AC/PC Reorientation — acpc_reorient • spm12r

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

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