I am trying to analyze an old fMRI dataset using fmriprep. However, all images are in mnc format. I managed to convert mnc to nii, named files following BIDS and created all other required event tsv files and the participant JSON file. The only thing left is the BOLD JSON file, I wonder what are the mandatory fields in BOLD JSON to be able to run fmriprep? I tried without BOLD JSON and got an error about missing TR. Do you think if I just put one field (RepetitionTime) it will be safe to run fmriprep? Or do you know if there are any existing python code that could read mnc file and generate a BIDS valid JSON? Any hints would also be welcome. Thanks a lot.
According to the BIDS specification, you need RepetitionTime, VolumeTiming/SliceTiming, and TaskName. Other fields such as the phase encoding direction, can be helpful for fieldmapless SDC, for example, but not required for basic fmriprep functions. If you have the raw dicoms still, you may be best off running dcm2nii on them to get BIDS-compliant json files.
Thanks a lot @Steven, unfortunately, I don’t have the raw dicoms… May I ask if you know the corresponding fields of VolumeTiming/SliceTiming in dicom header? In mnc file header I do have, hopefully all of the dicom header like dicom_0x0018:el_0x0080 = “1750” for RepetitionTime. But I could not find slice timing. Thanks again.
Unfortunately I do not know that. Perhaps, if you’re okay not doing slicetiming correction, you can not have that field, and add --ignore slicetiming and --skip-bids-validation to the fmriprep command, and maybe it will run.