Estimate an affine mapping and save its AFNI base-to-source matrix without requiring a resampled image.
Usage
ni_afni_allineate_estimate(
in_file,
reference,
out_matrix,
out_file = "NULL",
cost,
warp_type = "affine_general",
interpolation = "linear",
floatize = TRUE,
no_pad = FALSE,
zclip = FALSE,
weight_file = NULL,
source_mask = NULL,
overwrite = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. Source image to align. Required.
- reference
Character; file path. Fixed base image defining the reference frame. Required.
- out_matrix
Character; file path. Destination for AFNI base-to-source affine rows. Required.
- out_file
Character; file path. Optional resampled image; NULL suppresses image output.
- cost
Character; one of: "lpa+ZZ", "lpa+", "lpa", "lpc+ZZ", "lpc+", "lpc", "nmi", "mi", "hel", "crA", "crM", "crU", "ls". Cost function used for estimation. Required.
- warp_type
Character; one of: "shift_only", "shift_rotate", "shift_rotate_scale", "affine_general". Degrees of freedom for the estimated mapping.
- interpolation
Character; one of: "NN", "linear", "cubic", "quintic". Interpolation used during the fine estimation pass.
- floatize
Logical. Write a requested image output in floating-point format.
- no_pad
Logical. Disable base-image zero padding.
- zclip
Logical. Replace negative source and base values with zero.
- weight_file
Character; file path. Optional weight image on the reference grid.
- source_mask
Character; file path. Optional mask on the source grid.
- overwrite
Logical. Permit AFNI to overwrite existing output datasets.
- .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.