Segment T1 weighted MRI data using FSL FAST and write to file. Runs bet as a preprocessing step by default. — segment_t1_fsl • Spectroscopy Analysis Tools (spant)

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, out_dir = NULL, deface = FALSE, bet_fit = 0.5)

Arguments

mri_path: path to the volumetric T1 data.
out_dir: optional output directory. Defaults to the same directory as mri_path if not specified.
deface: deface the input T1 data before analysis. Defaults to FALSE.
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.