3dDWItoDT expects the gradient vectors in the form

x1 y1 z1
x2 y2 z2
...
xn yn zn

The program assumes a B0 volume to be first, and that is *not* included in the 1D file. If there are more B0 volumes, they may be added as lines of "0 0 0" in the order they appear in the dataset. If all three of your B0 volumes are acquired at the beginning, then there would two lines of "0 0 0" at the beginning of the 1D file.

If your data is in this form instead

x0,x1,x2,...,xn
y0,y1,y2,...,yn
z0,z1,z2,...,zn

then you can probably just transpose the existing file from rows to columns with 1dtranspose and remove the extra x0 y0 z0 line at the beginning.