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
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.
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
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...
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.
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?
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
(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
(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??
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
Hope you can help.
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....
On Mon, Apr 29, 2013 at 6:24 AM, Priscila Rojas Frias <[log in to unmask]>
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
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.....
0 0.99999934 0 0.3456666666
0 -0.9999956 0 -0.3456670000 <- same magnitude, different sign
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,
Dianne Patterson, Ph.D.
[log in to unmask]
University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
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