Commit 079f1c0b authored by mwaskom's avatar mwaskom

Tweak probabilistic labels example

parent e04e2920
"""
============================
Display Probabilistic Labels
============================
......@@ -16,37 +17,39 @@ brain = Brain("fsaverage", "lh", "inflated",
config_opts=dict(cortex="low_contrast"))
"""
The simplest way is to use add_label.
The easiest way to label any vertex that could be in the region is with
add_label.
"""
brain.add_label("BA1", color="darkblue")
brain.add_label("BA1", color="#A6BDDB")
"""
You can also threshold based on the probability of that
region being at each vertex.
You can also threshold based on the probability of that region being at each
vertex.
"""
brain.add_label("BA1", color="dodgerblue", scalar_thresh=.5)
brain.add_label("BA1", color="#2B8CBE", scalar_thresh=.5)
"""
It's also possible to plot just the label boundary, in case
you wanted to overlay the label on an activation plot to
asses whether it falls within that region.
It's also possible to plot just the label boundary, in case you wanted to
overlay the label on an activation plot to asses whether it falls within that
region.
"""
brain.add_label("BA45", color="firebrick", borders=True)
brain.add_label("BA45", color="salmon", borders=True, scalar_thresh=.5)
brain.add_label("BA45", color="#F0F8FF", borders=True, scalar_thresh=.5)
brain.add_label("BA45", color="#F0F8FF", alpha=.3, scalar_thresh=.5)
"""
Finally, with a few tricks, you can display the whole probabilistic map.
"""
label_file = join(environ["SUBJECTS_DIR"],
"fsaverage", "label", "lh.BA6.label")
subjects_dir = environ["SUBJECTS_DIR"]
label_file = join(subjects_dir, "fsaverage", "label", "lh.BA6.label")
prob_field = np.zeros_like(brain._geo.x)
ids, probs = io.read_label(label_file, read_scalars=True)
prob_field[ids] = probs
brain.add_data(prob_field, thresh=1e-5)
brain.add_data(prob_field, thresh=1e-5, colormap="RdPu")
"""
Adjust the colorbar to represent the coarseness of the probability
estimates more closely.
Adjust the colorbar to represent the coarseness of the probability estimates
more closely.
"""
brain.data["colorbar"].number_of_colors = 10
brain.data["colorbar"].number_of_labels = 11
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment