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Dear Jane, I have a question about using FSL's eddy after motion and EC/EPI correction using ExploreDTI on diffusion data. I don't have data of opposite phase encoding directions, so I would like to use the EPI correction in ExploreDTI, which is done with motion and eddy current correction. you don’t need opposite phase encodings if you only want to correct for eddy-currents and motion. It is only if you want to correct also for susceptibility induced distortions that you will need at least one pair of images with opposed phase encoding. Then, I would also like to use eddy to replace outliers in my data, but I do not want to have the data motion and eddy current-corrected again. Is there any way to do this? Or do you have any suggestions on how I could preprocess the data? Thank you! My suggestion would be to do all of the pre-processing with eddy. But if you prefer to use ExploreDTI for the motion and eddy current correction you can do as follows. 1. Run eddy, specifying the --repol flag so that you include outlier correction 2. Instead of using the “main” eddy output, use the file named “output name”.eddy_outlier_free_data. That is a 4D image file that has _not_ been corrected for motion or EC, but where all the outliers have been replaced by predictions. 3. Run ExploreDTI’s motion and EC correction on that file. Jesper Best wishes, Jane The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ________________________________ To unsubscribe from the FSL list, click the following link: 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