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Hi, Thanks for your reply. So you are saying that topup expects "1 0 0" vector for R >> L sequences independent of the image orientation (LAS, RAS, ALS...)? Is this the same with the --unwarpdir in fugue? Best, Chris On Wed, Dec 2, 2015 at 5:59 PM, Harms, Michael <[log in to unmask]> wrote: > > Hi, > I believe it depends on the orientation of your NIFTI file. If you have > an LAS oriented volume, then there is no inconsistency relative to > TOPUP/Faq examples -- i.e., P>>A and R>>L are both in the direction of > increasing index. > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: [log in to unmask] > > From: Chris Filo Gorgolewski <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Wednesday, December 2, 2015 6:53 PM > To: FSL - FMRIB's Software Library <[log in to unmask]> > Subject: [FSL] Describing phase encoding direction in topup > > Dear all, > I was trying to translate a the phase encoding vectors used in TOPUP from > the usual LR/RL, AP/PA to something more scanning object agnostic (afterall > I can run topup n a scan of a watermelon that does not have left/right, > anterior/posterior sides). From what I see in > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq there is some > inconsistency. > > For the second axis (y) if the phase encoding direction goes from zero to > maximum index the vector in --datain should be set to 0 1 0 (equivalent to > P >> A). If if the direction goes from maximum index to zero it should be > set to 0 -1 0. (equivalent to A >> P) This makes sense. > > However for the first axis (x) the situation is opposite. if the phase > encoding direction goes from zero to maximum index the vector in --datain > should be set to -1 0 0 (equivalent to L >> R). If if the direction goes > from maximum index to zero it should be set to 1 0 0 (equivalent to R >> L). > > Am I correct in my deductions? Is there a reason for this inconsistency? > > Best, > Chris Gorgolewski > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. >