Visualization of spectroscopy region

How can I visualize the spectroscopy region (MRS or CSI) on a structural image from dicom files with python.

Hi Jabit,

Our collection lists a couple of useful Python-based software packages for voxel visualization, for example FSL-MRS and MRS-voxel-plot. Copying in @wclarke and @nwduncan who developed the two tools in case you need help.


Unfortunately, MRS-voxel-plot can’t handle dicom images directly - you would need to create nifti format masks through some other means first and then work with those (Gannet or Osprey can do this easily, for example).

Regardless, I’d suggest reading the associated paper about minimum standards for the visual reporting of MRS data as it provides, I think, some useful pointers:

Hi, Perhaps spec2nii can help with the conversion to NIfTI. GitHub - wtclarke/spec2nii: Multi-format in vivo MR spectroscopy conversion to NIFTI


Unfortunately, our mri scanner data was not imported with spec2nii. I am investing the way to convert between the voxel coordinate of the image and the coordinate of the scanner with use of dicom data.

Hi @Jabit spec2nii is a separate program which can interpret dicom data. You can instal it on your computer and give it a try with your data.

Hi wclarke,
I am trying to use spec2nii with my dicom data.

How do I understand this code in
specDataCmplx = specData[0::2] + 1j * specData[1::2]

Please let me know if you have any information about MRS dicom data structure.

Hi Jabit, this is an operation that joins the real and imaginary parts of the signal into complex numbers.