def test_animate(tmpdir):
"""Test animation."""
_set_backend('auto')
brain = Brain(*std_args, size=100)
brain.add_morphometry('curv')
tmp_name = str(tmpdir.join('test.avi'))
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
pytest.raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def test_animate():
"""Test animation."""
_set_backend('auto')
brain = Brain(*std_args, size=100)
brain.add_morphometry('curv')
tmp_name = mktemp() + '.avi'
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
assert_raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def test_animate(tmpdir):
"""Test animation."""
_set_backend('auto')
brain = Brain(*std_args, size=100)
brain.add_morphometry('curv')
tmp_name = str(tmpdir.join('test.avi'))
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
pytest.raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def test_animate():
"""Test animation."""
_set_backend('auto')
brain = Brain(*std_args, size=100)
brain.add_morphometry('curv')
tmp_name = mktemp() + '.avi'
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
assert_raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def test_animate():
"""Test animation
"""
mlab.options.backend = 'auto'
brain = Brain(*std_args, config_opts=small_brain)
brain.add_morphometry('curv')
tmp_name = mktemp() + '.avi'
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
assert_raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def test_animate():
"""Test animation
"""
mlab.options.backend = 'auto'
brain = Brain(*std_args, config_opts=small_brain)
brain.add_morphometry('curv')
tmp_name = mktemp() + '.avi'
brain.animate(["m"] * 3, n_steps=2)
brain.animate(['l', 'l'], n_steps=2, fname=tmp_name)
# can't rotate in axial plane
assert_raises(ValueError, brain.animate, ['l', 'd'])
brain.close()
def visMorph(pathToSurface, overlay, outputPath, hemi):
'''
Display anything morphometric
'''
# check the overlay
if (not overlay == 'sulc' and not overlay == 'thickness'
and not overlay == 'curv'):
message = ('You specified %s as overlay, this doesn\'t make sense'
% (overlay))
raise Exception(message)
brain = Brain(pathToSurface, hemi, 'white')
brain.add_morphometry(overlay)
brain.save_montage(outputPath, ['l', 'm'], orientation='v')
brain.close()
def test_morphometry():
"""Test plotting of morphometry."""
mlab.options.backend = 'test'
brain = Brain(*std_args)
brain.add_morphometry("curv")
brain.add_morphometry("sulc", grayscale=True)
brain.add_morphometry("thickness")
brain.close()
def test_morphometry():
"""Test plotting of morphometry."""
mlab.options.backend = 'test'
brain = Brain(*std_args)
brain.add_morphometry("curv")
brain.add_morphometry("sulc", grayscale=True)
brain.add_morphometry("thickness")
brain.close()
def test_morphometry():
"""Test plotting of morphometry."""
_set_backend()
brain = Brain(*std_args)
brain.add_morphometry("curv")
brain.add_morphometry("sulc", grayscale=True)
brain.add_morphometry("thickness")
brain.close()
def test_morphometry():
"""Test plotting of morphometry."""
_set_backend()
brain = Brain(*std_args)
brain.add_morphometry("curv")
brain.add_morphometry("sulc", grayscale=True)
brain.add_morphometry("thickness")
brain.close()
def plot_brains(axes, palette):
lat_ax, med_ax = axes
lat_color, med_color = palette
b = Brain("fsaverage", "lh", "pial",
background="white", size=(1200, 1200))
b.add_morphometry("curv", grayscale=True, min=-.5, max=.5,
colormap="Greys", colorbar=False)
b.add_label("roi_labels/lh.ifs.label", alpha=.9, color="#feb308")
b.add_label("roi_labels/lh.mfc.label", alpha=.9, color="#cf6275")
mlab.view(160, 70)
lat_ax.imshow(crop(b.screenshot()), rasterized=True)
mlab.view(15, 90)
med_ax.imshow(crop(b.screenshot()), rasterized=True)
b.close()
for ax in axes:
ax.set_axis_off()
from surfer._commandline import parser
args = parser.parse_args(sys.argv[1].split())
# Get a dict of config override options
confkeys = ["size", "background", "cortex"]
argdict = args.__dict__
config_opts = dict([(k, v) for k, v in argdict.items() if k in confkeys and v])
# Load up the figure and underlying brain object
b = Brain(args.subject_id, args.hemi, args.surf, args.curv,
args.title, config_opts=config_opts)
# Maybe load some morphometry
if args.morphometry is not None:
b.add_morphometry(args.morphometry)
# Maybe load an overlay
if args.overlay is not None:
if args.range is not None:
args.min, args.max = args.range
b.add_overlay(args.overlay, args.min, args.max, args.sign)
# Maybe load an annot
if args.annotation is not None:
if not args.borders:
args.borders = any([args.overlay, args.morphometry])
b.add_annotation(args.annotation, args.borders)
# Maybe load a label
brain = Brain("fsaverage", "both", "pial",
background="dimgray")
if not brain.patch_mode:
brain.show_view("frontal")
"""
Because the morphometry files generated by
recon-all live in a predicatble location,
all you need to call the add_morphometry
method with is the name of the measure you want.
Here, we'll look at cortical curvatuve values,
and plot them for both hemispheres.
"""
brain.add_morphometry("curv")
"""
Each of the possible values is displayed in an
appropriate full-color map, but you can also
display in grayscale. Here we only plot the
left hemisphere.
"""
brain.add_morphometry("sulc", hemi='lh', grayscale=True)
"""
You can also use a custom colormap and tweak its range.
"""
brain.add_morphometry("thickness",
colormap="PuBuGn", min=1, max=4)
print __doc__
from surfer import Brain
brain = Brain("fsaverage", "both", "pial", views="frontal",
config_opts=dict(background="dimgray"))
"""
Because the morphometry files generated by
recon-all live in a predicatble location,
all you need to call the add_morphometry
method with is the name of the measure you want.
Here, we'll look at cortical curvatuve values,
and plot them for both hemispheres.
"""
brain.add_morphometry("curv")
"""
Each of the possible values is displayed in an
appropriate full-color map, but you can also
display in grayscale. Here we only plot the
left hemisphere.
"""
brain.add_morphometry("sulc", hemi='lh', grayscale=True)
"""
The Brain object can only hold one morphometry
overlay at a time, so adding a new one removes
any existing overlays.
"""
brain.add_morphometry("thickness")
from surfer import Brain
print(__doc__)
brain = Brain("fsaverage", "both", "pial", views="frontal",
background="dimgray")
"""
Because the morphometry files generated by
recon-all live in a predicatble location,
all you need to call the add_morphometry
method with is the name of the measure you want.
Here, we'll look at cortical curvatuve values,
and plot them for both hemispheres.
"""
brain.add_morphometry("curv")
"""
Each of the possible values is displayed in an
appropriate full-color map, but you can also
display in grayscale. Here we only plot the
left hemisphere.
"""
brain.add_morphometry("sulc", hemi='lh', grayscale=True)
"""
You can also use a custom colormap and tweak its range.
"""
brain.add_morphometry("thickness",
colormap="PuBuGn", min=1, max=4)
"""
from os import environ
from os.path import join
import numpy as np
from surfer import Brain
from nibabel.freesurfer import read_label
print(__doc__)
brain = Brain("fsaverage", "lh", "inflated")
"""
Show the morphometry with a continuous grayscale colormap.
"""
brain.add_morphometry("curv",
colormap="binary",
min=-.8,
max=.8,
colorbar=False)
"""
The easiest way to label any vertex that could be in the region is with
add_label.
"""
brain.add_label("BA1", color="#A6BDDB")
"""
You can also threshold based on the probability of that region being at each
vertex.
"""
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
from surfer import Brain
brain = Brain("fsaverage",
"both",
"pial",
views="frontal",
config_opts=dict(background="dimgray"))
"""
Because the morphometry files generated by
recon-all live in a predicatble location,
all you need to call the add_morphometry
method with is the name of the measure you want.
Here, we'll look at cortical curvatuve values,
and plot them for both hemispheres.
"""
brain.add_morphometry("curv")
"""
Each of the possible values is displayed in an
appropriate full-color map, but you can also
display in grayscale. Here we only plot the
left hemisphere.
"""
brain.add_morphometry("sulc", hemi='lh', grayscale=True)
"""
The Brain object can only hold one morphometry
overlay at a time, so adding a new one removes
any existing overlays.
"""
brain.add_morphometry("thickness")
from surfer import Brain
print(__doc__)
brain = Brain("fsaverage", "both", "inflated", views="lateral",
background="white")
"""
You can also use a custom colormap and tweak its range.
"""
brain.add_morphometry("thickness",
colormap="Blues", min=1, max=4,
colorbar=False)
brain.save_image('./figures/elements_fig_concept_anatomy.png')
"""
from os import environ
from os.path import join
import numpy as np
from surfer import Brain
from nibabel.freesurfer import read_label
print(__doc__)
brain = Brain("fsaverage", "lh", "inflated")
"""
Show the morphometry with a continuous grayscale colormap.
"""
brain.add_morphometry("curv", colormap="binary",
min=-.8, max=.8, colorbar=False)
"""
The easiest way to label any vertex that could be in the region is with
add_label.
"""
brain.add_label("BA1_exvivo", color="#A6BDDB")
"""
You can also threshold based on the probability of that region being at each
vertex.
"""
brain.add_label("BA1_exvivo", color="#2B8CBE", scalar_thresh=.5)
"""
It's also possible to plot just the label boundary, in case you wanted to
