Flatmap Demo Reference¶

File: /Users/iancharest/Documents/codex/cvncode/cvnpy/examples/flatmap_demo.py

Purpose¶

flatmap_demo.py renders cortical flatmaps with optional stat overlays, thresholding, colorbar, bilateral composition, inflated insets, and layered SVG output.

Common Commands¶

Flatmap, both hemispheres¶

.venv/bin/python examples/flatmap_demo.py \
  --subject-dir /Users/iancharest/data/nsd_fsaverage \
  --hemi both \
  --surftype full.flat.patch.3d \
  --view 0,0,0 \
  --out out/fullflat_bihemi.png

Real stat file, symmetric color limits, threshold¶

.venv/bin/python examples/flatmap_demo.py \
  --subject-dir /Users/iancharest/data/nsd_fsaverage \
  --hemi both \
  --stat-file /Users/iancharest/Downloads/rcnn-mpnet/encoding/subj01/shared_pred/test_corr.npy \
  --symmetric-clim \
  --absthreshold 0.05 \
  --show-colorbar \
  --out out/subj01_corr_thresh005.png

Add insets + layered SVG¶

.venv/bin/python examples/flatmap_demo.py \
  --subject-dir /Users/iancharest/data/nsd_fsaverage \
  --hemi both \
  --stat-file /Users/iancharest/Downloads/rcnn-mpnet/encoding/subj01/shared_pred/test_corr.npy \
  --show-colorbar \
  --show-insets \
  --out out/subj01_corr_insets.png \
  --out-svg out/subj01_corr_insets.svg

Inputs¶

Subject / surf resolution¶

--subject and optional --subjects-dir
or --subject-dir (preferred for explicit local data)

Statistical values¶

--stat-map <metricname>: reads surface metric by name
--stat-file <path.npy>: loads values from numpy file

--stat-file shape expectations: - n_lh + n_rh: split into LH and RH - n_lh: LH only - n_rh: RH only

Core Visual Options¶

--cmap (default cmapsign4)
--clim min,max
--symmetric-clim/--no-symmetric-clim
--absthreshold <float>
--background <metric-or-scalar> (default curv)
--show-colorbar/--no-show-colorbar

Threshold behavior: - pixels with abs(value) <= absthreshold render background curvature (gray) - above threshold render stat colormap

Bilateral Layout¶

When --hemi both: - LH and RH are independently rendered, rotated, trimmed, then composed side-by-side - defaults: - --lh-rotate-deg -90 - --rh-rotate-deg 90

Useful controls: - --pair-gap-px - --pair-margin-px - --pair-bg-gray (for white figure use 1.0)

Insets¶

--show-insets
--inset-viewname (default lateral)
--inset-imageres
--inset-size-frac
--inset-margin-px

Insets are rendered from surftype='inflated' using the same stat values and color settings.

Flatmap Artifact Controls¶

These are exposed for boundary/edge artifact tuning: - --flat-support-ratio - --trim-extrapolation-px - --flat-prune-artifact-faces - --flat-prune-quantile - --flat-prune-factor - --flat-filter-sparse-vertices - --flat-sparse-vertex-quantile - --flat-sparse-vertex-factor - --flat-edge-trim-steps - --flat-margin-frac - --flat-fill-small-holes-px

SVG Layering¶

Use --out-svg for layered export. The output includes IDs for: - curv - stat - labels_lh - labels_rh - colorbar - inset_lh, inset_rh (if enabled)

This enables downstream vector overlays for ROI workflows.