Uses recon-all to generate surfaces and parcellations of structural data
Usage
ni_freesurfer_recon_all(
FLAIR_file = NULL,
T1_files = NULL,
T2_file = NULL,
args = NULL,
base_template_id = NULL,
base_timepoint_ids = NULL,
big_ventricles = NULL,
brainstem = NULL,
directive = "all",
expert = NULL,
flags = NULL,
hemi = NULL,
hippocampal_subfields_T1 = NULL,
hippocampal_subfields_T2 = NULL,
hires = NULL,
longitudinal_template_id = NULL,
longitudinal_timepoint_id = NULL,
mprage = NULL,
openmp = NULL,
parallel = NULL,
subject_id = NULL,
subjects_dir = NULL,
use_FLAIR = NULL,
use_T2 = NULL,
xopts = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- FLAIR_file
Character; file path. Convert FLAIR image to orig directory
- T1_files
Character or numeric vector. name of T1 file to process
- T2_file
Character; file path. Convert T2 image to orig directory
- args
Character. Additional parameters to the command
- base_template_id
Character. base template id
- base_timepoint_ids
Character or numeric vector. processed timepoint to use in template
- big_ventricles
Logical. For use in subjects with enlarged ventricles
- brainstem
Logical. Segment brainstem structures
- directive
Character; one of: "all", "autorecon1", "autorecon2", "autorecon2-volonly", "autorecon2-perhemi", "autorecon2-inflate1", "autorecon2-cp", "autorecon2-wm", "autorecon3", "autorecon3-T2pial", "autorecon-pial", "autorecon-hemi", "localGI", "qcache". process directive
- expert
Character; file path. Set parameters using expert file
- flags
Character or numeric vector. additional parameters
- hemi
Character; one of: "lh", "rh". hemisphere to process
- hippocampal_subfields_T1
Logical. segment hippocampal subfields using input T1 scan
- hippocampal_subfields_T2
Character or numeric vector. segment hippocampal subfields using T2 scan, identified by ID (may be combined with hippocampal_subfields_T1)
- hires
Logical. Conform to minimum voxel size (for voxels < 1mm)
- longitudinal_template_id
Character. longitudinal base template id
- longitudinal_timepoint_id
Character. longitudinal session/timepoint id
- mprage
Logical. Assume scan parameters are MGH MP-RAGE protocol, which produces darker gray matter
- openmp
Integer. Number of processors to use in parallel
- parallel
Logical. Enable parallel execution
- subject_id
Character. subject name
- subjects_dir
Character; directory path. path to subjects directory
- use_FLAIR
Logical. Use FLAIR image to refine the pial surface
- use_T2
Logical. Use T2 image to refine the pial surface
- xopts
Character; one of: "use", "clean", "overwrite". Use, delete or overwrite existing expert options file
- .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.