create an anatomical segmentation for the geometric transfer matrix (GTM).
Usage
ni_freesurfer_gtm_seg(
subject_id,
args = NULL,
colortable = NULL,
ctx_annot = NULL,
dmax = NULL,
head = NULL,
keep_cc = NULL,
keep_hypo = NULL,
no_pons = NULL,
no_seg_stats = NULL,
no_vermis = NULL,
out_file = "gtmseg.mgz",
output_upsampling_factor = NULL,
subseg_cblum_wm = NULL,
subsegwm = NULL,
upsampling_factor = NULL,
wm_annot = NULL,
xcerseg = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- subject_id
Character. subject id Required.
- args
Character. Additional parameters to the command
- colortable
Character; file path. colortable
- ctx_annot
Character or numeric vector. annot lhbase rhbase : annotation to use for cortical segmentation (default is aparc 1000 2000)
- dmax
Numeric. distance threshold to use when subsegmenting WM (default is 5)
- head
Character. use headseg instead of apas+head.mgz
- keep_cc
Logical. do not relabel corpus callosum as WM
- keep_hypo
Logical. do not relabel hypointensities as WM when subsegmenting WM
- no_pons
Logical. do not add pons segmentation when doing —xcerseg
- no_seg_stats
Logical. do not compute segmentation stats
- no_vermis
Logical. do not add vermis segmentation when doing —xcerseg
- out_file
Character; file path. output volume relative to subject/mri
- output_upsampling_factor
Integer. set output USF different than USF, mostly for debugging
- subseg_cblum_wm
Logical. subsegment cerebellum WM into core and gyri
- subsegwm
Logical. subsegment WM into lobes (default)
- upsampling_factor
Integer. upsampling factor (default is 2)
- wm_annot
Character or numeric vector. annot lhbase rhbase : annotation to use for WM segmentation (with –subsegwm, default is lobes 3200 4200)
- xcerseg
Logical. run xcerebralseg on this subject to create apas+head.mgz
- .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.