NeuroLang Example based Implementing a NeuroSynth Query

import warnings

warnings.filterwarnings("ignore")

from pathlib import Path
from typing import Iterable

import nibabel
import nilearn.datasets
import nilearn.image
import nilearn.plotting
import numpy as np
import pandas as pd
from neurolang import ExplicitVBROverlay, NeurolangPDL
from neurolang.frontend.neurosynth_utils import get_ns_mni_peaks_reported

Data preparation

data_dir = Path.home() / "neurolang_data"

Load the MNI atlas and resample it to 4mm voxels

mni_t1 = nibabel.load(
    nilearn.datasets.fetch_icbm152_2009(data_dir=str(data_dir / "icbm"))["t1"]
)
mni_t1_4mm = nilearn.image.resample_img(mni_t1, np.eye(3) * 4)

Dataset created in /home/circleci/neurolang_data/icbm/icbm152_2009

Downloading data from https://osf.io/7pj92/download ...
 ...done. (2 seconds, 0 min)
Extracting data from /home/circleci/neurolang_data/icbm/icbm152_2009/e05b733c275cab0eec856067143c9dc9/download..... done.

Probabilistic Logic Programming in NeuroLang

nl = NeurolangPDL()

Adding new aggregation function to build a region overlay

@nl.add_symbol
def agg_create_region_overlay(
    i: Iterable, j: Iterable, k: Iterable, p: Iterable
) -> ExplicitVBROverlay:
    mni_coords = np.c_[i, j, k]
    return ExplicitVBROverlay(
        mni_coords, mni_t1_4mm.affine, p, image_dim=mni_t1_4mm.shape
    )

Load the NeuroSynth database

peak_data = get_ns_mni_peaks_reported(data_dir)
ijk_positions = np.round(
    nibabel.affines.apply_affine(
        np.linalg.inv(mni_t1_4mm.affine),
        peak_data[["x", "y", "z"]].values.astype(float),
    )
).astype(int)
peak_data["i"] = ijk_positions[:, 0]
peak_data["j"] = ijk_positions[:, 1]
peak_data["k"] = ijk_positions[:, 2]
peak_data = peak_data[["i", "j", "k", "id"]]

nl.add_tuple_set(peak_data, name="PeakReported")
study_ids = nl.load_neurosynth_study_ids(data_dir, "Study")
nl.add_uniform_probabilistic_choice_over_set(
    study_ids.value, name="SelectedStudy"
)
nl.load_neurosynth_term_study_associations(
    data_dir, "TermInStudyTFIDF", tfidf_threshold=1e-3
)

Downloading data from https://github.com/neurosynth/neurosynth-data/raw/master/data-neurosynth_version-7_coordinates.tsv.gz ...
 ...done. (1 seconds, 0 min)
Downloading data from https://github.com/neurosynth/neurosynth-data/raw/master/data-neurosynth_version-7_metadata.tsv.gz ...
 ...done. (0 seconds, 0 min)
Downloading data from https://github.com/neurosynth/neurosynth-data/raw/master/data-neurosynth_version-7_vocab-terms_source-abstract_type-tfidf_features.npz ...
 ...done. (0 seconds, 0 min)
Downloading data from https://github.com/neurosynth/neurosynth-data/raw/master/data-neurosynth_version-7_vocab-terms_vocabulary.txt ...
 ...done. (0 seconds, 0 min)

TermInStudyTFIDF: typing.AbstractSet[typing.Tuple[str, str, float]] = (9862924, '001', 0.0553942161114) ...

with nl.scope as e:
    e.Activation[e.i, e.j, e.k] = e.PeakReported(
        e.i, e.j, e.k, e.s
    ) & e.SelectedStudy(e.s)
    e.TermAssociation[e.t] = e.SelectedStudy(e.s) & e.TermInStudyTFIDF(
        e.s, e.t, ...
    )
    e.ActivationGivenTerm[e.i, e.j, e.k, e.PROB[e.i, e.j, e.k]] = e.Activation(
        e.i, e.j, e.k
    ) // e.TermAssociation("auditory")
    e.ActivationGivenTermImage[
        agg_create_region_overlay(e.i, e.j, e.k, e.p)
    ] = e.ActivationGivenTerm(e.i, e.j, e.k, e.p)

    img_query = nl.query((e.x,), e.ActivationGivenTermImage(e.x))

result_image = img_query.fetch_one()[0].spatial_image()
img = result_image.get_fdata()
plot = nilearn.plotting.plot_stat_map(
    result_image, threshold=np.percentile(img[img > 0], 95)
)
nilearn.plotting.show()