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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]>
>>> 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
>>>
>>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=72139C7E463068D5F
>>>
>>> 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]> 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
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ---------------
>>>>> 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/>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>