Please make sure you are using the latest release (v1.2.20181114). You only need to select "output folder" once - that just tells the program where you want to save the covnerted data. After that you drag and drop the DICOM folders onto the toolbar of the dcm2niix GUI and it will convert the files for you. By the way, if you want to quickly view DICOM images (and do not care about converting them), you can drag and drop the DICOM folder onto the main MRIcroGL window - unless the dcm2nii GUI dialog is visible it assumes you just want to look at your images.