Make a binary volume from a Freesurfer label
Usage
ni_freesurfer_label2_vol(
annot_file,
aparc_aseg,
label_file,
seg_file,
template_file,
args = NULL,
fill_thresh = NULL,
hemi = NULL,
identity = NULL,
invert_mtx = NULL,
label_hit_file = NULL,
label_voxel_volume = NULL,
map_label_stat = NULL,
native_vox2ras = NULL,
proj = NULL,
reg_file = NULL,
reg_header = NULL,
subject_id = NULL,
surface = NULL,
vol_label_file = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- annot_file
Character; file path. surface annotation file Required.
- aparc_aseg
Logical. use aparc+aseg.mgz in subjectdir as seg Required.
- label_file
Character or numeric vector. list of label files Required.
- seg_file
Character; file path. segmentation file Required.
- template_file
Character; file path. output template volume Required.
- args
Character. Additional parameters to the command
- fill_thresh
Character. thresh : between 0 and 1
- hemi
Character; one of: "lh", "rh". hemisphere to use lh or rh
- identity
Logical. set R=I
- invert_mtx
Logical. Invert the registration matrix
- label_hit_file
Character; file path. file with each frame is nhits for a label
- label_voxel_volume
Numeric. volume of each label point (def 1mm3)
- map_label_stat
Character; file path. map the label stats field into the vol
- native_vox2ras
Logical. use native vox2ras xform instead of tkregister-style
- proj
Character or numeric vector. project along surface normal
- reg_file
Character; file path. tkregister style matrix VolXYZ = R*LabelXYZ
- reg_header
Character; file path. label template volume
- subject_id
Character. subject id
- surface
Character. use surface instead of white
- vol_label_file
Character; file path. output volume
- .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.