TOPUP image alignment issues

[Elizabeth Castro]

Hi Frank,

I am having an issue with the alignment of my images when doing the topup preprocessing step. I have three images for each participant: B1000, B2000, and a reverse phase encoding image, and the images when viewed in 3D Slicer are all nicely aligned with each other. I created a multi-shell scheme in DSI Studio with the B1000 and B2000 images following the instructions to merge scans at multiple time points. This step included resampling to T1w/T2w to align the SRC files to the common space, and I believe this is where the alignment of the B1000 and B2000 image got changed compared to the PE image. As you can see these are my results from topup:

 

I have tried using FSL’s topup process, however I can’t get past the FSLmerge step since my images are throwing a size match error, and when viewed in FSLeyes the PE image is shifted far from the other images. I wanted to see if you had any solution for this alignment issue in DSI Studio, or knew of anyway to correct this issue? I’d very much like to continue my progress using DSI Studio, so let me know your thoughts please! I have also sent one participant’s data for you to look through if necessary.

[Fang-Cheng Yeh]

Could you upload the data for me to check?

Frank

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