Dear Kevin,
> Thank you for getting back to me.
>
> Here is a dropbox link of screen shots of a slice from our data.
> https://www.dropbox.com/sh/blg5sbyqd9jg4xf/AAApqiFA11WsfRufHAtjQ0NTa?dl=0
> (I could not attach images due to the size limit)
>
> Raw DTI - shows a slice with signal attenuation
> Eddy 5.0.11 with repol - fixes this slice
> Eddy 5.0.11 with no repol - does not fix this slice
> Eddy 6.0.1 with repol - fixes this slice
> Eddy 6.0.1 with no repol - also fixes this slice
>
> As you can see in the screen capture, there is huge difference in the slice between 5.0.11 vs 6.0.1.
> If 6.0.1 without "repol option" is not replaceing the outliers, would you please let us know what is happening here?
> (We did not use other eddy options here)
hmm, that does indeed look strange. I don’t have an explanation off the top of my head.
If you use slice-to-volume registration I can see how that could lead to a de facto outlier replacement since the predictions are then used to fill in the movement-related gaps in the data. But you say that you are not using “other eddy options” here, so that doesn’t seem like a likely explanation.
The other option would be that a bug has been introduced in the code that stores the original slices and brings them back at the end. Maybe I can use your data to check for that?
I am afraid that I won’t have time to look at it this or next week. So if you are happy for me to use your data, can you please send me a reminder after next week and I will give you instructions how to upload your data?
Jesper
>
> Best wishes,
> Kevin
>
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