This function calls fslorient's help
fslorient.help()Prints help output and returns output as character vector
if (have.fsl()){
fslorient.help()
}
#> Usage: fslorient <main option> <filename> where the main option is one of: -getorient (prints FSL left-right orientation) -getsform (prints the 16 elements of the sform matrix) -getqform (prints the 16 elements of the qform matrix) -setsform <m11 m12 ... m44> (sets the 16 elements of the sform matrix) -setqform <m11 m12 ... m44> (sets the 16 elements of the qform matrix) -getsformcode (prints the sform integer code) -getqformcode (prints the qform integer code) -setsformcode <code> (sets sform integer code) -setqformcode <code> (sets qform integer code) -copysform2qform (sets the qform equal to the sform - code and matrix) -copyqform2sform (sets the sform equal to the qform - code and matrix) -deleteorient (removes orient info from header) -forceradiological (makes FSL radiological header) -forceneurological (makes FSL neurological header - not Analyze) -swaporient (swaps FSL radiological and FSL neurological) Note: the stored data order is never changed here - only the header info. To change the data storage use fslswapdim. e.g. fslorient -forceradiological myimage fslorient -copysform2qform myimage fslorient -setsform -2 0 0 90 0 2 0 -126 0 0 2 -72 0 0 0 1 myimage