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DICOM importing

DICOM importing in SPM

  1. Click “DICOM Import”.
  2. Select a bunch of DICOM files (e.g. all the files in a series).
  3. Select an output folder (this could be the same folder the DICOM files are in, or a different folder).
  4. Your files start converting.

If there are no errors, you should be good to go with Nifti files, ready for analysis. Note that with the default SPM options, it may make sense to do this conversion one folder at a time, but if you change defaults.dicom.root (see below), or use a custom script, you may be able to convert a whole study in one go.

Options

There are a couple of options for DICOM importing which can be set in spm_defaults. To edit, type edit spm_defaults from the Matlab prompt, and look for the following lines:

defaults.images.format = 'img';

defaults.dicom.root    = 'flat';

By setting defaults.images.format to “nii”, DICOM importing will automatically produce single-file Nifti files (.nii) rather than .img/.hdr pairs. For the various settings available for defaults.dicom.root, type edit spm_dicom_convert, which provides options for sorting DICOM files into folders. For a single subject, “series” may be the best, as it will attempt to split converted images by series (which is often what you want). Note that the way this works will probably depend on the specific implementation of your scanner software etc.