nimare.transforms.ImagesToCoordinates

class ImagesToCoordinates(merge_strategy='fill', cluster_threshold=None, remove_subpeaks=False, two_sided=False, min_distance=8.0, z_threshold=3.1)

Bases: nimare.base.Transformer

Transformer from images to coordinates.

New in version 0.0.8.

Parameters

• merge_strategy ({“fill”, “replace”, “demolish”}, optional) – Strategy for how to incorporate the generated coordinates with possible pre-existing coordinates. Default=”fill”. Descriptions of the options:

  • "fill": only add coordinates to study contrasts that do not have coordinates. If a study contrast has both image and coordinate data, the original coordinate data will be kept.

  • "replace": replace existing coordinates with coordinates generated by this function. If a study contrast only has coordinate data and no images or if the statistical threshold is too high for nimare to detect any peaks the original coordinates will be kept.

  • "demolish": only keep generated coordinates and discard any study contrasts with coordinate data, but no images.

• cluster_threshold (int or None, optional) – Cluster size threshold, in voxels. Default=None.

• remove_subpeaks (bool, optional) – If True, removes subpeaks from the cluster results. Default=False.

• two_sided (bool, optional) – Whether to employ two-sided thresholding or to evaluate positive values only. Default=False.

• min_distance (float, optional) – Minimum distance between subpeaks in mm. Default=8mm.

• z_threshold (float) – Cluster forming z-scale threshold. Default=3.1.

Notes

The raw Z and/or P maps are not corrected for multiple comparisons. Uncorrected z-values and/or p-values are used for thresholding.

get_params(deep=True)

Get parameters for this estimator.

Parameters

deep (bool, optional) – If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns

params (dict) – Parameter names mapped to their values.

classmethod load(filename, compressed=True)

Load a pickled class instance from file.

Parameters

• filename (str) – Name of file containing object.

• compressed (bool, optional) – If True, the file is assumed to be compressed and gzip will be used to load it. Otherwise, it will assume that the file is not compressed. Default = True.

Returns

obj (class object) – Loaded class object.

save(filename, compress=True)

Pickle the class instance to the provided file.

Parameters

• filename (str) – File to which object will be saved.

• compress (bool, optional) – If True, the file will be compressed with gzip. Otherwise, the uncompressed version will be saved. Default = True.

set_params(**params)

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as pipelines). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Returns

self

transform(dataset)

Create coordinate peaks from statistical images.

Parameters

dataset (nimare.dataset.Dataset) – Dataset with z maps and/or p maps that can be converted to coordinates.

Returns

dataset (nimare.dataset.Dataset) – Dataset with coordinates generated from images and metadata indicating origin of coordinates (‘original’ or ‘nimare’).

Examples using nimare.transforms.ImagesToCoordinates

Transform images into coordinates

Compare image and coordinate based meta-analyses on 21 pain studies