Using synthetic field map from synbold-disco with fmriprep

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Hi @Bennett1, and welcome to neurostars!

I believe a basic step-by-step is something like:
Using RAW data:

  1. Run SynBOLD-DisCo without topup (--no_topup)
  2. Take the synthesized undistorted BOLD-contrast image (BOLD_s_3D.nii.gz), place in the fmap folder, give it a name such as sub-xx_ses-xx_acq-synbold_dir-PA/AP_epi.nii.gz, where the dir-<> label is the opposite of what your original BOLD is.
  3. Make your own JSON. Just needs a few fields: (1) TotalReadoutTime - make it whatever you define at runtime or the default (1 second), (2) PhaseEncodingDirection - make it the opposite as your original image (so add or remove the minus sign), (3) Add the IntendedFor and/or B0FieldSource/Identifier fields to link the fieldmap to your BOLD image. The JSON should be called sub-xx_ses-xx_acq-synbold_dir-PA/AP_epi.json.
  4. Run fMRIPrep as normal (of course, do not --ignore fieldmaps or --use-syn-sdc, otherwise the fmaps may be not used)

Best,
Steven

EDIT: While this probably works fine with just 1 T1 image, I now wonder if it would be better to use the preprocessed T1 template in the case of multiple T1s. That would make the workflow a little more complicated, since it would involve something like running sMRIPrep (of fMRIPrep with --anat-only) first, then making the synthesized image, and then doing the rest of fMRIPrep (passing in the preprocessed anatomical derivatives with the --anat-derivatives flag). I might give this a shot since I have a 7T dataset with multiple T1 images.

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