Dear Colleen,
> I would like to know if it is possible to use "eddy" on our data. Our DTI images were acquired with single-shot EPI (SENSE factor 2.5) on a 3T ‘Acheiva’ scanner (Philips, Best, the Netherlands). Two runs were collected in each subject, with 32 gradient directions (b = 800 s/mm3) and one b0 in each run. Sixty 2.2-mm axial slices were acquired for each volume, with 0.9 mm in-plane reconstructed resolution. We also acquired a non-EPI axially acquired T2-weighted image. Is it possible to average the two runs together and then run eddy? Can we still use eddy even though we do not have opposite phase encoding directions?
yes, eddy does not require opposing PE directions. How well it works will depend a little on how your b-vecs are distributed. I know that some Phillips protocols have a rather funny distribution of b-vecs and I have seen problems with running eddy on such data sets.
You do need at least one pair of b0 volumes with opposing PE directions if you want to run topup in order to estimate the susceptibility induced off-resonance field. If you have that, you can then pass the topup output (field estimate) into eddy, which means that eddy will correct the data also for susceptibility distortions.
If you don’t have that, you can still run eddy and correct your data for eddy currents and movement.
In your case, if the contrast in your T2-image is sufficiently similar to the b0-images, you may be able to use your T2 in lieu of a reversed-PE b0. In that case you stick one of your b0:s followed by the T2 image in a 4D file and make an acqparams.txt file looking something like
0 1 0 0.05
0 -1 0 0.00005
provided that the PE-direction in your EPI images is A<->P (if it is in the L<->R direction you put the 1 and -1 in the first column instead).
Jesper
> Thanks,
> Colleen
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