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FYI just tried latest version of dcm2nii (12/2012) and gives exactly same bvec files i.e. with opposite sign for vector elements. Best wishes, Priscila On 30 April 2013 18:39, Priscila Rojas Frias <[log in to unmask]> wrote: > Hi Michael, Dianne & Jesper, > > Looking at the results.txt file I attached previously, and the bvec files > from our A->P and P->A acquisitions, it seems like every vector is rotated > by ~180deg. I.e. > > bvec1 > 0 0.99999803304672 0 ...... > 0 -0 0.99999803304672 ..... > 0 0.0019999903161 0.0019999903161 ..... > > bvec2 > 0 -0.99999803304672 0 ...... > 0 -0 -0.99999803304672 ...... > 0 0.0019999903161 0.0019999903161 ..... > > and dividing bvec1 by bvec2 gives > NaN -1 NaN ........ > NaN NaN -1 ........ > 0 1 1 ....... > > > So my reading of this is that column 1 refers to the B0, column 2 to a > gradient along +/-X and column 3 to a gradient along +/- Y. > > Another interesting feature of the bvec files is that the location of the > 2 values that *never* change between bvec files are the ones equal to > 0.0019999903161, i.e. in position Z2 and Z3. Is that a bit weird? > > We looked with gdcmdump at one of the DICOM files and it had the following > info: > > (0019,100e) FD -0.561148\-0.23185\0.794581 # 24,3 > DiffusionGradientDirection > (0019,1027) FD 148\312\-172\655\-361\199 # 48,6 > B_matrix > > Obviously this will be different for the 65 images acquired, but I'm not > sure how to use this information to find out about the problem we're facing. > > Hope you can make sense of this? > > Best wishes, > > Priscila > > > 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]<https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26E%3Dquoted-printable%26P%3D8596348%26B%3D--B_3450165509_4932671%26T%3Dtext%252Fhtml%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%26E%3Dquoted-printable%26P%3D8596348%26B%3D--B_3450165509_4932671%26T%3Dtext%252Fhtml%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%26E%3Dquoted-printable%26P%3D8596348%26B%3D--B_3450165509_4932671%26T%3Dtext%252Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> > > > Date: Tuesday, April 30, 2013 10:59 AM > > To: FSL - FMRIB's Software Library <[log in to unmask]<https://www.jiscmail.ac.uk/cgi-bin/webadmin?LOGON=A3%3Dind1304%26L%3DFSL%26E%3Dquoted-printable%26P%3D8596348%26B%3D--B_3450165509_4932671%26T%3Dtext%252Fhtml%3B%2520charset%3DUS-ASCII%26pending%3D> > > > 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%26E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%252Fhtml%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%26E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%252Fhtml%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%26E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%252Fhtml%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%26E%3Dquoted-printable%26P%3D8543413%26B%3D--B_3450160256_4689374%26T%3Dtext%252Fhtml%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%26E%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%26E%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%26E%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 >