SynthStrip is a deep-learning skull-stripping tool that produces accurate brain masks across MRI contrasts (T1w, T2w, FLAIR, EPI, CT). Bundled with FreeSurfer 7.3+ as the mri_synthstrip command.
Usage
ni_freesurfer_synthstrip(
in_file,
out_file = NULL,
mask_file = NULL,
sdt_file = NULL,
border = NULL,
gpu = NULL,
threads = NULL,
no_csf = NULL,
model = NULL,
args = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. Input volume to skull strip (any MRI contrast) Required.
- out_file
Character; file path. Skull-stripped image output
- mask_file
Character; file path. Binary brain mask output
- sdt_file
Character; file path. Signed distance transform output
- border
Integer. Mask border threshold in mm (default 1)
- gpu
Logical. Use the GPU for inference
- threads
Integer. Number of CPU threads
- no_csf
Logical. Exclude CSF from the brain mask (uses the SynthStrip-CSF model)
- model
Character; file path. Path to alternate model weights file
- args
Character. Additional parameters passed verbatim to mri_synthstrip
- .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.