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Automatic plotting of activation maps

The module fff2.viz.activation_maps provides functions to plot visualization of activation maps in a non-interactive way.

2D cuts of an activation map can be plotted and superimposed on an anatomical map using matplotlib. In addition, Mayavi2 can be used to plot 3D maps, using volumetric rendering. Some emphasis is made on automatic choice of default parameters, such as cut coordinates, to give a sensible view of a map in a purely automatic way, for instance to save a summary of the output of a calculation.

An example

from fff2.viz.activation_maps import plot_map, mni_sform, \
        coord_transform

# First, create a fake activation map: a 3D image in MNI space with
# a large rectangle of activation around Brodmann Area 26
import numpy as np
mni_sform_inv = np.linalg.inv(mni_sform)
map = np.zeros((182, 218, 182))
x, y, z = -6, -53, 9
x_map, y_map, z_map = coord_transform(x, y, z, mni_sform_inv)
map[x_map-30:x_map+30, y_map-3:y_map+3, z_map-10:z_map+10] = 1

# And now, visualize it:
plot_map(map, mni_sform, cut_coords=(x, y, z), vmin=0.5)

This creates the following image:

../_images/activation_map.png

The same plot can be obtained fully automaticaly, by using auto_plot_map() to find the activation threshold vmin and the cut coordinnates:

from fff2.viz.activation_maps import auto_plot_map
auto_plot_map(map, mni_sform)

In this simple example, the code will easily detect the bar as activation and position the cut at the center of the bar.

fff2.viz.activation_maps functions

coord_transform
find_activation
find_cut_coords
plot_map_2d
plot_map_3d
auto_plot_map
plot_niftifile

The plot_activation script

In addition to the above functions, callable from Python, there is also script plot_activation that can be used to easily render previews from Nifti files. It can also optionally output an html file, to summarize many maps on one screen.

In its simplest use, it is called like this:

plot_activation file1.nii file2.nii [...]

The plot_activation script has several many options:

-h, –help
show the help message and exit
-o DIR, –outdir=DIR
write all output to DIR
-f FILE, –htmlfile=FILE
write report to a html file FILE, useful when visualizing multiple files
-a FILE, –anat=FILE
use the given Nifti file as an anatomy
-M FILE, –mask=FILE
use the given Nifti file as a mask
-d, –no3d
don’t try to do a 3D view
-s, –sign
force activation sign to be positive
-c CUT_COORDS, –cut-coords=CUT_COORDS
Talairach coordinates of the 2D cuts
-m VMIN, –vmin=VMIN
Minimum value for the activation, used for thresholding