tract_masks

A set of scripts and functions for producing masks from a JSON file of tract end points (which can be parsed from a MRML file).

Requirements

1. @edickie's ciftify module: https://github.com/edickie/ciftify
2. Connectome work bench
3. FSL
4. The following python modules: docopt, nibabel, numpy
5. Also implicitly requires outputs from some commonly used pipelines (hcp, dtifit) for some functions to be run

Contents

tracts_cifti_mask.py:

Can generate a cifti file of masks for each tract in the JSON file. This file is just a
composition of the code in the other scripts.
	1. Uses tract_end_masks to make nifti masks for all end points for the tracts
	2. Smoothes the nifti masks by some given value
	3. Moves the smoothed nifti masks into MNI space
	4. Converts the masks to cifti format
	5. Merges the cifti masks into one single mask

tract_end_masks.py:

Will generate a set of simple nifti masks from the tract end points in the given JSON file

mni_transform.py:

Adapted from a function in Erin W. Dickie's ciftify/func2hcp module. Transforms a given fmri
image into MNI space

utils.py:

A mess of useful functions.