Plot dropout regions on the flatmap

A dropout region is a region with very low EPI signal. In pycortex a crosshatch is used to display such dropout regions.

The crosshatches are created using the reference nifti image file with a threshold. Setting the with_dropout=True parameter in quickflat.make_figure takes the reference nifti image file and computes a thresholded version of this using the following formula:

FIXME: .. code-block:: python

rawdata[rawdata==0] = np.mean(rawdata[rawdata!=0]) normdata = (rawdata - rawdata.min()) / (rawdata.max() - rawdata.min()) normdata = (1 - normdata) ** power

** (inkscape:4619): WARNING **: 21:53:23.280: Failed to wrap object of type 'GtkRecentManager'. Hint: this error is commonly caused by failing to call a library init() function.

import cortex
import numpy as np
np.random.seed(1234)

# Create a random pycortex Volume
volume = cortex.Volume.random(subject='S1', xfmname='fullhead')

# Plot a flatmap with the data projected onto the surface
# Highlight the curvature and dropout regions
_ = cortex.quickflat.make_figure(volume,
                                 with_curvature=True,
                                 with_dropout=True)