Dear Taylor,
Thanks for this. We have uploaded the file - all files should be in the zipped folder. We accidently uploaded a set of 'good' data too so feel free to use that as a comparison.
Many thanks,
Carolyn & Greta
-----Original Message-----
From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Taylor Hanayik
Sent: 25 November 2019 17:38
To: [log in to unmask]
Subject: Re: [FSL] Fieldmap misalignment in FEAT registration
Hi Carolyn,
Could you upload the files for one participant that would replicate the bad results you see? Also supply the call to fsl_prepare_fieldmap as you have used it here.
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=8094620179643F6A48
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
Analysis Research Software Engineer
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]
> On 25 Nov 2019, at 14:42, Carolyn McNabb <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> We have run into some registration issues in FEAT. For a handful of
> participants (most cases are fine), the fieldmap and highres images
> are severely misaligned. see here:
> https://www.koumurayama.com/experiments/GF/Pictures/Screenshot_fieldma
> p.png These participants' func_to_standard registrations are poorer
> than other participants so we believe this may be what is driving the difference.
> We have used the fmap_rads image and mag_brain images in the b0 unwarping tab in FEAT - as instructed on the fsl wiki.
>
> We were wondering if there is a possible solution to this problem. It seems strange that it is only occurring in a small subset of participants.
>
> Any advice you can give would be very helpful. Happy to provide any files you need.
>
> Many thanks,
> Carolyn and Greta
>
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