readsliceimg: Read MRI slice data

In dpmixsim: Dirichlet Process Mixture Model Simulation for Clustering and Image Segmentation

Description

readsliceimg reads MRI and mask data.

Usage

readsliceimg(fbase="t1_pn3_rf0", swap=FALSE)

Arguments

fbase

Indicates the dataset prefix of the MRI dataset to use. The prefix applies to data files: ‘{fbase}_slice_0092.nii.gz’, and ‘{fbase}_slice_0092_mask.nii.gz’. These data files were obtained from the BrainWeb repository of the McConnell Brain Imaging Center at the Montreal Neurological Institute. BrainWeb anatomical models uses MRI slices of dimension 181x217 pixels. The datasets included in the package for demonstration correspond to a T1 BrainWeb image for slice number 92, with 3% noise and 0% intensity non-uniformity.

swap

logical variable (default = FALSE) for choosing the right/left data display convention consistent with FSLVIEW

Details

The FSL tools may be used to prepare the MRI data and the mask required as data input. The package oro.nifti is used for reading gzipped NIFTI files.

Value

a list containing

fbase	dataset prefix of the dataset used in the analysis
niislice	slice data at all timepoints
mask	slice mask
nrow	number of rows
ncol	number of columns
swap	relative orientation used in the data setup

Author(s)

A. Ferreira da Silva, Universidade Nova de Lisboa, Faculdade de Ciencias e Tecnologia,
[e-mail].

References

Brandon Whitcher, Volker Schmid and Andrew Thornton, Package oro.nifti: Rigorous - NIfTI Input / Output, 2010.

FSL/FEAT Analysis tool, FMRIB Software Library (FSL) (www.fmrib.ox.ac.uk/fsl)

See Also

dpmixsim

Examples

## Not run: 
slicedata <- readsliceimg(fbase="t1_pn3_rf0", swap=FALSE)
print(str(slicedata))

## End(Not run)

dpmixsim documentation built on May 1, 2019, 7:29 p.m.