FSL slicetimer wrapper to perform slice timing correction
Usage
ni_fsl_slice_timer(
in_file,
args = NULL,
custom_order = NULL,
custom_timings = NULL,
global_shift = NULL,
index_dir = NULL,
interleaved = NULL,
out_file = NULL,
slice_direction = NULL,
time_repetition = NULL,
custom_timing_units = NULL,
timing_reference = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. filename of input timeseries Required.
- args
Character. Additional parameters to the command
- custom_order
Character; file path. filename of single-column custom interleave order file (first slice is referred to as 1 not 0)
- custom_timings
Character; file path. Single-column FSL forward shifts in fractions of TR. Negative values shift data backwards. custom_timing_units and timing_reference are required.
- global_shift
Numeric. Global forward shift in fractions of TR; 0 means no global shift.
- index_dir
Logical. slice indexing from top to bottom
- interleaved
Logical. use interleaved acquisition
- out_file
Character; file path. Requested corrected NIfTI path. slicetimer receives its extension-free stem and FSL appends the configured NIFTI or NIFTI_GZ suffix.
- slice_direction
Character; one of: "1", "2", "3". direction of slice acquisition (x=1, y=2, z=3) - default is z
- time_repetition
Numeric. Repetition time in seconds.
- custom_timing_units
Character; one of: "fraction_of_tr". Units contract for custom_timings; FSL accepts forward-shift fractions of TR only.
- timing_reference
Character; one of: "forward_shift_to_reference". Interpretation contract for custom_timings: every file value is a forward shift to the declared reference.
- .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.