Print

Print


Hello Jesper,

Yes, all b=700 volumes are collected in AP direction while all b=2000
volumes are collected in PA direction.

Thank you!
Mahmoud

On Mon, Aug 7, 2017 at 6:40 AM, Jesper Andersson <
[log in to unmask]> wrote:

> Dear Mahmoud,
>
> do you mean that all b=700 are acquired with one PE direction and all the
> b=2000 with that opposite direction?
>
> If so, I have never worked with data of that exact kind so you might need
> some trial and error to work out which is the better option. My guess, and
> hope, is that option 2 would be the best.
>
> Jesper
>
> > On 3 Aug 2017, at 18:30, Mahmoud <[log in to unmask]> wrote:
> >
> > Hello All,
> >
> > I have dMRI data collected on a Siemens Prisma machine as follows:
> >
> > Two shells (b=700 and 2000) with opposite PE directions (AP and PA
> respectively) and a different number of diffusion gradients (89 and 90
> respectively) but the number of b0 volumes are the same for both shells (7
> b0 volumes collected at the beginning of each shell).
> >
> > I wonder which of the following ways you recommend to correct for EC,
> Susceptibility, and motion correction:
> >
> > 1-
> > a) using "topup" to estimate the susceptibility map.
> > b) use "eddy" with the first shell only as the input (--imain=b700).
> > c) use "eddy" with the second shell only as the input (--imain=b2000).
> > d) use "fslmerge" to merge the eddy corrected outputs of steps b and c.
> > e) using "paste" to merge the bval and rotated bvec files from steps b
> and c into one bval and bvec file.
> >
> > or
> >
> > 2)
> > a) using "topup" to estimate the susceptibility map.
> > b) use "fslmerge" to merge the two shells as b700_2000.
> > c) using "paste" to merge the bval and bvec files of the two shells into
> one bval and bvec file.
> > d) use "eddy" with the merged shells as the input (--imain=b700_2000)
> and bval and bvec files of the above step.
> >
> >
> > Thank you!
> > Mahmoud
> >
> >
>