Has anyone come across this before? At our second MRI site, fMRIprep seems to be having issues with the distortion correction (Phillips scanner). It looks like it’s struggling with the high-intensity CSF. Distortion correction is 1 fMRI scan in the opposite phase encoding direction. Normally we have 4, but here is what the output looks like. Wondering if anyone has any advice on this?
(motion correction (mcflirt) on the resting AP and the PA distortion scan separately
calculate a mean time series image for each just by averaging across each voxel’s intensities over time
concatenate the two mean time series images together into a single 4D volume (using fslmerge) with the AP mean image as the first and the PA mean image as the second volume 4) motion correct (mcflirt) the concatenated mean images by making volume 0 (the AP image) as the reference volume (-refvol 0) and realigning the PA mean time series to it (typically there is a minimal change here but sometime people move quite a bit between the PA distortion scan the functional run). 5) run top-up to estimate the distortion field, and then I apply the top-up correction to the motion-corrected resting state AP scan.
Could you try running with nipreps/fmriprep:next? A number of fieldmap issues should be improved there, and it would be good to know if yours is covered. You can use --level minimal to run as little as possible. You will still get reports showing the quality of the SDC and an SDC-corrected BOLD reference file.
@AustinBipolar 23.2.0a1 is out, which is a pre-release. It is “feature complete”, in that everything we intend to have in 23.2.0 is in it, but we want to give some time for people to run tests and catch bugs before we make it the obvious latest release. We would love to hear from you about how it runs.
Hmm. Thanks for trying that out. Would it be possible to get a copy of this subject? Just one T1w, BOLD (can be truncated to ~50 volumes without affecting processing) and fieldmap would be good to try to see what’s going on.
Data type coercions may be a bit of whack-a-mole, so I hope they don’t pop up elsewhere. Running in minimal mode gets sensible looking results. I’ll run in full and check the outputs.
Hi,
I just wanted to post that the update version of fMRIprep appears to have fixed the issues we have had (currently the unstable version of the docker container). Here are the updated images which are now much closer to the top-up version. Thank you.
