five_tissue_gen: Generat a five-tissue-type (5TT) segmented tissue image...

In muschellij2/mrtrix: Port of MRTrix software

Description

Generat a five-tissue-type (5TT) segmented tissue image suitable for use in Anatomically-Constrained Tractography (ACT)

Usage

five_tissue_gen(infile, algorithm = c("fsl", "freesurfer"),
  outfile = NULL, crop = TRUE, amyg_hipp_gray = FALSE, mask = NULL,
  t2 = NULL, premasked = FALSE, lut = NULL, opts = "",
  verbose = TRUE, ...)

Arguments

infile	The input T1-weighted image
algorithm	algorithm to be used to complete segmentation
outfile	Output image file
crop	crop the resulting 5TT image to reduce its size (changed dimensions compared to input image)
amyg_hipp_gray	Represent the amygdalae and hippocampi as sub-cortical grey matter in the 5TT image
mask	Mask for brain
t2	T2-weighted image in addition to the default T1-weighted image; this will be used as a second input to FSL FAST
premasked	Indicate that brain masking has already been applied to the input image
lut	Manually provide path to the lookup table on which the input parcellation image is based (e.g. FreeSurferColorLUT.txt)
opts	Additional options to pass to function
verbose	Print diagnostic output
...	arguments to pass to std_opts

Value

Output filename

Examples

## Not run: 
infile = "~/Downloads/anat+seg.nii.gz"
t1 = "~/Downloads/t1.nii.gz"
response = five_tissue_gen(t1, algorithm = "freesurfer")

## End(Not run)

muschellij2/mrtrix documentation built on July 9, 2019, 9:15 a.m.