This function calls mcflirt's help
mcflirt.help()Prints help output and returns output as character vector
library(fslr)
if (have.fsl()){
mcflirt.help()
}
#> Usage: mcflirt -in <infile> [options] Available options are: -out, -o <outfile> (default is infile_mcf) -cost {mutualinfo,woods,corratio,normcorr,normmi,leastsquares} (default is normcorr) -bins <number of histogram bins> (default is 256) -dof <number of transform dofs> (default is 6) -refvol <number of reference volume> (default is no_vols/2)- registers to (n+1)th volume in series -reffile, -r <filename> use a separate 3d image file as the target for registration (overrides refvol option) -scaling <num> (6.0 is default) -smooth <num> (1.0 is default - controls smoothing in cost function) -rotation <num> specify scaling factor for rotation optimization tolerances -verbose <num> (0 is least and default) -stages <number of search levels> (default is 3 - specify 4 for final sinc interpolation) -fov <num> (default is 20mm - specify size of field of view when padding 2d volume) -2d Force padding of volume -sinc_final (applies final transformations using sinc interpolation) -spline_final (applies final transformations using spline interpolation) -nn_final (applies final transformations using Nearest Neighbour interpolation) -init <filename> (initial transform matrix to apply to all vols) -gdt (run search on gradient images) -meanvol register timeseries to mean volume (overrides refvol and reffile options) -stats produce variance and std. dev. images -mats save transformation matricies in subdirectory outfilename.mat -plots save transformation parameters in file outputfilename.par -report report progress to screen -help