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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
 
 
From: Jesper Andersson <[log in to unmask]>
To: [log in to unmask]
Date: Wed, 20 Feb 2019 13:22:39 +0000
Subject: Re: [FSL] ghosting appears when performing topup command on b0 images

Dear Mashid,
 
I have a data-set including phase encoding (1b0+80 dir RL & 1b0+80 dir LR). Using default config file b02b0.cnf (included in attachment), an image with ghosting around brain was appeared. I also tried to change the values of the --warpres but the results got worse.
 
I had a look at your data and ran topup on it. The results look perfectly fine to me, given the input data. The ghosting has not appeared as a consequence of topup. There are two bands (one in slices 31-38 and one in slices 62-90) with severe ghosting in your input data. topup only deals with the distortions, and will not do anything about the ghosting.
 
I also had no problem with applytopup on your data. I think in an earlier version of applytopup the display range was not set correctly, but that would only affect the initial range that fslview (and I assume that fsleyes does the same) displays your data with. Try changing your display range and I think you will see it has worked fine.
 
For future reference. If you stick all your files in a tar-ball before uploading them you will save time both for me and yourself. If you are not familiar with tar, just google “linux tar” and there will be lots of information.
 
Jesper
 
I don't know what is the main problem! I would appreciated if any one could help me with the resulted problem.
 
Regards,
Mahshid
 
 
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<b02b0.cnf>
 
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