Dear Fatihah,
>
> Thank you for your explanation. Yes, I do have two phase encode directions. These two phase encoding directions that I have created are same which is :
> 1 1 0 0.0005
> 1 1 0 0.0005
the crucial thing when we say that you need to have two phase encode directions is that they need to be _different_. I.e. you need to have acquired them with different phase encode direction.
If you haven’t already done it I suggest you take a look at the help pages for topup (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup) to get a little background on the principles behind.
>
> Since my phase encoding directions are same, so I assume my acqparams.txt contains a single line. Based on your suggestion, how to obtain two different phase encode direction?
I am afraid that if your phase encoding directions really are the same, i.e. all your data was acquired with the same phase-encode direction, there is nothing you can do at this stage to change that.
Jesper
>
> Thank you.
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Jesper Andersson
> Sent: Wednesday, 25 September, 2019 5:41 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Run Eddy and Topup
>
> Dear Fatihah,
>
>> Hi,
>>
>> Thank you for your reply. Fyi, I have already tried that both direction which are 1 0 0 and 0 1 0. Unfortunately, it states that error like this :
>>
>> Topup: msg=topup_clp::topup_clp: Mismatch between 004Tensor.nii and acqparams.txt
>>
>> So, any other reasons or idea how to resolve this problem?
>
> in order to run topup you need two (or more, but let's forget that) images acquired with opposing phase encode directions. Both these images need to be put into a single 4D file. And to match that the acqparams.txt file needs to have two lines each describing how the pertinent volume was acquired. It is never a valid thing to do to run topup with an acqparams.txt file that contains a single line.
>
> I think what you need to do first of all is to make sure that you have data acquired with two different phase encode directions. And when you have confirmed that we can start thinking about what your acqparams.txt should look like.
>
> Jesper
>
>>
>> Thank you.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of SUBSCRIBE FSL Anonymous.
>>
>>
>> Sent: Monday, 23 September, 2019 10:59 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Run Eddy and Topup
>>
>> By writing 1 1 0, you are indicating that phase encoding and thus the distortion happened in both the x and y axes (left/right and top/bottom).
>> Typically, it should just be one direction 1 0 0 or 0 1 0 so that x^2 + y^2 + z^2 = 1.
>>
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