Dear Jesper,
Thank you for your useful response and help. Also I apologize for "tar", surely I would use your advice. Actually, I have some doubts which I need your help.
1- Is the exciting of these ghosting would be problematic in next processing steps (for example: tensor estimation and tractography) ??
2- If it would be problematic, so what do you suggest to solve it ?
3- Do I need GPU in case of using "eddy" (with -jacobian) instead of applytopup ? actually I used and it ran without error just the message "eddy is running in GPU mode" appeared, but the image is completely gray! also changing the rang did not work!
4- what did you use as input of the --imain in the "applytopup" ? I mean that, "b0_RL+ all dir of dwi_RL , b0_RL+ all dir of dwi_RL" or all dir of dwi_RL & all dir of dwi_RL" ? since b0 volumes where corrected in topup
5- Some volumes of the DWI image contains bvals =5, am I supposed to split them from the each phase encoded DWI image and merge with corresponding b0 then, perform "topup" on the new merged b0 images?
Regards,
Mahshid