Dear Shereif,
> So I have AP and PA diffusion datasets, and for some reason their acqparams.txt files show slightly different readout times (e.g. 0.05953 vs 0.06048). After merging the datasets and applying topup successfully, I'm running into trouble running eddy.
>
> Since eddy reads one row of the acqparams.txt file, I'm not sure which readout time to use in that row. When I use the AP readout time, I get FA maps with a really bad artefact at the occipital pole, while the frontal lobes look like they're missing parts (almost like the images are shifted anteriorly). When I use the PA readout time, I get much better images, but I'm not sure if that's the right thing to do or not.
>
> I hope I explained my problem clearly.
I think there is some little misunderstanding how eddy uses the acqparams.txt file. Let us for the sake of an argument say that your diffusion data consists of six volumes, three AP followed by three PA and let us say that the readout times are 0.05 and 0.06 for the AP and PA respectively. Your (single) acqparams.txt file would then have two rows and be
0 -1 0 0.05
0 1 0 0.06
and your index.txt file would have six entries (one for each volume) and be
1 1 1 2 2 2
which tells eddy that the first three volumes have been acquired according to the first row (0 -1 0 0.05) and the next three volumes have been acquired according to the second row (0 1 0 0.06).
Hope this helps.
Jesper
>
> Who ever's reading this, thank you for taking the time!
>
> Shereif
|