Hi all,
we are using fmriprep to preprocess resting state and task based fmri scans and use field maps for susceptibility distortion correction (FMB (fieldmap-based) - phase-difference map; Phase-encoding direction AP). After SDC, across many subjects there are new frontal and parietal hypointensities just below the brain’s surface while the surface of the parietal and frontal brain appears strongly hyperintense. In the more severe cases, the frontal hyperintensities also come along with a bad frontal coregistration. Furthermore, in many of the subjects with those new hypo-/hyperintensities we also see occipital distortions after sdc. (see screenshots below)
Any ideas where those issues might stem from and how to address them? Thanks a lot for your help!
Best,
Till
Command used (and if a helper script was used, a link to the helper script or the command generated):
It often helps if you can determine at which stage the images started looking strange. For example, do the distortions appear in the images before any preprocessing, or only after the distortion correction step? If the dicoms and everything look fine up to the distortion correction step, try looking at the fieldmaps for participants with and without the distortions; poor quality fieldmaps can create distortions in otherwise-ok functional images.
I am working with Till on the data, so I would like to add, that the observed hypoconnectivity and poor frontal coregistration for some subjects co-occured with an incorrect co-registration bt the anatomical reference of the fieldmap and the BOLD scan
Following your comments and we checked the quality of the acquired fieldmaps, which look fine to my eyes
As you suggested we also ran fMRIprep (v 23.2.1) with the command --ignore fmap-jacobian, but this did not solve the problems presented by Till and seemed to reduce the SDC-induced distortions and hypointensities only insignificantly.
We are currently re-running our dataset with the additional flag --ignore fmaps, which is not the pipeline we wish to use but at least does not introduce artifacts. Do you have any other suggestions or ideas where this problem might be coming from? Any help where to look at is greatly appreciated.
