You can only process DTI files with multiple volumes, so look for the images with multiple volumes (e.g. the image with 128x128x81x31 has 31 volumes) which has a bvec and a bval file and bvec and bval files. While you have not provided details about your sequence, I wonder if tdti_ep2d_diff_MDDW_30_p2_20140507001838_3_c2a and dti_ep2d_diff_MDDW_30_p2_20140507001838_100_c2a are from the same acquisition, with series 3 being the raw data and series 100 being the motion corrected data. If this is the case, I would delete series 100 and in future set the scanner to not save motion corrected data. Using Eddy and TOPUP with the new "repol" function will do a much better job of cleaning up motion artifacts than what the scanner will do.