Dear Jesper,
Thank you for your quick and detailed response.
I have used topup via command line:
topup --imain=AP_PA.nii --datain=accparams.txt --out=topup
--iout=topup_unwarped.nii
The AP_PA.nii file contains two 3D b0 volumes with opposite phase
encoding direction (as mentioned below). Apart of the phase encoding
direction, the same scanning parameters were used for both volumes.
So the accparams.txt file has two lines (below)
The distortions in the frontal area are not as well corrected as I have
hoped for (see attached image).
I ran topup also with the same files but fed in fsl's b02b0.cfg file,
which I changed only to avoid subsampling. And the correction seems to
be improved. So I believe with a more elaborated search for good
parameters, I may be able to get a better correction.
Does topup register the b0 volumes (rigidly) before warping? Otherwise I
may have to consider to align my b0 volumes beforehand.
Thanks agian for you help
Stefan
On 2016-05-24 12:51, Jesper Andersson wrote:
> Dear Stefan,
>
>>
>> I try to correct my DWI for EPI distortions with topup. As know from
>> the FSL topup documentation, I need an acquisition file to feed the
>> scanning parameters to topup (--datain).
>> I have two b0 volume with opposite phase encoding direction A>>P and
>> P>>A, so my acquisition file would have two rows with
>>
>> 0 -1 0 X
>> 0 1 0 X
>>
>> However I have problems to define the X value.
>> First I have computed it according to the documentation with: X = echo
>> spacing(in ms) * (EPI factor/GRAPPA - 1) * 10^-3, which in my case
>> would be: X = 0.72 * (128/2 - 1) = 0.04536
>> Unfortunately, the result is not satisfying.
>
> I’ll reply to the readout time question below. Here I want to say that
> if the results are not satisfying, the readout time is not the issue.
> In what way are the results not satisfactory? What did your command
> line look like?
>
>>
>> -> Do I compute the value correctly?
>
> Yes
>
>> -> Is the result maybe a limit of topup, or can I compute the factor
>> in a different/more accurate way?
>
> No, the above is correct.
>
>> -> Why do I not have to consider partial Fourier acquisition, as this
>> influences the acq. time as well?
>
> The relevant thing is the off-resonance phase-evolution over the
> course of the acquisition, and that doesn’t change with partial
> Fourier. In the partial Fourier case there is an implicit assumption
> that the phase-evolution in the “unacquired” part is the same as in
> the acquired part.
>
> Jesper
>
>
>>
>>
>> Details of my scan from protocol:
>> Echo spacing = 0.72ms
>> EPI factor = 128
>> Bandwidth = 1698 Hz/Pxl
>> Further acquisition details from the dicom header in the screenshot,
>> attached to this e-mail.
>>
>> Hope you can help me.
>> Thank you very much in advance
>> Stefan
>>
>> <Capture.PNG>
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