Run coordinate-based meta-analyses on 21 pain studies

Collection of NIDM-Results packs downloaded from Neurovault collection 1425, uploaded by Dr. Camille Maumet.

Note

This will likely change as we work to shift database querying to a remote database, rather than handling it locally with NiMARE.

Start with the necessary imports

import os
import json
from glob import glob

import numpy as np
import pandas as pd
import nibabel as nib
from scipy.stats import t
from nilearn.masking import apply_mask
from nilearn.plotting import plot_stat_map

import nimare
from nimare.tests.utils import get_test_data_path

Load Dataset

dset_file = os.path.join(get_test_data_path(), 'nidm_pain_dset.json')
dset = nimare.dataset.Dataset(dset_file)

mask_img = dset.masker.mask_img

MKDA density analysis

mkda = nimare.meta.cbma.MKDADensity(kernel__r=10)
mkda.fit(dset)
corr = nimare.correct.FWECorrector(method='permutation', n_iters=10, n_cores=1)
cres = corr.transform(mkda.results)
plot_stat_map(cres.get_map('logp_level-voxel_corr-FWE_method-permutation'),
              cut_coords=[0, 0, -8], draw_cross=False, cmap='RdBu_r')

MKDA Chi2 with FDR correction

mkda = nimare.meta.cbma.MKDAChi2(kernel__r=10)
dset1 = dset.slice(dset.ids)
dset2 = dset.slice(dset.ids)
mkda.fit(dset1, dset2)
corr = nimare.correct.FDRCorrector(method='fdr_bh', alpha=0.001)
cres = corr.transform(mkda.results)
plot_stat_map(cres.get_map('consistency_z_FDR_corr-FDR_method-fdr_bh'),
              threshold=1.65, cut_coords=[0, 0, -8], draw_cross=False,
              cmap='RdBu_r')

MKDA Chi2 with FWE correction

corr = nimare.correct.FWECorrector(method='permutation', n_iters=10, n_cores=1)
cres = corr.transform(mkda.results)
plot_stat_map(cres.get_map('consistency_z'), threshold=1.65,
              cut_coords=[0, 0, -8], draw_cross=False, cmap='RdBu_r')

KDA

kda = nimare.meta.cbma.KDA(kernel__r=10)
kda.fit(dset)
corr = nimare.correct.FWECorrector(method='permutation', n_iters=10, n_cores=1)
cres = corr.transform(kda.results)
plot_stat_map(cres.get_map('logp_level-voxel_corr-FWE_method-permutation'),
              cut_coords=[0, 0, -8], draw_cross=False, cmap='RdBu_r')

ALE

ale = nimare.meta.cbma.ALE()
ale.fit(dset)
corr = nimare.correct.FWECorrector(method='permutation', n_iters=10, n_cores=1)
cres = corr.transform(ale.results)
plot_stat_map(cres.get_map('logp_level-cluster_corr-FWE_method-permutation'),
              cut_coords=[0, 0, -8], draw_cross=False, cmap='RdBu_r')

SCALE

ijk = np.vstack(np.where(mask_img.get_data())).T
scale = nimare.meta.cbma.SCALE(ijk=ijk, n_iters=10, n_cores=1)
scale.fit(dset)
plot_stat_map(scale.results.get_map('z_vthresh'), cut_coords=[0, 0, -8],
              draw_cross=False, cmap='RdBu_r')