Converting Dicom to NIfTI - tannerjared/MRI_Guide GitHub Wiki

My preferred tool is dcm2niix. That link provides installation and simple usage instructions. More complete instructions are available on the NITRC website.

The minimal command line call would be dcm2niix /path/to/dicom/folder. However, you may want to invoke additional options, for example the call dcm2niix -z y -f %p_%t_%s -o /path/ouput /path/to/dicom/folder will save data as gzip compressed, with the filename based on the protocol name (%p) acquisition time (%t) and DICOM series number (%s), with all files saved to the folder "output". For more help see help: dcm2niix -h.

There are other options for converting as well. If you have FreeSurfer installed, you can use the mri_convert tool.

If you are working within MatLab, you can use dicm2nii.