FSL prelude wrapper for phase unwrapping
Usage
ni_fsl_prelude(
complex_phase_file,
magnitude_file,
phase_file,
args = NULL,
end = NULL,
label_file = NULL,
labelprocess2d = NULL,
mask_file = NULL,
num_partitions = NULL,
process2d = NULL,
process3d = NULL,
rawphase_file = NULL,
removeramps = NULL,
savemask_file = NULL,
start = NULL,
threshold = NULL,
unwrapped_phase_file = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- complex_phase_file
Character; file path. complex phase input volume Required.
- magnitude_file
Character; file path. file containing magnitude image Required.
- phase_file
Character; file path. raw phase file Required.
- args
Character. Additional parameters to the command
- end
Integer. final image number to process (default Inf)
- label_file
Character; file path. saving the area labels output
- labelprocess2d
Logical. does label processing in 2D (slice at a time)
- mask_file
Character; file path. filename of mask input volume
- num_partitions
Integer. number of phase partitions to use
- process2d
Logical. does all processing in 2D (slice at a time)
- process3d
Logical. forces all processing to be full 3D
- rawphase_file
Character; file path. saving the raw phase output
- removeramps
Logical. remove phase ramps during unwrapping
- savemask_file
Character; file path. saving the mask volume
- start
Integer. first image number to process (default 0)
- threshold
Numeric. intensity threshold for masking
- unwrapped_phase_file
Character; file path. file containing unwrapepd phase
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.