FREESURFER SegStatsReconAll — ni_freesurfer_seg_stats_recon

This class inherits SegStats and modifies it for use in a recon-all workflow.

Usage

ni_freesurfer_seg_stats_recon_all(
  annot,
  lh_orig_nofix,
  lh_pial,
  lh_white,
  rh_orig_nofix,
  rh_pial,
  rh_white,
  ribbon,
  segmentation_file,
  subject_id,
  surf_label,
  transform,
  args = NULL,
  avgwf_file = NULL,
  avgwf_txt_file = NULL,
  brain_vol = NULL,
  brainmask_file = NULL,
  calc_power = NULL,
  calc_snr = NULL,
  color_table_file = NULL,
  cortex_vol_from_surf = NULL,
  default_color_table = NULL,
  empty = NULL,
  etiv = NULL,
  euler = NULL,
  exclude_ctx_gm_wm = NULL,
  exclude_id = NULL,
  frame = NULL,
  gca_color_table = NULL,
  in_file = NULL,
  in_intensity = NULL,
  intensity_units = NULL,
  mask_erode = NULL,
  mask_file = NULL,
  mask_invert = NULL,
  mask_thresh = NULL,
  multiply = NULL,
  non_empty_only = NULL,
  partial_volume_file = NULL,
  segment_id = NULL,
  sf_avg_file = NULL,
  subcort_gm = NULL,
  summary_file = NULL,
  supratent = NULL,
  total_gray = NULL,
  vox = NULL,
  wm_vol_from_surf = NULL,
  .cwd = NULL,
  .env = NULL,
  .engine = NULL,
  .profile = NULL,
  dry_run = FALSE,
  echo = interactive()
)

Arguments

annot: Character or numeric vector. subject hemi parc : use surface parcellation Required.
lh_orig_nofix: Character; file path. Input lh.orig.nofix Required.
lh_pial: Character; file path. Input file must be <subject_id>/surf/lh.pial Required.
lh_white: Character; file path. Input file must be <subject_id>/surf/lh.white Required.
rh_orig_nofix: Character; file path. Input rh.orig.nofix Required.
rh_pial: Character; file path. Input file must be <subject_id>/surf/rh.pial Required.
rh_white: Character; file path. Input file must be <subject_id>/surf/rh.white Required.
ribbon: Character; file path. Input file mri/ribbon.mgz Required.
segmentation_file: Character; file path. segmentation volume path Required.
subject_id: Character. Subject id being processed Required.
surf_label: Character or numeric vector. subject hemi label : use surface label Required.
transform: Character; file path. Input transform file Required.
args: Character. Additional parameters to the command
avgwf_file: Character or numeric vector. Save as binary volume (bool or filename)
avgwf_txt_file: Character or numeric vector. Save average waveform into file (bool or filename)
brain_vol: Character; one of: "brain-vol-from-seg", "brainmask". Compute brain volume either with brainmask or brain-vol-from-seg
brainmask_file: Character; file path. Load brain mask and compute the volume of the brain as the non-zero voxels in this volume
calc_power: Character; one of: "sqr", "sqrt". Compute either the sqr or the sqrt of the input
calc_snr: Logical. save mean/std as extra column in output table
color_table_file: Character; file path. color table file with seg id names
cortex_vol_from_surf: Logical. Compute cortex volume from surf
default_color_table: Logical. use $FREESURFER_HOME/FreeSurferColorLUT.txt
empty: Logical. Report on segmentations listed in the color table
etiv: Logical. Compute ICV from talairach transform
euler: Logical. Write out number of defect holes in orig.nofix based on the euler number
exclude_ctx_gm_wm: Logical. exclude cortical gray and white matter
exclude_id: Integer. Exclude seg id from report
frame: Integer. Report stats on nth frame of input volume
gca_color_table: Character; file path. get color table from GCA (CMA)
in_file: Character; file path. Use the segmentation to report stats on this volume
in_intensity: Character; file path. Undocumented input norm.mgz file
intensity_units: Character; one of: "MR". Intensity units
mask_erode: Integer. Erode mask by some amount
mask_file: Character; file path. Mask volume (same size as seg
mask_invert: Logical. Invert binarized mask volume
mask_thresh: Numeric. binarize mask with this threshold <0.5>
multiply: Numeric. multiply input by val
non_empty_only: Logical. Only report nonempty segmentations
partial_volume_file: Character; file path. Compensate for partial voluming
segment_id: Character or numeric vector. Manually specify segmentation ids
sf_avg_file: Character or numeric vector. Save mean across space and time
subcort_gm: Logical. Compute volume of subcortical gray matter
summary_file: Character; file path. Segmentation stats summary table file
supratent: Logical. Undocumented input flag
total_gray: Logical. Compute volume of total gray matter
vox: Character or numeric vector. Replace seg with all 0s except at C R S (three int inputs)
wm_vol_from_surf: Logical. Compute wm volume from surf
.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.

Value

An ni_result object.