I have some fMRI data that I’ve been trying to convert to BIDS format through my University’s Flywheel instance. I’m running into a problem because a couple of the scan runs are being split into multiple acquisitions by DCM2NIIX on Flywheel. All other scan runs process fine with this pipeline.
I had previously processed these data in a more low-tech way, using a GUI version of DCM2NII / DCM2NIIX, which produced produced single Nifti files for the runs in question.
In one case, it’s a functional run, which I ran all the way through FSL without issue previously. There should be 294 images in the run; it looks like now, one file has 130 images and the other has 164. (Looking back at the files from my old pipeline, the data type of BOLD runs for that subject is INT16, while for other subjects I’ve checked, it’s UINT16. But that’s true for other runs, not just the one at issue. Not sure if that helps…)
The other run at issue is a B0map run, and DCM2NIIX on Flywheel is giving 3 separate output files instead of 1. (So across 2 B0map DICOM sets for that session, there’s a total of 5 outputs where there should only be 3.)
Any ideas as to why this is happening, or how to fix it?