Hello, 

The filenames are important. BedpostX requires a folder which contains following files. (see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)

     Input directory: Use the browse button to select an input directory. That directory must contain the following files:

    data: A 4D series of data volumes. This will include diffusion-weighted volumes and volume(s) with no diffusion weighting.
    nodif_brain_mask: 3D binary brain mask volume derived from running bet on nodif (i.e. on a volume with no diffusion weighting).
    bvecs (with no file extension): An ASCII text file containing a list of gradient directions applied during diffusion weighted volumes. The order of entries in this file must match the order of volumes in data.

First, rename filenames through the following commands.

   cp 20080811_204605ACEprotocol415088s009a1001_eddy.nii.gz data.nii.gz
   cp b0_brain_mask.nii.gz nodif_brain_mask

Second, bvec processing. Did you use "fdt_rotate_bvecs"? 
I think that you performed the eddy current correction on the image but did not perform the bvec correction. 
if you rotate the bvecs, just type as follows. 
    cp 20080811_204605ACEprotocol415088s009a1001.bvec bvecs
If not, type the following lines. 
   fdt_rotate_bvecs 20080811_204605ACEprotocol415088s009a1001.bvec bvecs 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog

I hope this helps.

Best
Cheol