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

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")'

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

Arguments

mri_path

path to the volumetric T1 data.

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.