This function calls flirt's help
flirt.help()Prints help output and returns output as character vector
if (have.fsl()){
flirt.help()
}
#> FLIRT version 6.0Usage: flirt [options] -in <inputvol> -ref <refvol> -out <outputvol> flirt [options] -in <inputvol> -ref <refvol> -omat <outputmatrix> flirt [options] -in <inputvol> -ref <refvol> -applyxfm -init <matrix> -out <outputvol> Available options are: -in <inputvol> (no default) -ref <refvol> (no default) -init <matrix-filname> (input 4x4 affine matrix) -omat <matrix-filename> (output in 4x4 ascii format) -out, -o <outputvol> (default is none) -datatype {char,short,int,float,double} (force output data type) -cost {mutualinfo,corratio,normcorr,normmi,leastsq,labeldiff,bbr} (default is corratio) -searchcost {mutualinfo,corratio,normcorr,normmi,leastsq,labeldiff,bbr} (default is corratio) -usesqform (initialise using appropriate sform or qform) -displayinit (display initial matrix) -anglerep {quaternion,euler} (default is euler) -interp {trilinear,nearestneighbour,sinc,spline} (final interpolation: def - trilinear) -sincwidth <full-width in voxels> (default is 7) -sincwindow {rectangular,hanning,blackman} -bins <number of histogram bins> (default is 256) -dof <number of transform dofs> (default is 12) -noresample (do not change input sampling) -forcescaling (force rescaling even for low-res images) -minsampling <vox_dim> (set minimum voxel dimension for sampling (in mm)) -applyxfm (applies transform (no optimisation) - requires -init) -applyisoxfm <scale> (as applyxfm but forces isotropic resampling) -paddingsize <number of voxels> (for applyxfm: interpolates outside image by size) -searchrx <min_angle> <max_angle> (angles in degrees: default is -90 90) -searchry <min_angle> <max_angle> (angles in degrees: default is -90 90) -searchrz <min_angle> <max_angle> (angles in degrees: default is -90 90) -nosearch (sets all angular search ranges to 0 0) -coarsesearch <delta_angle> (angle in degrees: default is 60) -finesearch <delta_angle> (angle in degrees: default is 18) -schedule <schedule-file> (replaces default schedule) -refweight <volume> (use weights for reference volume) -inweight <volume> (use weights for input volume) -wmseg <volume> (white matter segmentation volume needed by BBR cost function) -wmcoords <text matrix> (white matter boundary coordinates for BBR cost function) -wmnorms <text matrix> (white matter boundary normals for BBR cost function) -fieldmap <volume> (fieldmap image in rads/s - must be already registered to the reference image) -fieldmapmask <volume> (mask for fieldmap image) -pedir <index> (phase encode direction of EPI - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z) -echospacing <value> (value of EPI echo spacing - units of seconds) -bbrtype <value> (type of bbr cost function: signed [default], global_abs, local_abs) -bbrslope <value> (value of bbr slope) -setbackground <value> (use specified background value for points outside FOV) -noclamp (do not use intensity clamping) -noresampblur (do not use blurring on downsampling) -2D (use 2D rigid body mode - ignores dof) -verbose <num> (0 is least and default) -v (same as -verbose 1) -i (pauses at each stage: default is off) -version (prints version number) -help