API reference

Datasets

Preprocessed fMRI datasets. Each class downloads what it needs on first use and returns data matrices in a chosen brain space.

Geometry, masks, parcellations, morphometry, and mappings for the standard surface spaces (onavg, fsaverage) and MNI volume grids.

geometry	Surface geometry.
mask	Standard cortical mask.
mapping	Get mapping (transform) from one space to another.
parcellation	Group-based parcellation.
morphometry	Group-based morphometry measure.
distances	Distances between vertices.
smooth	Get a smoothing matrix.
sls	Get a list of vertex indices for searchlight analysis.
tpl	Connectivity hyperalignment template.

Surface meshes, spheres, and surface alignment.

Surface
Sphere
Aligner	Aligns a surface to a template using Procrustes analysis.

Modeling, statistics, and benchmarking.

glm	General linear model.
isc	Compute inter-subject correlation (ISC) from data matrices.
pearsonr	Pearson correlation coefficient.
classification	Movie time point/segment classification accuracy.
stats.cronbach_alpha	Cronbach’s alpha.
stats.cronbach_alpha_ci	Confidence interval for Cronbach’s alpha.
stats.spearman_brown	Spearman-Brown prediction formula.
stats.spearman_brown_inv	Predicting required test length for a given reliability.
stats.noise_ceilings	Noise ceilings.
stats.normalize	Normalize the data to normal distribution.
linalg.safe_svd	Singular value decomposition without occasional LinAlgError crashes.
linalg.safe_polar	Polar decomposition without occasional LinAlgError crashes.
linalg.gram_pca	Principal component analysis (PCA) based on the Gram matrix.
linalg.ensemble_lstsq	Linear regression with k-fold bagging.
ensemble.kfold_bagging	Generate train and test indices for k-fold bagging.
ensemble.kfold_bagging_groups	Generate train and test indices for k-fold bagging with group constraints.
ensemble.permute_groups	Generate permutations of group members.

Render surface maps as 2D images.

File I/O, result caching, and archiving.

load	Load the file using the automatically determined function.
save	Save the data using the automatically determined format.
record	Run the function and save the returned output to file.
percentile
archive	Create a lzma compressed tar file from a list of files and/or directories.
archive_check	Check if the lzma file is correct by comparing it with the original files.
utils.monitor	Monitors function execution and records running time and system information.
utils.parse_record	Parse the timing information based on record.
utils.assert_sufficient_time	Check if remaining SLURM walltime is sufficient.