FastSurfer: GPU-accelerated brain segmentation and cortical surface reconstruction
Usage
ni_fastsurfer_run(
t1,
sid,
sd,
fs_license = NULL,
t2 = NULL,
seg_only = NULL,
surf_only = NULL,
device = NULL,
viewagg_device = NULL,
threads = NULL,
vox_size = NULL,
three_t = NULL,
no_asegdkt = NULL,
no_cereb = NULL,
no_hypothal = NULL,
no_cc = NULL,
no_biasfield = NULL,
no_surfreg = NULL,
no_fs_t1 = NULL,
py = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- t1
Character; file path. Input T1-weighted image Required.
- sid
Character. Subject ID Required.
- sd
Character; directory path. Subjects directory (output root) Required.
- fs_license
Character; file path. FreeSurfer license file
- t2
Character; file path. Optional T2-weighted image for hypothalamus segmentation
- seg_only
Logical. Run segmentation only (skip surface reconstruction, ~5 min)
- surf_only
Logical. Run surface reconstruction only (requires prior segmentation)
- device
Character; one of: "auto", "cpu", "cuda", "mps". Device for DNN inference
- viewagg_device
Character; one of: "cpu", "cuda". Device for view aggregation (use cpu to reduce VRAM usage)
- threads
Integer. Number of parallel threads
- vox_size
Character. Voxel size for processing (0.7-1.0 or 'min')
- three_t
Logical. Use the 3T atlas for talairach registration
- no_asegdkt
Logical. Skip whole-brain DKT segmentation
- no_cereb
Logical. Skip cerebellum segmentation
- no_hypothal
Logical. Skip hypothalamus segmentation
- no_cc
Logical. Skip corpus callosum segmentation
- no_biasfield
Logical. Skip bias field correction
- no_surfreg
Logical. Skip surface registration (spherical registration)
- no_fs_t1
Logical. Skip T1.mgz generation from conformed image
- py
Character. Python command to use (override default)
- .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.