import nipy.algorithms.statistics.empirical_pvalue as en
# Local import
from get_data_light import DATA_DIR, get_second_level_dataset
# parameters
verbose = 1
theta = float(st.t.isf(0.01, 100))
# paths
mask_image = os.path.join(DATA_DIR, 'mask.nii.gz')
input_image = os.path.join(DATA_DIR, 'spmT_0029.nii.gz')
if (not os.path.exists(mask_image)) or (not os.path.exists(input_image)):
get_second_level_dataset()
# Read the mask
nim = load(mask_image)
mask = nim.get_data()
# read the functional image
rbeta = load(input_image)
beta = rbeta.get_data()
beta = beta[mask > 0]
mf = plt.figure(figsize=(13, 5))
a1 = plt.subplot(1, 3, 1)
a2 = plt.subplot(1, 3, 2)
a3 = plt.subplot(1, 3, 3)
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
from nibabel import load
from nipy.labs import viz
from nipy.utils import example_data
# Local import
from get_data_light import get_second_level_dataset
# get the data
data_dir = get_second_level_dataset()
# First example, with a anatomical template
img = load(os.path.join(data_dir, 'spmT_0029.nii.gz'))
data = img.get_data()
affine = img.get_affine()
viz.plot_map(data, affine, cut_coords=(-52, 10, 22),
threshold=2.0, cmap=viz.cm.cold_hot)
plt.savefig('ortho_view.png')
# Second example, with a given anatomical image slicing in the Z direction
try:
anat_img = load(example_data.get_filename('neurospin', 'sulcal2000',
'nobias_anubis.nii.gz'))
anat = anat_img.get_data()
from nibabel import load
import nipy.algorithms.statistics.empirical_pvalue as en
import get_data_light
# parameters
verbose = 1
theta = float(st.t.isf(0.01, 100))
# paths
data_dir = os.path.expanduser(os.path.join('~', '.nipy', 'tests', 'data'))
mask_image = os.path.join(data_dir, 'mask.nii.gz')
input_image = os.path.join(data_dir, 'spmT_0029.nii.gz')
if (not os.path.exists(mask_image)) or (not os.path.exists(input_image)):
get_data_light.get_second_level_dataset()
# Read the mask
nim = load(mask_image)
mask = nim.get_data()
# read the functional image
rbeta = load(input_image)
beta = rbeta.get_data()
beta = beta[mask > 0]
mf = mp.figure(figsize=(13, 5))
a1 = mp.subplot(1, 3, 1)
a2 = mp.subplot(1, 3, 2)
a3 = mp.subplot(1, 3, 3)
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
from nibabel import load
from nipy.labs import viz
from nipy.utils import example_data
# Local import
from get_data_light import get_second_level_dataset
# get the data
data_dir = get_second_level_dataset()
# First example, with a anatomical template
img = load(os.path.join(data_dir, 'spmT_0029.nii.gz'))
data = img.get_data()
affine = img.get_affine()
viz.plot_map(data,
affine,
cut_coords=(-52, 10, 22),
threshold=2.0,
cmap=viz.cm.cold_hot)
plt.savefig('ortho_view.png')
# Second example, with a given anatomical image slicing in the Z direction
try: