Chris Markiewicz
Chris Markiewicz
It looks like an issue with Jacobian intensity correction when applying fieldmaps, which appears to be doing more harm than good in your data. If you add `--ignore fmap-jacobian` to...
What image are you looking at?
I'm not seeing what you're describing in `sub-03_task-mvpa_run-1_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz`, which is the only one I processed. I've looked through the first 20 volumes.
Sorry for letting this one fall through the cracks. If you're realigning your dataset to ACPC before passing to fMRIPrep, that could be a source of the behavior you see....
Orientations are always a bit backwards of how I want to think of them, and I think you're probably having that happen to you as well. The orientation describes a...
> 1. For some reason, the `anat/*_desc-ribbon_mask.nii.gz` file was the only `.nii.gz` file that was not binary identical (i.e., did not have identical MD5 hash). Comparison of the two files...
Since you're passing the affine, it's being converted back into the header format. If you use `affine=None`, the header will not be modified.
Can you `print(img.header)` for the `WMmgz` input image, the `WMnew` image, and then reload the file that you save and print its header too?
Oh, ```diff - WMnew = nb.freesurfer.mghformat.MGHImage(WM, affine=None, header=WMmgz) + WMnew = nb.freesurfer.mghformat.MGHImage(WM, affine=None, header=WMmgz.header) ```
Sorry for missing this. Yes, if you could share a subject (with only a single BOLD run) that exhibits this issue in 25.2.0, then we can look into it.