Hi,
For bedpostx, yes, I think is better to use the CUDA version.
The binaries are only included in the CentOS 6 distribution,
but you can compile the CUDA source code and it should work with Ubuntu and CUDA 7.5.
First you need to set some variables:
export FSLDEVDIR=$FSLDIR
export COMPILE_GPU=1
export CUDA='path to your CUDA directory' (/usr/local/cuda for instance)
You also need to set $FSLCONFDIR and $FSLMACHTYPE:
export FSLCONFDIR=$FSLDIR/config
export FSLMACHTYPE=`$FSLDIR/etc/fslconf/fslmachtype.sh`
And to compile it:
cd $FSLDIR/src/fdt
make install
Let me know if you find problems doing it.
Moises.