipped GIFTI (.gii.gz) surfaces; it previously failed on them.

neurosurf 0.1.0

  • Initial CRAN submission.