Hi Kerstin,
what kind of sequence are you using - a double gradient vs. spin echo fieldmapping? In any case, you should just use the echo time difference, not twice the value.
Schöne Grüße zurück, es muß spät bei Dir sein-
Andreas
PS: Hast Du in Würzburg studiert?
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library im Auftrag von Kerstin Pannek
Gesendet: Mo 22.09.2008 07:51
An: [log in to unmask]
Betreff: Re: [FSL] AW: [FSL] AW: [FSL] fugue distortion correction on dti stretches CC
Hi Andreas,
you are right, I managed to make another mistake, that "fixed" the
problem - my bad, it worked only once...
Still I think the trouble is when I generate the fieldmap. Is it correct
that asym is 2x echo time difference? I read this somewhere, and it
seems to work, but maybe just another mistake that cancels out another -
I seem to be good at that today...
Gruesse ins schoene Frankenland!
Kerstin
Andreas Bartsch wrote:
> Hi Kerstin,
>
> are you sure? I would definitely NOT expect a large difference to be introduced by an echo time difference error of 0.04ms.
> Cheers-
> Andreas
>
> ________________________________
>
> Von: FSL - FMRIB's Software Library im Auftrag von Kerstin Pannek
> Gesendet: Mo 22.09.2008 02:59
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] fugue distortion correction on dti stretches CC - solved
>
>
>
> Hi all
> It turned out the problem was in the generation of the fieldmap itself.
> The echo times I used were inaccurate - OsiriX (not the current version)
> reported echo times of 7.40 and 4.90, while ImageJ reported 7.38 and 4.92.
> Cheers
> Kerstin
>
> Kerstin Pannek wrote:
>
>> Hi Andreas
>> Using --unwarpdir=y- is actually what I did for this subject,
>> resulting in the overstretched CC. The size and shape of the brain
>> seem correct when doing so. When I don't use --unwarpdir=y-, the whole
>> image is distorted even more.
>> Cheers
>> Kerstin
>>
>> Andreas Bartsch wrote:
>>
>>> Hmmh, maybe your have negative blip encoding? A least you could try
>>> to reverse the sign for y.
>>> Cheers-
>>> Andreas
>>>
>>> ________________________________
>>>
>>> Von: FSL - FMRIB's Software Library im Auftrag von Kerstin Pannek
>>> Gesendet: Fr 19.09.2008 09:02
>>> An: [log in to unmask]
>>> Betreff: [FSL] fugue distortion correction on dti stretches CC
>>>
>>>
>>>
>>> Hi all!
>>> I would like to use fugue to correct distortions on my dti data using a
>>> field map.
>>>
>>> I did the following:
>>> 1) eddy_correct dti data
>>> 2) extract and bet b0 image
>>> 3) bet magnitude, mask fieldmap with betted magnitude
>>> 4) warp magnitude (fugue -w)
>>> 5) flirt -dof 6 warped magnitude to betted b0
>>> 6) apply flirt transform to masked fieldmap
>>> 7) unwarp dti data (fugue -u)
>>> 8) dtifit
>>> 9) flirt -dof 6 FA to structural (T1)
>>>
>>> I found that the corpus callosum in the FA map (and corrected b0 image)
>>> is "stretched" when compared to the structural image (see attachment).
>>> The screenshot shows the structural image, overlaid in red with FA
>>> (thresholded at 0.3).
>>> Does anyone know what might cause this problem, and how I could fix it?
>>> Thanks for your help!
>>>
>>> Cheers
>>> Kerstin
>>>
>>>
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