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AFNI AutoTLRC

Source: R/wrappers_auto.R
ni_afni_auto_tlrc.Rd

A minimal wrapper for the AutoTLRC script

Usage

ni_afni_auto_tlrc(
  base,
  in_file,
  args = NULL,
  no_ss = NULL,
  .cwd = NULL,
  .env = NULL,
  .engine = NULL,
  .profile = NULL,
  dry_run = FALSE,
  echo = interactive()
)

Arguments

base

Character. Reference anatomical volume. Usually this volume is in some standard space like TLRC or MNI space and with afni dataset view of (+tlrc). Preferably, this reference volume should have had the skull removed but that is not mandatory. AFNI's distribution contains several templates. For a longer list, use "whereami -show_templates" TT_N27+tlrc –> Single subject, skull stripped volume. This volume is also known as N27_SurfVol_NoSkull+tlrc elsewhere in AFNI and SUMA land. (www.loni.ucla.edu, www.bic.mni.mcgill.ca) This template has a full set of FreeSurfer (surfer.nmr.mgh.harvard.edu) surface models that can be used in SUMA. For details, see Talairach-related link: https://afni.nimh.nih.gov/afni/suma TT_icbm452+tlrc –> Average volume of 452 normal brains. Skull Stripped. (www.loni.ucla.edu) TT_avg152T1+tlrc –> Average volume of 152 normal brains. Skull Stripped.(www.bic.mni.mcgill.ca) TT_EPI+tlrc –> EPI template from spm2, masked as TT_avg152T1 TT_avg152 and TT_EPI volume sources are from SPM's distribution. (www.fil.ion.ucl.ac.uk/spm/) If you do not specify a path for the template, the script will attempt to locate the template AFNI's binaries directory. NOTE: These datasets have been slightly modified from their original size to match the standard TLRC dimensions (Jean Talairach and Pierre Tournoux Co-Planar Stereotaxic Atlas of the Human Brain Thieme Medical Publishers, New York, 1988). That was done for internal consistency in AFNI. You may use the original form of these volumes if you choose but your TLRC coordinates will not be consistent with AFNI's TLRC database (San Antonio Talairach Daemon database), for example. Required.

in_file

Character; file path. Original anatomical volume (+orig).The skull is removed by this scriptunless instructed otherwise (-no_ss). Required.

args

Character. Additional parameters to the command

no_ss

Logical. Do not strip skull of input data set (because skull has already been removed or because template still has the skull) NOTE: The -no_ss option is not all that optional. Here is a table of when you should and should not use -no_ss +——————+————+—————+ | Dataset | Template | +==================+============+===============+ | | w/ skull | wo/ skull | +——————+————+—————+ | WITH skull | -no_ss | xxx | +——————+————+—————+ | WITHOUT skull | No Cigar | -no_ss | +——————+————+—————+ Template means: Your template of choice Dset. means: Your anatomical dataset -no_ss means: Skull stripping should not be attempted on Dset xxx means: Don't put anything, the script will strip Dset No Cigar means: Don't try that combination, it makes no sense.

.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.