Dear Johan,

I have had a look at your data and I am afraid that neither fieldmap (the SE or GE) look very good. I am not 100% sure exactly why that is, but I think that the problem is the very large distortions. It (topup) has come up with a quite creative solution where instead of pushing back all of the frontal intensity that has been pulled out, it pushes back some and leaves some, while doing the opposite for the reverse PE direction. The end result is an image pair (the --iout output) that looks surprisingly sane, but where the field is not what one would expect from a human head.

I have only seen this behaviour once before, and I haven’t got a solution for it. Essentially it is a situation where the non-linear optimisation (which is what topup does) has two minima, and topup falls into the wrong one. For future acquisitions I would suggest using some IPAT (a factor 2 should be sufficient) to reduce the distortions. For the current data I can only suggest experimenting with the config file to see if you can get it to take a different path and find the other minimum.

Sorry I cannot be of more help.

Jesper

On 23 Aug 2017, at 04:09, Johan <[log in to unmask]> wrote:

Dear Matt,

I uploaded a tarball (a second one - the first one isn't good) to the FSL upload site for inspection. I also have a screenshot but it's too big for the FSL mailinglist to accept, so I also uploaded it to the FSL upload site.


Thanks again and best wishes
Johan



On Wed, Aug 23, 2017 at 11:48 AM, Matt Glasser <[log in to unmask]> wrote:
The images you sent were not sufficient to evaluate the issue.  Perhaps if you have some mid sagittal slices after distortion correction in which you can see some clear anatomy and compare the T1w to the fMRI.  

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Johan <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, August 22, 2017 at 8:34 PM

To: <[log in to unmask]>
Subject: Re: [FSL] HCP Topup Unwarping advice

Dear Matt,

I did actually carefully check the scans how they compare to the Anatomy - the T1. I extracted the boundary between WM and GM of the T1 scan, and compared to that boundary (and also the T1). The thing is I see too much dropout in a region where normally you wouldn't expect any dropout normally - it's too much in the 'middle' of the EPI scan. As if somehow things get too compressed, or something outside of the brain where signal is more random, gets pushed inside (but this just a guess on my part). Also when I calculate the match between T1 and EPI, using fsl FLIRT's brr cost function, I get lower values for the GE-corrected scans, indicating a better fit.

I sent an example 'package' of our results (topup files for GE and SE + instructions), including T1 and T1 boundary to Jesper (well - will do in a few minutes). If you wish I can also send it to you for inspection.

Thanks for your time and best wishes
Johan





On Wed, Aug 23, 2017 at 11:14 AM, Matt Glasser <[log in to unmask]> wrote:
Like I said on the HCP list what is most important is comparing anatomy that is within the distorted region but not the dropped out region.  This is how you evaluate the quality of the distortion correction, not on the size of the dropped out region.

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Johan <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, August 22, 2017 at 8:05 PM

To: <[log in to unmask]>
Subject: Re: [FSL] HCP Topup Unwarping advice

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
Johan









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?

Peace,

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jesper Andersson <[log in to unmask]K>
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?

Jesper

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.

<image.png>



Best wishes
Johan






On Tue, Aug 22, 2017 at 6:02 PM, Jesper Andersson <[log in to unmask]k> 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.

Jesper

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
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


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Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
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