def get_anat(cls):
from nipy.utils.data import templates
if cls.anat is not None:
return cls.anat, cls.anat_sform, cls.anat_max
filename = templates.get_filename(
'ICBM152', '1mm', 'T1_brain.nii.gz')
if not os.path.exists(filename):
raise OSError('Cannot find template file T1_brain.nii.gz'
'required to plot anatomy. Possible path: %s'
% filename)
anat_im = load(filename)
anat = anat_im.get_data()
anat = anat.astype(np.float)
anat_mask = ndimage.morphology.binary_fill_holes(anat > 0)
anat = np.ma.masked_array(anat, np.logical_not(anat_mask))
cls.anat_sform = anat_im.get_affine()
cls.anat = anat
cls.anat_max = anat.max()
return cls.anat, cls.anat_sform, cls.anat_max
def find_mni_template():
""" Try to find an MNI template on the disk.
"""
from nipy.utils.data import templates, DataError
try:
filename = templates.get_filename(
'ICBM152', '1mm', 'T1_brain.nii.gz')
if os.path.exists(filename):
return filename
except DataError:
pass
possible_paths = [
('', 'usr', 'share', 'fsl', 'data', 'standard', 'avg152T1_brain.nii.gz'),
('', 'usr', 'local', 'share', 'fsl', 'data', 'standard', 'avg152T1_brain.nii.gz'),
]
if 'FSLDIR' in os.environ:
fsl_path = os.environ['FSLDIR'].split(os.sep)
fsl_path.extend('data', 'standard', 'avg152T1_brain.nii.gz')
possible_paths.append()
for path in possible_paths:
filename = os.sep.join((path))
if os.path.exists(filename):
return filename
