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 : https://brainder.org/download/flair/

../../_images/ex_add_nifti.png
from __future__ import print_function
import numpy as np

from visbrain import Brain
from visbrain.objects import VolumeObj, CrossSecObj, SourceObj
from visbrain.io 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
object
"""
vb = Brain(source_obj=s_obj, vol_obj=vol_obj, cross_sec_obj=cross_sec_obj)
vb.show()

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

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