All scripts

Link directory contents

iter_link	Iterates through source directory linking each file to destination directory.
merge_hcp	Creates new directory with links to HCP data

NIFTI/GIFTI/CIFTI to dataframes

to_dataframe	Converts a NIFTI/GIFTI/CIFTI file into a pandas dataframe
to_dataframe_tree	Converts related files loaded from a tree into a pandas dataframe.

create/analyze CIFTI files

cifti.convert	Converts between CIFTI formats (NIFTI, HDF5, and zarr)
cifti.correlate	Correlates two CIFTI files
cifti.ptx2dconn	Converts probtrackX to dconn
cifti.smooth	Smooths the values in the GIFTI or CIFTI file across the surface

Functional MRI scripts

function.normalize

Normalizes the functional MRI data based on the noise level and concatenates results

Gyral coordinate system

gcoord.gen	Generates the gyral coordinates in a volume
gcoord.gui
gcoord.mult	Converts dyads into gyral coordinate system
gcoord.split	Extract radial, sulcal, and gyral orientations from gyral coordinate NIFTI file
gcoord.transition	Extract fibre orientation transition boundary

ProbtrackX helpers

ptx.select_vertex

Selects vertices on surface to run tractography from

Splits voxel-wise job into multiple sub-jobs

split.merge	Merge result from individual runs
split.run	Run part of the voxel-wise job
split.submit	Submits a job using a mask in multiple parts

GIFTI surfaces

surface.from_mask	Creates a surface covering the mask
surface.from_ridge	Assigns each vertex the value from the closest ridge (BUGGY)
surface.gradient	Computes the feature similarity with the neighbouring vertices
surface.roi_dist_gifti	For every vertex computes the distance to the closest point in a ROI
surface.smooth	Smooths the surface mesh
surface.watershed	Creates maps of gyri or sulci using watershed algorithm

Surface parcellations

parcel.cluster	Clusters the surface based on provided features
parcel.combine	Combines two parcellations into a single parcellation by multiplying them
parcel.discretise	Discretizes a continuous variable
parcel.random	Randomly parcellates a surface
parcel.spectral	Parcellates the surface based on clustering similar fingerprints

Tree helper functions

tree.extract

Extract filenames from a FileTree

Various

round_bvals

Rounds the input b-values