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Dear Jesper Thanks for your response. I have uploaded the input data which was used in command topup and applytopup from the link you privided. (dataset belongs to WU-Minn HCP Lifespan Pilot Data https://db.humanconnectome.org/app/template/Login.vm;jsessionid=F125A42455E0451FE15865C55E149C44 [https://db.humanconnectome.org/app/template/Login.vm;jsessionid=F125A42455E0451FE15865C55E149C44]). One more thing, after applying applytopup command the corrected output image is gray. Also using eddy instead of applytopup with -lsr, is completely a gray square not an image. Regards Mahshid From: Jesper Andersson <[log in to unmask]> To: [log in to unmask] Date: Tue, 19 Feb 2019 09:58:04 +0000 Subject: Re: [FSL] ghosting appears when performing topup command on b0 images Dear Mahshid, I would need to see your data in order to say what is going on here. Can you please tar all files alluded to on you command line and upload them to https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F [https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F] Jesper On 19 Feb 2019, at 09:39, Mahshid Fouladivanda <[log in to unmask] [mailto:[log in to unmask]]> wrote: Dear fsl experts, 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 don't know what is the main problem! I would appreciated if any one could help me with the resulted problem. Regards, Mahshid To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 [https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1]<b02b0.cnf> To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 [https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1] ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1