SPM has a DICOM conversion utility that works with many different variations of the DICOM format. It is accessible via the button "DICOM Import" that will redirect you to the batch interface:
SPM -> Util -> DICOM Import
You will then have access to a number of options such as the choice of single file ('.nii') or dual files ('.img/.hdr') NIfTI output format.
If you encounter problems with your DICOM data, please email the SPM mailing list with details about your scanner and acquisition settings (an example of a DICOM file might be useful). This will contribute to make the DICOM conversion utility even more robust.
If you have problems with SPM's DICOM Import, popular alternatives include:
- dcm2nii by Chris Rorden, (part of the image viewer MRIcron)
- MRIConvert from the Lewis Center for Neuroimaging, University of Oregon.
At the bottom of the webpage for dcm2nii there is a longer list of alternative DICOM conversion tools.