Okay – I have made the same experience with MPRAGEs before, also T1 doesn’t seem to be as well suited to reconstruct the trajectory, but in general it seems to work for me. In some cases, you can’t delineate all 4 contacts of both electrodes, however, sometimes the uppermost contact seems to show a slightly larger artifact. Since the contacts are equidistant, this might help to place the contacts correctly. Also, you might want to estimate the distance between the electrode contacts, which is usually slightly greater than 2 mm (or 3 mm in 3387 electrodes) depending how much warping has been done in the normalization process. The distance should be displayed in the Manual Review window.
When doing the first reconstructions, I agree that it sometimes feels a bit difficult where to exactly place the contacts, but after about 10 reconstructions, in my experience one gets a confident feeling about where to put them.
If you happen to have some imaging data from 3387 electrodes, it might be easier to start with those as well.
But in any case I’m happy that there were no further technical errors so far.