Dear Holly,
not being able to run topup (because you don't have at least one volume with reversed phase encoding) does not prevent you from using eddy. You just run eddy "as usual", but without the --topup parameter. You will then have the missing files you list below.
When you run eddy without the --topup your data will not be corrected for susceptibility distortions (same as with eddy_correct), but you will get a much better correction for eddy currents and subject movement.
I should also mention that there is a method and software developed by Kurt Schilling et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394453/) that uses topup and the anatomical (T1 or T2) scan to estimate a fieldmap that can then be input as the --topup parameter to eddy. I haven't tried it myself, but I have had good reports about it.
Best regards Jesper
On 09/08/2022, 19:36, "FSL - FMRIB's Software Library on behalf of Holly Sullivan-Toole" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Hi, I ran an in-house version of the eddy_correct command (I can share via email) on a set of DWI data for which I did not have field maps to perform topup. As a result, I did not get the below movement-reports as output. Is there a way that I can get analogous information without using eddy? I am trying to use voxel displacement/movement as a covariate in TBSS analyses and (in the future) tractography analyses.
my_eddy_output.eddy_movement_rms
my_eddy_output.eddy_restricted_movement_rms
my_eddy_output.eddy_outlier_report
Thanks!
Holly
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