Dear Rodrigo,
>
> I have the same question and issue (check below). What is confusing for me is whether *.acqp.txt should be only 2 lines (if A>P and P>A directions were used) or if it should include the same number of volumes in my 4D DWI volume (in my case 398, so 398x4 or only 2by4?) .
as a general rule you should have as many lines in your acqp.txt as you have volumes in your input to topup. I used to recommend having more than two volumes (i.e. use some of the interspersed b0 volumes from the diffusion data set), but with more recent versions of eddy that is no longer really necessary. So to keep things simple I would recommend just two input volumes to topup and two lines in your acqp.txt file.
>
> In my case, I have two b0s with A>P and P>A phase encoding. I successfully applied topup (only in two mean b0-values per phase encoding direction).
Unless the two b0 volumes are acquired consecutively I would be careful with averaging them before feeding them to topup. It can complicate things if there are any movement between them. I would either use only one b0 from each PE direction, and I would chose the ones that come first in the diffusion data sets. Provided that they look fine.
>
> No I created a index.txt file with (199 1s and 199 -1), each representing a>P and P>a enconding directions.
>
> In the acqp.txt file, I tried both options (2by4 matrix, or 398by4 matrix) and I still get the same error.
> Wondering if anybody has any suggestions on how to solve this.
The 2x4 should be fine. The index is simply an index into the acqp.txt file, indicating if the first line or the second line should be used for that volume. So the index values should be 1 (to indicate the first line) or 2 (to indicate the second line). It won’t know what to do with an index of -1.
Jesper
>
> Thanks in advance,
>
> Rodrigo
>
>
>
> Error Message:
>
> eddy: msg=Mismatch between --index and --acqp
> terminate called after throwing an instance of 'EDDY::EddyException'
> what(): eddy: msg=Mismatch between --index and --acqp
>
>
>
> acqp.txt: cat acqp.txt (also tried with the same lines repeated 398 times, as the number of DWI volumes I have)
> 0 1 0 0.096
> 0 -1 0 0.096
>
> index.txt: cat index.txt
> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
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