FSL FUGUE set of tools for EPI distortion correction
Usage
ni_fsl_fugue(
args = NULL,
asym_se_time = NULL,
despike_2dfilter = NULL,
despike_threshold = NULL,
dwell_time = NULL,
dwell_to_asym_ratio = NULL,
fmap_in_file = NULL,
fmap_out_file = NULL,
fourier_order = NULL,
icorr = NULL,
icorr_only = NULL,
in_file = NULL,
mask_file = NULL,
median_2dfilter = NULL,
no_extend = NULL,
no_gap_fill = NULL,
nokspace = NULL,
pava = NULL,
phase_conjugate = NULL,
phasemap_in_file = NULL,
poly_order = NULL,
save_unmasked_fmap = NULL,
save_unmasked_shift = NULL,
shift_in_file = NULL,
shift_out_file = NULL,
smooth2d = NULL,
smooth3d = NULL,
unwarp_direction = NULL,
unwarped_file = NULL,
warped_file = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- args
Character. Additional parameters to the command
- asym_se_time
Numeric. set the fieldmap asymmetric spin echo time (sec)
- despike_2dfilter
Logical. apply a 2D de-spiking filter
- despike_threshold
Numeric. specify the threshold for de-spiking (default=3.0)
- dwell_time
Numeric. set the EPI dwell time per phase-encode line - same as echo spacing - (sec)
- dwell_to_asym_ratio
Numeric. set the dwell to asym time ratio
- fmap_in_file
Character; file path. filename for loading fieldmap (rad/s)
- fmap_out_file
Character; file path. filename for saving fieldmap (rad/s)
- fourier_order
Integer. apply Fourier (sinusoidal) fitting of order N
- icorr
Logical. apply intensity correction to unwarping (pixel shift method only)
- icorr_only
Logical. apply intensity correction only
- in_file
Character; file path. filename of input volume
- mask_file
Character; file path. filename for loading valid mask
- median_2dfilter
Logical. apply 2D median filtering
- no_extend
Logical. do not apply rigid-body extrapolation to the fieldmap
- no_gap_fill
Logical. do not apply gap-filling measure to the fieldmap
- nokspace
Logical. do not use k-space forward warping
- pava
Logical. apply monotonic enforcement via PAVA
- phase_conjugate
Logical. apply phase conjugate method of unwarping
- phasemap_in_file
Character; file path. filename for input phase image
- poly_order
Integer. apply polynomial fitting of order N
- save_unmasked_fmap
Logical. saves the unmasked fieldmap when using –savefmap
- save_unmasked_shift
Logical. saves the unmasked shiftmap when using –saveshift
- shift_in_file
Character; file path. filename for reading pixel shift volume
- shift_out_file
Character; file path. filename for saving pixel shift volume
- smooth2d
Numeric. apply 2D Gaussian smoothing of sigma N (in mm)
- smooth3d
Numeric. apply 3D Gaussian smoothing of sigma N (in mm)
- unwarp_direction
Character; one of: "x", "y", "z", "x-", "y-", "z-". specifies direction of warping (default y)
- unwarped_file
Character; file path. apply unwarping and save as filename
- warped_file
Character; file path. apply forward warping and save as filename
- .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.