This function calls Freesurfer command passed to func
fs_cmd(
func,
file,
outfile = NULL,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
opts = "",
verbose = TRUE,
samefile = FALSE,
opts_after_outfile = FALSE,
frontopts = "",
add_ext = TRUE,
bin_app = "bin",
...
)
If retimg
then object of class nifti. Otherwise,
Result from system command, depends if intern is TRUE or FALSE.
(character) Freesurfer function
(character) image to be manipulated
(character) resultant image name (optional)
(logical) return image of class nifti
(logical) If retimg, should file be reoriented when read in?
Passed to readnii
.
(logical) to be passed to system
(character) operations to be passed to func
(logical) print out command before running
(logical) is the output the same file?
(logical) should opts
come after
the outfile
in the Freesurfer command?
(character) options/character to put in before filename
(logical) should the extension be added to
the outfile
(character) appendix to add to get_fs
additional arguments passed to system
.