Add Nifti volume

Import a custom Nifti volume that can be then used in the cross-section or volume tab. To this end, the python package nibabel must be installed and custom Nifti volume must be downloaded. When the volume is loaded into the GUI, it’s accessible from the Brain/Cross-sections and Brain/Volume tab.

This script use a custom nifti volume downloadable at :

from __future__ import print_function
import numpy as np

from visbrain import Brain
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj
from import download_file

"""Download two NIFTI files
path_1 = download_file('GG-853-GM-0.7mm.nii.gz')
path_2 = download_file('GG-853-WM-0.7mm.nii.gz')

"""Define four sources sources and a Source object
s_xyz = np.array([[29.9, -37.3, -19.3],
                  [-5.33, 14.00, 20.00],
                  [25.99, 14.00, 34.66],
                  [0., -1.99, 10.66]])
s_obj = SourceObj('MySources', s_xyz)

"""Define a volume object and a cross-section object
vol_obj = VolumeObj(path_1)
cross_sec_obj = CrossSecObj(path_2)

"""Localize a source in the cross-section object
cross_sec_obj.localize_source(s_xyz[2, :])

"""Define a Brain instance and pass the source, volume and cross-section
vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj)

Total running time of the script: ( 0 minutes 0.000 seconds)

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