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	GUI for interacting with gyral coordinate scripts
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

Multiple diffusion encoding (MDE)

MDE.btensor	Extracts b-tensor for given sequence
MDE.fit_dispersion	Fit dispersing zeppelin model (single Bingham)
MDE.generate_data	Module to generate fake mutiple diffusion encoding data under the Gaussian assumption
MDE.micro_anisotropy	Extracts micro-anisotropy from mean signal
MDE.spherical_mean	Computes spherical mean signal

Metadata beyond bvals/bvecs

sidecar.index	Indexes the volumes into shells based on the sidecar
sidecar.merge	Merges multiple sidecars into one

Non-Gaussian noise

non_central_chi.correct	Corrects MRI signal for the noise floor
non_central_chi.variance	Estimates the variance of the noise assuming a non-central chi distribution

Scatter plots

plot.scatter_dconn	Scatter plot of dense connectomes
plot.scatter_dscalar	Scatter plot of dense scalar files
plot.scatter_gifti	Scatter plot of gifti files

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
tree.from_jal	Copies files matching short name from jalapeno

Bibtex scripts

bibtex.query	Query pubmed and adds result to bibtex file
bibtex.update	Updates entries in an existing bibtex file

Various

mask_dlabel	Masks out part of a dlabel file based on a dscalar file
round_bvals	Rounds the input b-values