Dara,
I notice your data is from Siemens VA30. Siemens started adding in a lot of sequence details with VB11, which I think was released in the year 2005. Therefore, the DICOM images from these devices is impoverished, and this limits what dcm2niix can extract. While the Allegra was a ground breaking scanner for its day, there have been a lot of improvements over the last two decades.
If you do want to use these, take heart that for FSL tools If your readout time is identical for all acquisitions you don't neccessarily have to specify a valid value in this column (you can e.g. just set it to 1), but if you do specify correct values the estimated field will be correctly scaled in Hz, which may be a useful sanity check. Presumably, your readout time is identical across sequences, so just inset a plausible value, e.g. "TotalReadoutTime": 0.018,
You should also be aware that you are trying to remove the geometric distortions in a gradient echo EPI scan. The typical ways to do this are to either:
- fieldmap method: Acquire a gradient echo fieldmap and use a tool like FUGUE.
- pepolar method: Acquire a pair of spin echo EPI data with the same slice centers and angulation as your gradient echo EPI and estimate the distortion with a tool like TOPUP, applying the warp fields to your gradient echo data.
As discussed previously the BIDS specification explicitly requires pepolar to be Spin Echo. The issue is that gradient echo has both spatial distortion and signal loss, while the spin-echo should recover the signal (so the image is distorted, but the signal is moved and either compressed or rarefied). While some people do apply TOPUP and similar tools to gradient echo pepolar data, I think you need to be realistic about the performance and visually inspect each dataset.