"""
If you don't have access to a Nifti file, download one of the volume available
at https://brainder.org/download/flair/.
"""
path_to_nifti1 = os.getenv("HOME") # Path to the Nifti file
file_nifti1 = 'GG-853-GM-0.7mm.nii.gz' # Name of the Nifti file
path1 = os.path.join(path_to_nifti1, file_nifti1)
"""
Load the Nifti file. The read_nifti function load the data and the
transformation to convert data into the MNI space :
"""
data1, header1, tf1 = read_nifti(path1)
# print(header1)
# Add the volume to the GUI :
vb.add_volume('Volume1', data1, transform=tf1)
print('Add Volume1 to the list of volumes : ', vb.volume_list())
# You can add multiple volumes :
path_to_nifti2 = os.getenv("HOME")
file_nifti2 = 'GG-853-WM-0.7mm.nii.gz'
path2 = os.path.join(path_to_nifti2, file_nifti2)
data2, header2, tf2 = read_nifti(path2)
vb.add_volume('Volume2', data2, transform=tf2)
print('Add Volume2 to the list of volumes : ', vb.volume_list())
# Set the cross-section to be centered on the last source :
vb.cross_sections_control(pos=s_xyz[3, :],
volume='Volume2',
cmap='gist_stern',
split_view=True)
"""
import os
from visbrain import Brain
from visbrain.io import read_nifti
"""Import the volume and the associated affine transformation
"""
volume_name = 'GG-853-WM-0.7mm'
path_to_nifti = os.getenv("HOME")
file_nifti = 'GG-853-WM-0.7mm.nii.gz'
path = os.path.join(path_to_nifti, file_nifti)
data, header, tf = read_nifti(path)
vb = Brain()
# Add the volume to the GUI
vb.add_volume(volume_name, data, transform=tf)
"""Set the cross-section to be centered on the slice (70, 171, 80) with the
gist_stern colormap.
"""
vb.cross_sections_control(center=(70, 171, 80),
volume=volume_name,
cmap='gist_stern')
"""Display the 3D volume using the translucent rendering method.
"""
vb.volume_control(volume_name, cmap='TransFire', rendering='translucent')
"""Finally, rotate the scene and hide the main brain.
"""
vb.rotate(custom=(142, 12))
vb.brain_control(visible=False)
vb.show()