Hi NeuroStars!
I’m relatively new to fmriprep and preprocessing multi-echo task data (with version 22.1.1). We are currently not using tedana. Instead, we are using AROMA on the optimally combined data. I’ve seen conflicting information about how to SDC is being performed/best practices.
I’m using the first echo of the dir-PA as the fieldmap (e.g., sub-AT000012_acq-multiecho_dir-PA_echo-1_epi.nii.gz) per this thread Multi-echo pepolar fieldmaps BIDS spec/SDCFlows grayzone.
I then edit the .json file’s IntendedFor field and list all the dir-AP bold files (echo 1-4). When I run this, I get individual fmapid files for each echo (e.g., sub-AT000012_fmapid-auto00002_desc-epi_fieldmap.nii.gz).
From my understanding of this thread (Multi-echo, fmriprep 21.0.2 distortion correction, the -t task selection parameter, and tedana - #12 by jrdalenberg) it seems that SDC is then applying different SDC to each echos. This may be fine if you are using tedana after?
As I’m hoping to use the optimally combined data without tedana, how do I ensure the same SDC is being applied to all the echos of the same task?
Thank you so much!
Kate