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Dianne: You said you get identical b-vecs between A/P and P/A phase encoded acquisitions under Skyra VD13. Is that using Siemen's product ep2d_diff sequence, or are you using the CMRR MB sequence? -- 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: Priscila Rojas Frias <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Tuesday, April 30, 2013 9:36 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] Applytopup Hi Dianne, Michael and Jesper, We've been trying a few things and asking some questions, and thought it might be worth feeding back to you... Data conversion with either MRIConvert or dcm2nii (Chris Rorden's tool) both give the same output - i.e. bvec files with vectors of opposite sign depending on the phase encoding direction. From Dianne's comment below this sounds like a bug in Siemens' header information. Rather than throw away the diffusion data from 25 scans, we would like to see if it is possible to analyse the data as they are. Some questions: (1) is it possible that the *reported* diffusion vector has been rotated by 180 degrees, but the data were acquired properly? Could we confirm this by looking at the opposite blipped data and picking an image with the same applied gradient to see if the shearing is in the same direction? (2) Does it matter that the acquisitions have different acquisition vectors? I know that sounds silly, and assuming that we want to average pairs of undistorted images with the same applied gradient then this will clearly be important, but if the gradients are opposite in direction, and the same sampling scheme was used, presumably the same directions *should* have been sampled, just at different points in the acquisition. (3) When the diffusion tools require that we specify a single bvec file that describes the 2 acquisitions, can we just concatenate the 2 bvec files - so the differences are accounted for? (4) Or would we need to re-order the data as stored on disk so that the different diffusion directions appear at the same point in the 4D volume? (5) We have used Applytopup on these data - just to see if it was working - and we get something sensible out from it. If we first ran eddy_correct then Applytopup (we should have done this first time around), would you expect us to get nonsense from Applytopup? I.e. if the hifi output is really averaging volumes acquired with equal and opposite diffusion directions, presumably the shearing effect would be blurred out?? You can see that we really don't want to throw the data away! So any help in understanding this problem and salvaging the experiment would be much appreciated. Hope you can help. Best wishes, Priscila Hi Priscila, I too have been attempting to use topup and applytopup. For our images, the bvecs for the A-P image are equivalent to the bvecs for the P-A image. Our scanner is a Seimens Skyra with vd13 on it.... -Dianne On Mon, Apr 29, 2013 at 6:24 AM, Priscila Rojas Frias <[log in to unmask] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8212491%26B%3D--089e0160c76a3a2e1804db804309%26T% 3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D> > wrote: > 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 > > 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..... > > 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 > -- Dianne Patterson, Ph.D. Research Scientist [log in to unmask] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8212491%26B%3D--089e0160c76a3a2e1804db804309%26T% 3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D> or [log in to unmask] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8212491%26B%3D--089e0160c76a3a2e1804db804309%26T% 3Dtext%252Fhtml%3B%2520charset%3DISO-8859-1%26pending%3D> University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) 621-9877 ============== "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." - George Bernard Shaw