For Siemens users who get “_Eq” images: this occurs because Siemens scanners can generate the same series (0020,0011) and instance (0020,0013) number for the same slice acquired for two echoes. In this example, where the fieldmap had 36 slices, saving the data direct from the console would store 72 DICOM files, but when the images got exported the PACS archiving thought there were duplicates and only saved 36 (in this case, 5 from one echo and 31 from another).
This is not a fault of dcm2niix: it correctly identifies that the provided images from a given echo do not have equidistant slices. The Siemens files are technically legal (the DICOM standard does not require unique instance numbers), but it does disrupt many archiving systems. While it would be terrific if Siemens helped disambiguate their images, they have had consistent behavior for about a decade. Therefore, when this happens I recommend rescuing the original files from your scanner and validating/updating your storage system to handle this situation.