acpc_reorient: AC/PC Reorientation

In muschellij2/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

AC/PC Reorientation

Description

Function that AC/PC re-orients the images for SPM spatial normalization routine. Uses nii_setOrigin from http://www.mccauslandcenter.sc.edu/CRNL/sw/spm8/spm.zip

Usage

acpc_reorient(
  infiles,
  modality = c("T1", "T2", "CT", "fMRI"),
  spmdir = spm_dir(),
  verbose = TRUE,
  install_dir = NULL,
  ...
)

Arguments

infiles	(character) Files to reorient. First file will be used to estimate AC/PC, then rest will be transformed
modality	T1, T2, CT, fMRI (T2*)
spmdir	(character) path for SPM12. If NULL, assumes SPM12 is in matlabpath and so is spm8/toolbox Must have nii_setOrigin installed. In system.file("", package="spm12r") from http://www.mccauslandcenter.sc.edu/CRNL/sw/spm8/spm.zip
verbose	(logical) Print diagnostic output
install_dir	directory to download SPM12
...	Arguments to pass to run_matlab_code

Value

Exit code from MATLAB. If not zero, there was an error

muschellij2/spm12r documentation built on Aug. 31, 2022, 9:49 p.m.