Loading and Querying the Destrieux et al. Atlas’ Left Hemisphere

Uploading the Destrieux regions NeuroLang and executing a simple query.

import warnings

warnings.filterwarnings("ignore")


from matplotlib import pyplot as plt
import nibabel as nib
from nilearn import datasets, plotting
from neurolang.frontend import NeurolangDL

Initialise the NeuroLang probabilistic engine.

nl = NeurolangDL()

Load the Destrieux example from nilearn as a fact list

atlas_destrieux = datasets.fetch_atlas_destrieux_2009()
atlas_labels = {
    label: str(name.decode('utf8'))
    for label, name in atlas_destrieux['labels']
}


nl.add_atlas_set('destrieux_atlas', atlas_labels, nib.load(atlas_destrieux['maps']))

Dataset created in /home/circleci/nilearn_data/destrieux_2009

Downloading data from https://www.nitrc.org/frs/download.php/11942/destrieux2009.tgz ...
 ...done. (0 seconds, 0 min)
Extracting data from /home/circleci/nilearn_data/destrieux_2009/2a2e5a5707983d509d9319c692c867ab/destrieux2009.tgz..... done.

destrieux_atlas: typing.AbstractSet[typing.Tuple[str, neurolang.regions.ExplicitVBR]] = ('Background', Region(VBR= affine:[[   2.    0.    0.  -76.]
 [   0.    2.    0. -109.]
 [   0.    0.    2.  -64.]
 [   0.    0.    0.    1.]], voxels:[[ 0  0  0]
 [ 0  0  1]
 [ 0  0  2]
 ...
 [75 92 73]
 [75 92 74]
 [75 92 75]])) ...

Add utility function

@nl.add_symbol
def startswith(prefix: str, s: str) -> bool:
    return s.startswith(prefix)

Query all left hemisphere regions superior to the temporal superior sulucs and anterior to the central sulcus

with nl.scope as e:
    e.on_left_hemisphere[e.x] = (
            e.destrieux_atlas(e.l, e.x) & e.startswith('L S', e.l)
    )

    result = nl.query((e.r,), e.on_left_hemisphere(e.r))

Visualise results

subplots = plt.subplots(
    nrows=len(result), ncols=1,
    figsize=(10, 5 * len(result))
)[1]

for (r, subplot) in zip(result, subplots):
    region = r[0]
    plotting.plot_roi(region.spatial_image(), axes=subplot)