Sprout from master 2014-02-06 17:27:54 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'Changes for osx 109'
Cherrypick from master 2014-07-08 16:29:20 UTC Matthew Webster <mwebster@fmrib.ox.ac.uk> 'check for bvacs/bvals .txt files':
    CUDA/bedpostx_gpu
    bedpostx
    eddy_correct
Cherrypick from master 2012-09-04 15:58:14 UTC Stamatios Sotiropoulos <stam@fmrib.ox.ac.uk> 'Hide grad_nonlin options':
    dtifitOptions.h
Delete:
    CUDA/bedpostx_multigpu_LSF
    CUDA/bedpostx_multigpu_PBS.sh
    RLR_MAP_routines.cpp
    RLR_MAP_routines.h
    doc/fdt_bedpostx.html
    doc/fdt_bedpostx_parallel.html
    doc/fdt_biggest.html
    doc/fdt_display.html
    doc/fdt_dtifit.html
    doc/fdt_eddy.html
    doc/fdt_images/eddy.gif
    doc/fdt_images/eddy.tif
    doc/fdt_images/eddy2.gif
    doc/fdt_images/fdt_bedpost.gif
    doc/fdt_images/fdt_bedpost.tiff
    doc/fdt_images/fdt_bedpostx.gif
    doc/fdt_images/fdt_fa.gif
    doc/fdt_images/fdt_fa_big.png
    doc/fdt_images/fdt_gui.gif
    doc/fdt_images/fdt_gui.tiff
    doc/fdt_images/fdt_l1.gif
    doc/fdt_images/fdt_lines.gif
    doc/fdt_images/fdt_lines_subs.gif
    doc/fdt_images/fdt_probtrackx.gif
    doc/fdt_images/fdt_rgb.gif
    doc/fdt_images/fdt_rgb_subs.gif
    doc/fdt_images/fdt_seeds2targets_quant_eg.gif
    doc/fdt_images/fdt_seeds2targets_thal.gif
    doc/fdt_images/fdt_simple_tract3.gif
    doc/fdt_images/fdt_spherical_polars.gif
    doc/fdt_images/fdt_twomasks_tracts.gif
    doc/fdt_images/fdt_vecreg.gif
    doc/fdt_images/fdt_vectors.jpg
    doc/fdt_images/fdt_vectorsx.jpg
    doc/fdt_images/fdt_xfibres_axial.png
    doc/fdt_images/fdt_xfibres_coronal.png
    doc/fdt_images/fsl-bg.jpg
    doc/fdt_images/fsl-logo.jpg
    doc/fdt_images/fslview_dti.gif
    doc/fdt_images/fslview_x.gif
    doc/fdt_images/gui_intro.gif
    doc/fdt_images/gui_intro.tif
    doc/fdt_images/qboot.gif
    doc/fdt_pipeline.html
    doc/fdt_probtrackx.html
    doc/fdt_reg.html
    doc/fdt_surface.html
    doc/fdt_thresh.html
    doc/fdt_top.html
    doc/fdt_utils.html
    doc/fdt_vecreg.html
    doc/index.html
    nldtifit.cpp
    nldtifit.h
    rubix.cc
    rubix.h
    rubix_parallel.sh
    rubix_postproc.sh
    rubix_preproc.sh
    rubixoptions.cc
    rubixoptions.h
    rubixvox.cc
    rubixvox.h