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Dear Jesper,

Thanks so much for your helps.

I would ask one more question. I used mricron to calculate the bvecs. But
the v1 images are distorted and the lines are not aligned with the fa
images. Also bvecs are different between subjects. I thought the
acquisition protocol should have been the same for all the subjects. Is
mricron a reliable tool for bvecs calculation?

Bests

Arman

On Aug 30, 2017 12:34, "Jesper Andersson" <[log in to unmask]>
wrote:

> Dear Arman,
>
> Thanks so much for your response.
>
> As Helen had also an EPI set with just one PE diresction I thought maybe
> she had found a way to resolve the problem of topup for just one PE
> direction. So how had she done that?
>
>
> In her case she had one pair of images acquired with different
> PE-directions from which she could calculate the field with topup. She then
> applied that to a “full” data set that was acquired with only one PE
> direction. This is a fairly typical way of doing it. It is more unusual
> that people acquire the “full” data set with different PE-directions.
>
> What does she mean by blipup/blipdown images? I thought they should have
> been the first b=0 volumes of different EPI sets with different PE
> directions.
>
>
> Those are simply shorter ways of saying “image acquired with positive
> PE-blips” (blipup) and “image acquired with negative PE-blips” (blipdown).
>
>
> Among the data which have been delivered to me I have an EPI set with 35
> gradient directions which I don't know how to determine the PE direction.
> Besides I have also two phase images and two magnitude images acquired with
> two different echo times.
>
>
> The two phase and magnitude images that you have is an alternative way of
> estimating the susceptibility field. That a look at the FSL help pages for
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE/Guide information about what
> they are and how to use the FSL tools to transform these into a useful
> fieldmap.
>
> Once you have that you can use the --field option in eddy to pass that
> fieldmap into eddy for doing the eddy current and motion correction. In
> order to do that you need to make sure that you find out the PE-direction
> of your data. This should be fairly easy by comparing the images to the
> example images you see here https://fsl.fmrib.ox.ac.
> uk/fsl/fslwiki/eddy/Faq#What_if_I_still_really_want_to_
> have_an_.22accurate.22_--acqp_file.3F.
>
> The difficulty in your case will be to work out the “total readout time”.
> In order to do that you will need some information about the sequence that
> was used. Chances are that you need to wait for your colleagues to return
> from vacation to find that out.
>
> Another thing you need to take care of when using a “traditional” fieldmap
> with eddy is to make sure it is accurately registered to the first volume
> in the data set that you feed into eddy.
>
> Jesper
>
>
>
> Would you please help me to find how I can use these informations to
> correct my EPI for distortion and motion? Your help is highly appreciated.
> Everyone here is on holiday and I am left alone.
>
> Bests
>
> Arman
>
>
>