What you’ll need to undistort an EPI data series

Field maps

You must have collected field (or "phase") maps. You need the raw data for these – before Bruker reconstruction. The undistortion tool will perform the reconstruction. Commonly, you will have collected three field maps – phase1a, phase1b and phase1c. These will be in three numbered directories within the subject directory: e.g.

000484.bd1/10

000484.bd1/11

000484.bd1/12

You need to know which is which – although they are almost always collected in the order 1a, 1b, 1c

EPI header file

You’ll need either the .brkhdr or imnd file from any one of your EPI dataseries. This contains information about the slice angle that the tool needs. If you’ve used pvconv.pl rather than ImageJ to convert your data to Analyse format, this will produce the .brkhdr file. Otherwise, the imnd file will be in the numbered session directory of the raw data.

Mean EPI

You’ll need a mean of your EPIs that you wish to undistort. Usually, you should use the mean produced by the output of realignment.

The EPIs you want to undistort

The .mat file of all of these must be the same, and the same as the mean. This will be the case if you have resliced your EPIs after realignment.