Hello everyone,
I have some spectroscopy data (PRESS and MEGAPRESS) acquired from the Siemens Skyra system in Dicom format. I am trying to convert the Dicom files to Raw format for the LC model.
I also tried using OSPREY but it threw an error after loading the job file. I have attached the log file below for reference. Could someone provide me with a solution?
Thanks in advance
LogFile.txt (1.4 KB)
Hi @samuel2496,
thanks for reaching out.
It looks like it is trying to load your Dicom files as if they were NIfTI-MRS files. Could you share the jobfile that you have used? If you have done this through the GUI you can find it in the output folder as .json file.
Best,
Helge
Hi @Helge,
Thank you for your reply. Yes, the input was a nifti-mrs file. I converted the dicom files to nifti using spect2nii.
I have attached the jobfile as a text document below.
json_job.txt (642 Bytes)
Best
Berkins
Ok - this makes more sense now. So this is the MEGA-PRESS data then.
Could you check whether the data is correctly separated into dynamics and edited scans in spec2nii by extracting the header from the .nii file (spec2nii extract …)? The sub-spectra dimension has to have the name DIM_EDIT so that it is loaded correctly.
If this is not the case you have to extract the header from each dataset and correct this and putt it back into the nii file with spec2nii insert.
Helge
Ok, @Helge, I extracted the header file as mentioned but I could not find the DIM_EDIT. I have attached the header file below. Could you please have a look at it? If it is of any help, I can share a sample data for you to have a look at.
header.txt (715 Bytes)
Thank you
Berkins
Hi @samuel2496,
Sure. Happy to take a look at this. Can you share the DCM data because it seems like the issue is at the conversion level.
Best,
Helge
Hi @Helge, can you share your email or drive link for me to send or upload the data? Or should I share it in a drive?