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Another thought: The April 2011 version of dcm2nii is rather old. I'd get the newest version, and try it both with and without b-vec rotation applied (there are flags for controlling that), and compare what it returns to the actual b-vector as it is stored in the DICOM itself. 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: Michael Harms <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Tuesday, April 30, 2013 11:18 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] Applytopup The fact that the 180 flip of the b-vectors is not present in ALL the vectors is rather troubling, but also potentially informative. The DICOMs should contain B_matrix information (0019 0027, I believe) -- I'd look at that to see if that provides any clues. Also, I haven't used it, but my understanding is that the 'dicom2nrrd' converter includes an option to derive b-vectors from the B_matrix (precisely because of the issues encountered with inaccurate b-vectors in VB13 and VB15). So, you might want to see what that converter gives you regarding b-vectors. And, I'd get your local Siemen's engineer involved as well. They should be able to direct you to someone in Siemen's that can either confirm whether there is a bug in VD11, or explain what is going on. 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: Priscila Rojas Frias <[log in to unmask]> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> Date: Tuesday, April 30, 2013 10:59 AM To: FSL - FMRIB's Software Library <[log in to unmask]> Subject: Re: [FSL] Applytopup Hi Michael I've attached two example bvec files with opposite-blipped acquisition as well as a 'result' file where we divided the values from the first bvec file over the values from the second bvec file. I believe there are only two values that do not have opposite signs and result in a value of 1 when divided. result=s002a001 ./ s005a001 Thanks again, Priscila Is EVERY reported b-vector direction in your opposite-blipped acquisition 180 deg, or just some of them? Earlier you said that "most, but not all" have the opposite sign. If that is indeed the case, is it reproducible? i.e., if you run in a phantom, and slightly change the angulation of the acquisition, do you get the exact same pattern of b-vectors that are 180 opposite ? I would want to figure out exactly what is going on before I try to figure out what to do with the data in eddy/topup. 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] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%2 52Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> From: 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%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%2 52Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%2 52Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> > Date: Tuesday, April 30, 2013 9:36 AM To: FSL - FMRIB's Software Library <[log in to unmask] <https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26 E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%2 52Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> > 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