Using synthetic field map from synbold-disco with fmriprep

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Hi all,

Thanks to all the contributors to this interesting and useful thread! I have tried fmriprep23.# for a couple of fMRI runs either using its fieldmap-less or with fieldmap susceptibility distortion correction on a couple of datasets, however they all made more distortions (discussed in a thread here). Thus, I am now trying SynBOLD to see whether I can get a detour for that SDC part of fmriprep. Also, I am currently using an old dataset with no fieldmap data available.

So far, results from the SynBOLD (BOLD_u.nii.gz) are amazingly good (by means of distortion and matching with T1), however, while trying to utilize it into fMRIprep I encountered some issues:

  1. Using the method by @Steven did not solve the issue. Of note, it can be also because of my new fmriprep version and its buggy SDC. Check the frontal and brainstem regions:
    image

  2. I ran the pipeline suggested @jsein, with slight difference:
    – Letting TOPUP be done by SynBOLD
    – No --stripped or --motion_correct flags; I am also curious why these flags were used in the first place if the data was not either stripped or motion-corrected.
    The results of SDC ran by fmriprep (sub-#_ses-#_task-rest_space-T1w_desc-preproc_bold.nii.gz) are better (top image) but still worse than the BOLD_u.nii.gz generated by SynBOLD (bottom image). Both are in the T1w space for better comparison:
    image
    image

Is there a way to pass the BOLD_u.nii.gz to the fmriprep and do not have the issues mentioned here? I haven’t tried it yet but was thinking of:

  1. Running SynBOLD with --no_smoothing flag to avoid double-smoothing
  2. Pass BOLD_u_3D.nii.gz as “sbref” in the fmriprep to be used for mcflirt and motion regressor estimation.
  3. Use rBOLD.par to de-“motion correct” the BOLD_u.nii.gz. However, I do not know whether it is possible or not.

I also wonder whether it is possible to run fmriprep on BOLD_u.nii.gz and pass the rBOLD.par into the confounds pipeline of fmriprep separately.

Best,
Amir

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