Dcm2bids with multi-echo BOLD data

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1

Hi Neurostars’ers,

Thanks in advance for reading this!

We’re using fmriprep_23.1.4. We have collected a BOLD fMRI dataset with multiple-echos (which we intend to analyze with fMRIprep and TEDANA). The dataset includes a pair of short AP-PA acquisitions for calculating fieldmaps. Each scan also has a single-band reference image. Based on dcm2bids_helper, this results in the following nifti files:

1a. Short AP sbref
1b. Short AP echo 1
1c. Short AP echo 2
1d. Short AP echo 3

2a. Short PA sbref
2b. Short PA echo 1
2c. Short PA echo 2
2d. Short PA echo 3

3a. Long PA sbref
3b. Long PA echo 1
3c. Long PA echo 2
3d. Long PA echo 3

I was wondering what the best approach is for running dcm2bids on this dataset. Specifically:

  1. Should the fieldmaps be based only on the shortest echo time, which has the best contrast? Or is there a way to define a fieldmap based on the optimal sum of echos?
  2. Should we simply ignore the sbref scans for the short scans that we collected for fieldmapping?

Many thanks!
Roey

2

You should have an SBRef for each echo - and I would use the shortest echo SBRef for fieldmap related parts of processing. I don’t think an optimal combination would help you, as you say the contrast is good.

3

Thank you for your advice, @dowdlelt!
And you’re absolutely right. We do have an SBRef per echo.

(For future reference, a similar quesiton had been discussed here before)