help > dcm2nii and Siemens mosaic dicom
Jan 12, 2017  02:01 AM | Suzanne Witt
dcm2nii and Siemens mosaic dicom

I downloaded MRIcro v1.8.7 and am trying to use dcm2nii to convert Siemens mosaic dicom files of EPI data into 4D nifti format.  I am not having much luck, as the resulting nifti images are still just the montages of slices.  However, if I use the dcm2niigui that came with the old version of MRIcro (2013), everything works perfectly, with each time point of the 4D nifti file corresponding to a volume of stacked slices.  I will add that these dicom files are not coming directly off the scanner but rather being exported as anonymized dicom files from a Sectra PACS server.

Just to add to my confusion, I experience the exact opposite situation when converting Siemens mosaic dicom files for DTI scans exported as anonymized dicom files from the same Sectra PACS server.  This conversion does not work with the old dcm2niigui but does work with the new dcm2nii that comes with MRIcronGL.

Am I missing some setting/option that will allow the new dcm2nii program to properly handle EPI data saved in Siemens mosaic dicom format?  It would be nice to be able to use a single dicom to nifti converter for all of my Siemens data rather than having to switch back and forth between the programs depending on the sequence type.

Thanks in advance,

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dcm2nii and Siemens mosaic dicom
Jan 12, 2017