Choosing between ANTs SyN fieldmapless and a GRE fieldmap for distortion correction

1

Hi there! New to QSIprep and wondering whether or not to use fieldmapless distortion correction (ANTs SyN). We do collect a GRE fieldmap at the beginning the scan protocol, but it is not collected close in time to the diffusion scan- there is about 45 minutes of functional and structural scans between the GRE fieldmap and the start of the DSI sequence. In this case, is it more appropriate to use this GRE fieldmap for distortion correction or use the fieldmapless algorithm instead?

2

Hi @aiadipaolo and welcome to neurostars!

I almost always recommend a real fieldmap to the fieldmapless method, but you can also try SynB0-DisCo (GitHub - MASILab/Synb0-DISCO: Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps) to generate a fieldmap before running qsiprep, which is a promising alternative to the SyN method directly incorporated in qsiprep.

You can always try running all three and benchmarking them for your study.

Best,
Steven

3

Thanks so much for the recommendation, Steven- I will try that!