Dear Andreas,
In order to solve the misalignment issue we tried the following:
- fslreorient2std both the T1 anatomical image and the gradient field map images
- Try to run Melodic with each phase encoding direction to see whether
one of it will solve the issue
None of this helped.
Any ideas?
Thank you very much,
ines
On Mon, Apr 20, 2015 at 9:11 PM, Andreas Bartsch <[log in to unmask]> wrote:
> Well, at least in the bad case the distortion correction actually seems to
> have introduced additional distortions in AP - from what I can tell in the
> low res jpeg.
> So something is definitely not right here.
> Cheers,
> Andreas
>
> Am 20.04.15 18:21 schrieb "InĂªs Violante" unter <[log in to unmask]>:
>
>>Dear Andreas,
>>
>>When you mentioned a bad z-shift do you think that the phase enconding
>>direction for these subjects could be different?
>>
>>Thanks
>>
>>ines
>>
>>On Mon, Apr 20, 2015 at 5:14 PM, Li, Lucia M <[log in to unmask]>
>>wrote:
>>> Dear Andreas,
>>> Thank you for replying.
>>> Yes, we use the BBR option in the registration step.
>>> Lucia
>>> ________________________________________
>>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
>>>Andreas Bartsch [[log in to unmask]]
>>> Sent: Monday, April 20, 2015 4:36 PM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] B0 unwarping misalignment
>>>
>>> Hi,
>>>
>>> this looks like bad z-shift.
>>> Do you use FSL's latest version, i.e. BBR?
>>> Cheers,
>>> Andreas
>>>
>>> Am 20.04.15 15:31 schrieb "Lucia M Li" unter <[log in to unmask]>:
>>>
>>>>Dear FSL users & experts,
>>>>
>>>>We were hoping to get some help on an issue we've had with our unwarping
>>>>step (run as part of running a single-session melodic).
>>>>
>>>>We noticed that for a couple of people in our study, the "fieldmap to
>>>>highres" registration looks seriously displaced - see link:
>>>>https://dl.dropboxusercontent.com/u/22466029/FieldmapAlignment/Missalign
>>>>me
>>>>nt.jpg
>>>>
>>>>The majority of our scans have registered very well however - see link:
>>>>https://dl.dropboxusercontent.com/u/22466029/FieldmapAlignment/GoodAlign
>>>>me
>>>>nt.png
>>>>
>>>>We were wondering if anyone could advise on what might have caused this
>>>>displacement in a few people only (scanned using the same scanner/
>>>>parameters, fieldmaps prepared using the same parameters & unwarped with
>>>>the same parameters)?
>>>>We were also wondering what effect this has on the final data (the final
>>>>func to highres looks ok) and what we can do to correct it?
>>>>
>>>>Many thanks in advance for your help.
>>>>
>>>>Kind regards,
>>>>Lucia
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