Example Gallery¶

Datasets Examples ¶

Examples demonstrating how to create, manipulate, plot datasets.

Dataset Arithmetic

Dataset Arithmetic

Map from Volume to Vertex Data

Map from Volume to Vertex Data

Plot Volume Data

Plot Volume Data

Plot Vertex Data

Plot Vertex Data

Plot 2D Vertex Data

Plot 2D Vertex Data

Plot 2D Volume Data

Plot 2D Volume Data

Plot RGB Vertex Data

Plot RGB Vertex Data

Plot RGB Volume Data

Plot RGB Volume Data

Plot Data with Alpha Values

Plot Data with Alpha Values

Examples with fsaverage ¶

Examples showing how to use PyCortex to visualize data on fsaverage.

Upsample data from a lower resolution fsaverage template to fsaverage for visualization

Upsample data from a lower resolution fsaverage template to fsaverage for visualization

Examples with HCP fs_LR data ¶

Examples showing how to use PyCortex to visualize HCP fs_LR 32k data, both on the HCP template and resampled to fsaverage.

Visualize HCP fs_LR data on the HCP template and on fsaverage

Visualize HCP fs_LR data on the HCP template and on fsaverage

Importing Surfaces Examples ¶

Examples demonstrating how to import surfraces from other software (e.g. FreeSurfer, fmriprep).

Import fmriprep output

Import fmriprep output

Quickflat Examples ¶

Examples demonstrating how to create flatmaps.

Plot sulci on the flatmap

Plot sulci on the flatmap

Plot dropout regions on the flatmap

Plot dropout regions on the flatmap

Save a 2D static flatmap as SVG

Save a 2D static flatmap as SVG

Save a 2D static flatmap as PNG

Save a 2D static flatmap as PNG

Plot cutouts on the flatmap

Plot cutouts on the flatmap

Plot ROIs on the flatmap

Plot ROIs on the flatmap

Plot which vertices are inside the same voxels

Plot which vertices are inside the same voxels

Animate a series of volumes as a GIF

Animate a series of volumes as a GIF

Ignore NaN (not-a-number) values in thickness mapping

Ignore NaN (not-a-number) values in thickness mapping

Plotting a zoomed view of one ROI

Plotting a zoomed view of one ROI

Plot a 2D static flatmap

Plot a 2D static flatmap

Plot with advanced compositing

Plot with advanced compositing

Quickstart Examples ¶

Examples demonstrating how to get started with pycortex.

Plot Example Retinotopy in Web Viewer

Plot Example Retinotopy in Web Viewer

Finding out where the config and filestore are

Finding out where the config and filestore are

Plot Example Retinotopy Flatmaps

Plot Example Retinotopy Flatmaps

Surface Analysis Examples ¶

Examples demonstrating operations and analyses done on brain surfaces.

Tissot’s Indicatrix

Tissot's Indicatrix

Plotting Geodesic Paths

Plotting Geodesic Paths

Plotting Geodesic Distances

Plotting Geodesic Distances

Flatmap Distortion

Flatmap Distortion

Plot and Use Subsurface Tools

Plot and Use Subsurface Tools

Interpolate Data

Interpolate Data

Bumpy Flatmaps

Timeseries Examples ¶

Examples for the click-a-voxel timeseries panel in the WebGL viewer (Open Controls -> movie -> timeseries).

Timeseries of RGB Vertex Data

Timeseries of RGB Vertex Data

Inspect Encoding-Model Predictions and Timeseries

Inspect Encoding-Model Predictions and Timeseries

Utility Examples ¶

Examples demonstrating how to do all sorts of beautiful things using pycortex.

Get Vertices for an ROI

Get Vertices for an ROI

Voxel distance from surface

Voxel distance from surface

Mosaic plot

Transform from Subject to MNI Space

Transform from Subject to MNI Space

Get ROI Voxel Mask

Get ROI Voxel Mask

Transform from MNI to Subject Space

Transform from MNI to Subject Space

Multi-panels figures

Multi-panels figures

Get ROI Index Volume

Get ROI Index Volume

WebGL Examples ¶

Examples demonstrating how to make beautiful interactive 3-D viewers

Create a 3D WebGL Viewer

Create a 3D WebGL Viewer

Create a static viewer

Create a static viewer

Dynamic viewer with html template

Dynamic viewer with html template

Static viewer with html template

Static viewer with html template

Create a 3D WebGL Viewer with Multiple Datasets

Create a 3D WebGL Viewer with Multiple Datasets

Plot 3D Brain Views Headlessly (No Browser)

Plot 3D Brain Views Headlessly (No Browser)

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