I am trying to apply fMRIprep to data from a Philips scanner using topup for distortion correction. I’m confused about some issues related to overcoming limited data in the Philips DICOM headers
– Before using fmriprep, our lab had been calculating Total Readout Time using the Spinoza/OSF method described here: OSF . The problem is, Estimated Total Readout Time values calculated by dcm2niix differ from that method by a factor of 2, beyond any slight differences from using different formulas, in our data.
I think this may have something to do with the reported 2x SENSE acceleration factor in the image headers. As I understand it, acceleration needs to be taken into account in some versions of the formula for total readout time. However, our headers include a field for “EchoTrainLength”, which I believe corresponds to (EPI factor + 1) after taking into account acceleration.
When I try to compute the Total Readout Time myself using header data with the formula ((“WaterFatShift” x (“ReconMatrixPE”-1))/(3.4 x “ImagingFrequency” x “EchoTrainLength”)), I get a similar value to what the Spinoza/OSF formula produces. This makes me wonder if dcm2niix is handling the acceleration factor erroneously.
– I also noticed that the total readout time value shouldn’t really matter in most cases, as long as it doesn’t vary between the blip_up and blip_down images (which it doesn’t for us), and as long as images don’t need to be precisely scaled. My question for the fmriprep team regards the latter: is it OK for fmriprep if the total readout time value is incorrect but consistent between scans?
– Finally, because Philips scan headers don’t distinguish between A–>P and P–>A phase encoding directions, I saw elsewhere that it’s best to take the PhaseEncodingAxis value from dcm2niix, and just set the direction to opposing directions for field map data. But now I see that fmriprep is also asking for phase encoding direction to be set on functional images. Does it matter if this is precisely correct (i.e., does it matter if this is j vs. j- for functional images)?