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Hi,
The SPM interface currently does not support voxel-based FDR. The MATLAB version of SPM readily provides this functionality, however, if you change your SPM defaults accordingly. There is no easy way to achieve this in nipype. I believe that FDR is a very useful way of correcting for multiple comparisons when analyzing fMRI data. Other users share this view because a similar PR has already been made by Lorenzo here. The changes proposed in my PR are minimally invasive and thus are very unlikely to cause any problems with respect to backward compatibility.
List of changes proposed in this PR (pull-request)
I hope you will find these changes useful as well.