We are seeing some strange results of the susceptibility distortion correction in fmriprep v21.0.2. It appears to stretch the brain too far in many participants, making alignment with the structural data worse. The data has A>P phase encoding direction and we use phase difference fieldmaps to do SDC…

Hi, A few questions: does this happen in all, or just some participants? have you tried the fieldmap-less method? does this error persist in v22.0.0? what scanner manufacturer do the images come from? If GE, this discussion may be useful: fMRIPrep 20.2.3 directly measured B0 map SDC correction cr…

Thank you for your questions, Steven! Below are the answers: More clearly in some participants than others, but visible in the vast majority Have not tried this, but will look at it in the next couple days Have not tried this yet. Do you expect it to make a difference? I don’t see major changes to…

I suggest looking at the field maps and/or single band reference images; abnormalities in those can lead to strangely distorted functional runs after preprocessing. This topic has such a case: Repeated fmriprep distortion; perhaps from susceptibility distortion , and I summarized it and a few other …

I aslo met the same problems. Many subjects have the unusual SDC and even I rerun the preprocessing. Some good results become the distorted reuslts. Did you solve the problem?

Same here, Yukun! Unfortunately, we still see problems when using fieldmapless correction; the SDC distortion doesn’t seem to depend on the quality of our fieldmaps. We also see normal results when processing the same scan with an older version of fmriprep so we plan to revert back to v20. However, …

Do you confirm that the SDC method used in all these problematic cases are with the Phase Difference Fieldmap method? One could look at the implementation of this correction method in fmriprep v20 and in fmriprep v21 (i.e. in SDCFlows as SDC was excised from FMRIPREP at this point) to see if there …

Thanks. I will keep you posted if we make any progress.

Unfortunately, the fmriprep v22 seems have same problem. I rerun the preprocessing with v22. I used 8 subjects to test and half of them have different bad correction. Even some of runs have good correction in the previous preprocessing. I post some information in this link. [image] …

If you are interested in this question，I have show my problem in this link. [image] The SDC of fMRIPrep v21-22 seems not robust! Hi, there. I used the fmriprep to do proprocessing recently. After checking the report, I found many subjects have wrong SDC corr…

Unusual susceptibility distortion correction for fmriprep v21.0.2?

YukunQu September 28, 2022, 3:28am 10

If you are interested in this question，I have show my problem in this link.