In muschellij2/ct.malf.templates: Template Images for Multi-Atlas Label Fusion ('MALF') for Computed Tomography ('CT') Images

Data Disclaimer

A summary of this message is seen when you load in the package:

library(ct.malf.templates)

Where is the Data located?

The ct_malf_images is the general workhorse function for returning the data from the MALF templates.

mi = ct_malf_images()
names(mi)

The return is a list of filenames, broken into images (raw T1-weighted scans) and masks (binary brain masks).

Derivative Functions

The ct_malf_template_images, ct_malf_template_labels, ct_malf_template_brains, ct_malf_template_masks functions all call ct_malf_images and take the relevant element of the list for easier use.

MASS Derivatives

The ct_mass_images function was created. It simply returns the images and the brain masks. Generally, these are used for MASS (multi-atlas skull stripping), which is a bit more specific (but more widely-applicable) applicatio of label fusion:

mi = ct_mass_images()
names(mi)
head(ct_mass_template_images())
head(ct_mass_template_masks())

The large difference is that ct_mass_images (and the derivative functions) simply take the n_templates argument for the number of templates to return (from 1 to 35).

What to use them with?

Using the extrantsr::malf function, these functions can be used for MALF. The images/brain images are passed into the template.images argument and the structures/brain masks are passed into the template.structs argument.

Why have you not shown me a MALF example?

We have not included this code in the vignettes due to install times for extrantsr as a Suggests package.

muschellij2/ct.malf.templates documentation built on May 23, 2019, 8:33 a.m.