Dear Matt,

We have (tried) to be really contentious w.r.t. matching echo dwell time, in-plane resolution, # k-lines (EPI factor or iPat), partial Fourier (it matches the EPI), voxel sizes, tot. slices, orientation and bandwidth. Anything basically that could taper with the amount of time spent reading out one slice of k-space (which is the main thing w.r.t. distortions). We also were careful in the analysis w.r.t. possible motion happening between acquisition of SE Fieldmap and following functionals too.

The only thing different, as far as we could see, is that we used the Scanner's own SE - EPI instead of the HCP SE-EPI. I'm trying to get those installed so I can compare those with what we have so far.

I will upload a sample dataset that we have to the URL Jesper gave me!

This scan is, from the 4 scans that we did, the most 'sensitive' to distortions (about 2-3 voxels) due to a res of 2mm ^3 and 106x160 matrix. Partial F is 6/8th for both fieldmap and functionals.

Thanks and best wishes

On Tue, Aug 22, 2017 at 9:55 PM, Matt Glasser <[log in to unmask]> wrote:
Also, did you match the geometry between SE and GE images and the echo spacing?  What kind of scanner do you have?



From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jesper Andersson <[log in to unmask]UK>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, August 22, 2017 at 5:04 AM
To: <[log in to unmask]>
Subject: Re: [FSL] HCP Topup Unwarping advice

Dear Johan,

that does indeed look unusual. I think the best would be if I could take a look at your data. To do so, can you please send me the input files into topup for the SE and the GE cases and also a small sample (a couple of volumes) of the GE data that you want to correct? Please put all file in a tar-ball and upload it to

Can you please also send me an email with the exact commands you used for running topup and applytopup?


On 22 Aug 2017, at 09:44, Johan <[log in to unmask]> wrote:

Dear Jesper,

I could send you the Magnitudes that I have for you to inspect. Here the SE stuff does look a bit better/more tidy. However the EPI, when topup-SE-corrected have quite big 'holes' frontally that I really don't trust is normal dropout - or at least, it looks quite unsubtle.

This figure is about the EPI - left = SE unwarped right = GE unwarped.


Best wishes

On Tue, Aug 22, 2017 at 6:02 PM, Jesper Andersson <[log in to unmask]uk> wrote:
Dear Johan,

what does the --iout output look like for SE and GE-EPI respectively. I would expect the former to look better, i.e. less difference between AP and PA after topup. If not, I think something must be going wrong.

When then applying these maps to the GE-EPI images those wont _look_ as good, because the GE-EPI images also has dropout in those same areas as there are distortions. It can be surprisingly difficult to distinguish dropout from distortion, no matter how trained your eye.


On 22 Aug 2017, at 08:33, Johan <[log in to unmask]> wrote:

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

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

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  (fax 222717)
[log in to unmask]

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