FSL TOPUP for BOLD data

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Hello experts,

I have data in BIDS format with functional data in /BIDS/func/sub_task_rest_BOLD.nii.gz and related json file as well as reverse phase encoding data in /BIDS/fmap/sub_dir-PA_run_02_epi.nii.gz and related json. How can I use the topup tool to get the fmap in HZ and the related json file? Where can I get the parameters for the acqparams.txt? I hope that experts can provide feasible code.

Thank you very much for your kind considerations and I am looking forward to your reply.

Neal

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Hi @Yi_Zheng, and welcome to neurostars!

Fmriprep can preprocess your BOLD data, including TOPUP. Documentation here: fMRIPrep: A Robust Preprocessing Pipeline for fMRI Data — fmriprep version documentation

Best,
Steven

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