SynthMorph image registration: deep-learning, contrast-agnostic affine and deformable registration. Bundled with FreeSurfer 7.4+ as 'mri_synthmorph register' and distributed standalone as the freesurfer/synthmorph Docker image.
Usage
ni_freesurfer_synthmorph_register(
moving,
fixed,
out_moving = NULL,
out_fixed = NULL,
trans = NULL,
inverse = NULL,
header_only = NULL,
model = NULL,
init = NULL,
extent = NULL,
threads = NULL,
gpu = NULL,
resample = NULL,
args = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- moving
Character; file path. Moving image to register to the fixed image Required.
- fixed
Character; file path. Fixed (target) image Required.
- out_moving
Character; file path. Save moving image resampled into fixed space
- out_fixed
Character; file path. Save fixed image resampled into moving space
- trans
Character; file path. Save transform mapping moving to fixed
- inverse
Character; file path. Save inverse transform mapping fixed to moving
- header_only
Logical. Adjust voxel-to-world matrix only (no resampling)
- model
Character; one of: "joint", "deform", "affine", "rigid". Registration model
- init
Character; file path. Initial affine transform (LTA, mat, or txt)
- extent
Integer. Registration FOV side length in mm (default 256)
- threads
Integer. Number of CPU threads
- gpu
Logical. Use the GPU for inference
- resample
Logical. Resample fixed image to moving space
- args
Character. Additional parameters passed verbatim to mri_synthmorph register
- .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.