Fieldmaps

In a nutshell, the information we need to create a VDM in SPM (see calculate VDM module in SPM batch):

  • blip direction

  • echo time

  • total EPI readout time

Inferring blip direction and echo time from a dataset that has sufficient metadata is usually simple.

But total EPI readout time is not mentioned, so it has to be computed from the information we have, it is not entirely clear how (see the comments with a lot of ??? in getTotalReadoutTime).

Things that are yet unclear:

  • is it actually possible to compute total EPI readout time that SPM needs from the info in a typical dataset with fieldmaps like openneuro/ds001168?

  • If it is not then that is an issue because it means some BIDS dataset are not usable with SPM.

Things to keep an eye on: the code from this repo from the fMRIprep team could have answers for us.

bidsCreateVDM()

setBatchCoregistrationFmap() setBatchCreateVDMs() setBatchComputeVDM()

getBlipDirection() getMetadataFromIntendedForFunc() getTotalReadoutTime() getVdmFile()