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ecc is usually done before bet, even in fdt. cheers- andreas ________________________________________ Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt Glasser [[log in to unmask]] Gesendet: Freitag, 10. September 2010 17:51 An: [log in to unmask] Betreff: Re: [FSL] DTI pipeline questions Dunno why it says that on the website. You can actually use eddy_correct to correct for motion between averages if you concatenate the runs (and then split the runs back out and average them). Only way averaging before eddy_correct could make sense is if you registered each DWI volume to its corresponding volume in the other averages first and then ran eddy_correct. I did this before when I had low SNR data and many averages and eddy_correct didn't handle this unaveraged images very well. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Torsten Ruest Sent: Friday, September 10, 2010 10:43 AM To: [log in to unmask] Subject: [FSL] DTI pipeline questions Dear all, I have just some simple questions: on the fdt_pipeline site it says to do the averaging of several acquisitions before the eddy current correction. I thought it may be better afterwards in case the subject has moved, thus movements will be taking into account before the averaging. Also at which stage would you do the bet brain extraction, before or after the eddy current correction. I saw in the practical that it's been done before, while on another site (http://www.cabiatl.com/CABI/resources/dti-analysis/) it was done after. I may think before is better, but since the scull of the same subject may give some additional information, it may be better after. Thanks in advance for suggestions for these questions that kept me sleepless for a while :) Cheers, Torsten