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Hello Priscila, Was your diffusion data obtained by any chance on a VB17 platform using the CMRR MB sequence with the polarity inverted via the check box on the Sequence/Special tab? If so, it has recently come to light that a bug exists with the VB17 version such that the reported diffusion directions are inverted between the blip-up, blip-down acquisitions, even though the actual directions were not. 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] On 4/29/13 9:09 AM, "Jesper Andersson" <[log in to unmask]> wrote: >Dear Priscila, > >> Hello. I have been asked to analyse a set of diffusion data and to do >>so I have been following the topup steps on the fsl website. I have come >>to the stage of "applytopup" and I am unsure about ordering of the data >>and the corresponding acqparams.txt file. I have been told that the data >>were acquired in 2 series, the first with blip down (A->P) and the >>second blip up (P->A), phase encoding was in the y-direction. Is this >>the correct way to interpret this? >> >> My acqparams.txt file looks like this: >> 0 -1 0 0.065 >> 0 1 0 0.065 >> > >You should use the same acqparams.txt file for applytopup as was used for >topup. The data should be organised such that all volumes in a file >pertains to the same row in acqparams.txt. > >I think that this page >https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplyto >pup >explains it reasonably well. > > >> I also wondered whether having .bvec files with opposite sign (+/-) >>indicates that the data has not been collected using identical >>protocols. I understand that the numbers stored in the 2 .bvec files >>associated with each series correspond to the x, y and z components for >>each diffusion direction, but when I look at the values they differ in >>sign between the 2 series..... >> > >It does indeed sound as if your diffusion vectors are different for the >two acquisitions. If you don't want do run eddy, i.e. if you rely on some >other tools for movement and eddy current correction, that is not a >problem. The diffusion signal is expected to be identical for v and -v >(where v is a diffusion vector) so there is no problem with pooling the >data and using either of the bvec files. > >However, if you want to run eddy that is NOT a good situation. What you >want for eddy to work is data with the same/similar diffusion signal but >different distortions. This can be achieved by sign-swapping either the >phase-encode direction or the diffusion-gradient direction. BUT if you >swap both you have effectively swapped the distortions twice leading to >similar/identical distortions in the two images and then there is no >differential signal to drive the correction. > >Jesper > > >> e.g. file1.bvec >> >> 0 0.99999934 0 0.3456666666 >> ........ >> 0 ........ >> ........ >> 0 ........ >> >> e.g. file2.bvec >> >> 0 -0.9999956 0 -0.3456670000 <- same magnitude, different sign >> ........ >> 0 ........ >> ........ >> 0 ........ >> >> According to the applytopup help page, once I have used it I will be >>left with a single set of images, but which bvec file should I use? >> >> >> I would really appreciate your input on this. >> >> Thanks in advance, >> >> Priscila >>