If I understand correctly you are only loading a subset of your dicom sequences at a time? If so, you can do the downsampling within Slicer. Just use the ResampleScalarVolume and specify the output spacing (in mms) you’d like. This will preserve coordinate system of the original DICOMs, and you can segment/directly measure distances/etc…
Alternatively, you can try to use the Fiji’s Import->Image Sequence with virtual stack option to load your entire dicom and subsample there. Though I never tried with such large datasets…