Print

Print


Hi Stephen,

Yes, we did carefully check all major dropout-susceptible regions of the
brain and still found that the GE AP/PA 'way' somehow produced more
'complete/better looking' EPIs. The output we get from the GE AP/PA looks
quite reasonable, whereas the SE AP/PA produced scans looking actually a
bit worse with more dropout where we didn't suspect it. We got the same
kind of result for four different kinds of EPI scans, making me thing that
either our SE AP/PA protocol isn't optimal in some way (or I am just doing
something wrong in the analysis).

But I still wish to figure out what's the deal with our SE AP/PA scans
(se_ep2d based), exactly because in theory SE approach should work better
due to absence of signal dropout in the AP and PA scans.

In our analysis, we just used basic topup to get the unwarping data - then
did applytopup to unwarp functionals - being careful about orientation
issues. Just as written in the tutorials. We didn't mask or anything.

Could I possibly as a test obtain one of your SpinEchoFieldMap AP/PA scans
as well as a functional (and how it should be looking once it's unwarped)?

Thanks and best wishes
Johan







On Tue, Aug 22, 2017 at 4:00 PM, Stephen Smith <[log in to unmask]> wrote:

> Hi - GE AP/PA data is not recommended because this has the serious
> dropouts in the areas being most affected also by distortions - have you
> checked in those areas for performance of the unwarping?
>
> This email list is the best venue for sending these questions,
> Cheers, Steve.
>
>
> On 22 Aug 2017, at 06:54, Johan <[log in to unmask]> wrote:
>
> Dear experts,
>
> If I have a rather complicated question regarding Topup, SpinEcho
> Fieldmaps with AP / PA phase encoding directions, who would you suggest I
> contact?
>
> I have some data that i'd like to send. We obtained GE and SE AP and PA
> scans, and although SE AP/PA combination pair is recommended, for our case
> GE AP/PA seems to work better. We're not confusing this with the dual-echo
> B0 Fieldmaps.
>
> Thanks and best wishes
> Johan
>
>
>
> ------------------------------------------------------------
> ---------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis,  Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 222726 <+44%201865%20222726>  (fax 222717)
> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------
> ---------------
>
> Stop the cultural destruction of Tibet <http://smithinks.net>
>
>
>
>
>
>