help > dcm2nii and Siemens mosaic dicom
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Jan 12, 2017  10:01 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,

Apr 28, 2017  12:04 PM | Ahmed Khalil - Center for Stroke Research Berlin
RE: dcm2nii and Siemens mosaic dicom
Hi Suzanne,

Did you ever figure out what the problem was? I'm having the same kind of trouble (it works on Siemens mosaic DICOMs from one scanner, but not the other).

Best wishes,
Jul 12, 2019  09:07 PM | bcsccn - Boston College
RE: dcm2nii and Siemens mosaic dicom
I am having the same problem, has anyone been able to figure out the answer?
Jul 13, 2019  12:07 PM | Chris Rorden
RE: dcm2nii and Siemens mosaic dicom
Can you cofirm you are using the latest version of dcm2niix (1.0.20190410)?
 For a graphical interface, make sure you are using MRIcroGL version 1.2.20190410. If you are using the command line, use version you can get the latest version (1.0.20190410) from Github

If you are having problems with the latest version, the first thing I would do is check the providence of your image. dcm2niix uses the proprietary Siemens CSA header to glean a lot of information about your sequence, so make sure this was not removed by a DICOM anonymization stage.

Finally, if you are using a Siemens Vida scanner (software XA10, XA11), you need to be very careful to NEVER save data to mosaic format, as Siemens strips relevant information from Vida mosaics (technically the XA10 mosaics are not valid DICOMs as they lack Type 1 attributes). This is not a limitation of dcm2niix, but rather a limitation of the files Siemens generates.

If none of these thoughts resolve your problem, please post a new issue on the dcm2niix Github page.