Automated plotting of neuroimaging maps from Python using Connectome Workbench.

This package is intended for users who want to generate images which illustrate scalar data on a brain surface, from within their Python scripts.

Installation

Step 1. Make sure you have Connectome Workbench v1.3+ installed.

• If running wb_view from a terminal yields command not found, see https://www.humanconnectome.org/software/connectome-workbench/
• If you have Workbench 1.2 or below installed, you will get an error message

Step 2. Install wbplot and dependencies.

• Clone the repository and install manually: git clone https://github.com/jbburt/wbplot.git
• Or just use pip: pip install wbplot

Usage

Assuming x is a NumPy array containing scalar values mapped onto each of the 360 parcels in the Human Connectome Project's MMP1.0 parcellation:

from wbplot import pscalar
pscalar("/path/to/image.png", x)

Assuming y is a NumPy array containing dense scalar values mapped onto the 59412 surface vertices in a standard bilateral 32k surface mesh:

from wbplot import dscalar
dscalar("/path/to/image.png", y)

Notes

• wbplot currently only supports cortical data. Parcellated data must also be in the HCP MMP1.0 parcellation. Dense data must be registered to a standard 32k surface mesh.
• Down the line I'd be open to adding subcortical support and other functionality if people are interested.
• More detailed explanations of the functionality can be found in the scripts in the examples directory.

Change Log

• 1.0.14 Fixed an issue that caused wbplot to break when using nibabel>=3.2.0.
• 1.0.13 Attempted to fix a bug which threw an error on Windows machines. FOLLOW-UP: Due to Connectome Workbench itself, Windows is currently NOT SUPPORTED.
• 1.0.12 Fixed bug in list of available colormaps; ROY-BIG-BL and videen_style are now supported.
• 1.0.11 Dependency version updates.
• 1.0.10 Patched keyword argument bug in wbplot.dscalar.
• 1.0.9 Fixed bug in images.check_dscalars().
• 1.0.8 Fixed it for real now.
• 1.0.7 Fixed type checking bug in images module.
• 1.0.6 Added errors raised to docstrings and cleaned up a few files.
• 1.0.5 Last patch didn't fix the problem.
• 1.0.4 ImageParcellated loaded into dense scenes resulted in error messages printed to console.
• 1.0.3 Entirely changed the way data are read from and written to, to circumnavigate permissions issues.
• 1.0.2 Error in MANIFEST.in -- not all necessary data files included in build.
• 1.0.1 Small error in README.
• 1.0 Initial release.