I am considering preprocessing a dataset using fMRIPrep, and I would like to leverage both T2 and T2* images to improve geometrical distortion correction of the BOLD images, following the approach described in 10.1111/j.1552-6569.2010.00470.x, as no fieldmap is available for this dataset.
Specifically, my idea is to register the EPI to the T2*, then the T2* to the T2, and finally the T2 to the T1w. As described in the paper, this would allow for an approximate distortion correction by warping the mean EPI image onto the non-EPI T2* image, with the resulting transformation then applied to all BOLD volumes.
From what I understand, this type of custom distortion correction step is not directly supported in fMRIPrep with single-echo data. Do you have any recommendations for how such a procedure could be integrated into or used in combination with fMRIPrep? Would another pipeline such as C-PAC be better suited for implementing this kind of strategy?
Thank you very much for your time and any guidance!
Thank you, Steven! I’ll look into this. Do you happen to have any resources comparing both methods, or at least comparing more common distortion correction techniques and/or their influence on the true signal? I apologize for asking, but I’m struggling to see the advantage of using synthetic fieldmaps when I have access to real data that could potentially help. However, I’m still relatively new to these preprocessing steps, so any additional insights would be greatly appreciated.
Hi — I would like to follow-up on this. I am quite interested in incorporating omni’s distortion correction into my fmriprep-based preprocesisng pipeline, but I would like to avoid performing some similar correction steps twice.
Do you have any advice on the best way to go, e.g., feed fmriprep with omni’s corrected EPI images instead of raw ones and disable --use-syn-sdc, or place omni’s synthetic fieldmaps in fmap/ with custom json files, to force fmriprep to use them?
Place the synthetic field maps in fmap folder with epi suffix, including opposite phasencoding direction and IntendedFor fields in json to link it to bold.
Could you confirm that this is the correct output image feed for the synthetic fmap /func/sub-xxxx_ses-xxx_task-rest_acq-Siemens_bold/epi_proc_1_distortion_correction/iteration2_synthetic_epispace.nii?
The bold is oriented LAS, while the synthetic image generated by omni is RAS, like the T1w and T2w images. Do you think this mismatch could cause errors? Should I flip the bold to RAS to avoid potential problems?