@JosetAEtzel or @effigies , do either of you have any insights into this terrible fmriprep distortion correction issue? Some labs are encountering this and others are not. It is really worrying. Is it related to the FOV not quite getting the whole brain? That is my only theory at the moment. ; (

@dpat @JosetAEtzel I I think there are two issues right now. One related to masks when estimating/applying fieldmaps, and the other related to not applying a Jacobian modulation (down-weighting false signal pile-up). I think these can interact, so I'm trying to resolve Jacobians first.

@effigies
Thank you so much for taking this on. I am inquiring about sharing the bad dataset with you, if that would be useful.

@dpat Took about 2 months longer than I hoped, but we've got a release for you to test: https://mas.to/@effigies/111449183587172464

@effigies I tried this out and the native space boldref images look so much better! However, the standard space image is still a bit weird. This is with fieldmap-based correction. I've linked to before and after pictures: https://www.dropbox.com/scl/fi/os8z5em74604n2l11u1kp/fmriprep_sdc-Before-and-After-boldref-images.pdf?rlkey=pan7n1l4y0ir0pmkbke0pbm8i&dl=0

@dpat Not sure they attached here. Would you care to open an issue?

@dpat Oh, I see. That is a much bigger effect than I expected. Is there any chance of getting ahold of your data?

@effigies absolutely. See dropbox: The data is deidentified. https://www.dropbox.com/scl/fi/9saxth9tk3hgu9u6kd2ho/bids_pest107.zip?rlkey=fhzgtvrf7y2cewv4u2w279p99&dl=0
This is the raw bids, not the derivatives. Let me know if you want the latter.

@dpat Nope, raw is great. Running now. Thanks!

@dpat I'm realizing in the images you sent, you used the HMC boldref. That's not distortion corrected at all. Have a look at the desc-coreg_boldref.nii.gz. Or the "Susceptibility distortion correction" reportlet compares them:

@dpat The distortion correction seems not ideal, but in line with the fieldmap provided. The main weirdness IMO is that there is significant signal pileup in the inferior frontal lobe, which will be an effect of Jacobian modulation. I'm a bit conflicted here, as that typically produces cleaner results.

@effigies Well, the results are certainly much improved. Do you have any suggestions going forward?