Siemens (TWIX) data import

MRS Software Osprey
1

Hello,

I just started MRS analysis.

I used Gannet to analyze Siemens’ MRS data before, but there is no segmentation function, so now I plan to use Osprey to analyze it. But the data only has. dat and. IMA files, and there is no. nii files in exampledata. Do I need to convert. IMA files into. nii files? Is there a tutorial on this (because the. nii file in exampledata includes T1w.nii and T1w_overlay.nii, but I don’t know how to distinguish them)?

In addition, I saw Osprey manuscript in osprey documentation/chapter 5 osprey GUI tutorial/5.8 quantification, but I don’t know how to get it. Where is it?

Thank you in advance for your answer! !

2

Hi @hanxue,

  1. Yes, you will need to convert your T1-weighted DICOM to NIfTI with any converter you like - we typically use rordenlab/dcm2niix: dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC (github.com) or just the batch converter in SPM.
  2. Once you have the T1 NIfTIs, you just list them in a separate files_nii array in the job file - you can check out the example job files for the other file formats (sdat/spar, dat) in the exampledata folder.
  3. The free version of the Osprey paper can be found at Osprey: Open-Source Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data - PMC (nih.gov).

Cheers,
Georg

3

Thank you very much. I’ll try to operate it.

Thank you！！