segment_t1_fsl: Segment T1 weighted MRI data using FSL FAST and write to...

In spant: MR Spectroscopy Analysis Tools

Segment T1 weighted MRI data using FSL FAST and write to file. Runs deface and bet as preprocessing steps by default.

Description

This function requires a working installation of FSL and uses the fslr package. You may need to specify the fsl install directory, eg: 'options(fsl.path = "/path/to/fsl")'

Usage

segment_t1_fsl(mri_path, deface = TRUE, bet_fit = 0.5)

Arguments

mri_path	path to the volumetric T1 data.
deface	deface the input T1 data before analysis. Defaults to TRUE.
bet_fit	fractional intensity threshold for bet brain extraction. Values should be between 0 and 1. Defaults to 0.5 with smaller values giving larger brain estimates.

spant documentation built on April 4, 2025, 1:40 a.m.