Note
Click here to download the full example code
Use NeuroVault statistical maps in NiMARE
Download statistical maps from NeuroVault, then use them in a meta-analysis, with NiMARE.
import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map
Conversion of Statistical Maps
Some of the statistical maps are T statistics and others are Z statistics.
To perform a Fisher’s meta analysis, we need all Z maps.
Thoughtfully, NiMARE has a class named ImageTransformer
that will
help us.
from nimare.transforms import ImageTransformer
# Not all studies have Z maps!
dset.images[["z"]]
z_transformer = ImageTransformer(target="z")
dset = z_transformer.transform(dset)
Out:
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.0.12rc1/lib/python3.7/site-packages/nilearn/image/resampling.py:602: RuntimeWarning: NaNs or infinite values are present in the data passed to resample. This is a bad thing as they make resampling ill-defined and much slower.
fill_value=fill_value)
All studies now have Z maps!
dset.images[["z"]]
Run a Meta-Analysis
With the missing Z maps filled in, we can run a Meta-Analysis and plot our results
from nimare.meta.ibma import Fishers
# The default template has a slightly different, but completely compatible,
# affine than the NeuroVault images, so we allow the Estimator to resample
# images during the fitting process.
meta = Fishers(resample=True)
meta_res = meta.fit(dset)
fig, ax = plt.subplots()
display = plot_stat_map(meta_res.get_map("z"), threshold=3.3, axes=ax, figure=fig)
fig.show()
# The result may look questionable, but this code provides
# a template on how to use neurovault in your meta analysis.
Out:
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.0.12rc1/lib/python3.7/site-packages/nilearn/plotting/img_plotting.py:348: FutureWarning: Default resolution of the MNI template will change from 2mm to 1mm in version 0.10.0
anat_img = load_mni152_template()
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.0.12rc1/lib/python3.7/site-packages/nilearn/_utils/niimg.py:62: UserWarning: Non-finite values detected. These values will be replaced with zeros.
"Non-finite values detected. "
Total running time of the script: ( 0 minutes 22.234 seconds)