Processing Data through fMRIprep without DICOMS

Hello everyone!

I have recently begun using fMRIprep for my lab’s data processing pipeline, and I am incredibly impressed with the results!

The reason I am writing this post is to ask a question about the BIDS data structure or, more specifically, a question about the sidecar (JSON) files used in the BIDS structure and fMRIprep. Our data is captured on a General Electric 3T Discovery Scanner and, up until later in 2018, did not output DICOM files, but instead, output proprietary GE p-pfiles. Where that becomes a problem is that, based on the BIDS tutorials I’ve read, the necessary JSON files needed for each subject are generated in the “dcm2niix” step of converting DICOMs to NIfTI format. For our older data that does not have DICOMs, however, this isn’t as easy of a task since dcm2niix will not work.

For a particular set of data, about half of the subject only have p-files, and the other have does have DICOM files that can go through dcm2niix. With this in mind, I wanted to run something by everyone to see if this idea would work:

If we create a JSON file via dcm2niix by using a subject who does have DICOMs, could we copy that JSON file into the directories for the subjects that only have p-files? I am not very well-versed in sidecar files, and I apologize for that, but to my understanding, throughout this particular set of data, all of the scanning parameters have been kept constant. If this is the case, would there be any problem using a master JSON file for this set of data? I know the JSON files have scan dates and other information that is particular to a certain individual, but for the purposes of our work, demographic information and scan dates are not needed.

In not so many words: would there be any information in a JSON file that would affect the function of fMRIprep that would be different between individuals when the scanning parameters are kept constant?

Thank you for reading.

Assuming the protocols really did not change, this would work fine. I wonder if the p-files were saved when multi-band was still a WIP (Work in progress) for the GE, and it is possible some parameters changed with the upgrade that allow DICOM export. While the BIDS JSON files are fine, be especially cautious if you have DWI sequences - the FSL format bvec gradient directions use the image itself as the frame of reference (e.g. the x,y,z directions refer to row, column, slice). If two DWI scans with identical parameters except the image angulation differs, the bvec files will be different. So if you acquire the same DWI scan from the same person, just adjusting the rotation of the scans, the bvecs will vary.

This project might help you spot differences.