Our Siemens scanner was recently upgraded and no longer exports regular dicoms- it now only provides enhanced dicoms.
This is an issue for our research team because we use the Nexstim device to provide neuronavigated TMS to patients and it is currently not compatible with enhanced dicoms. To use the device, we have to convert our files to NIfTI format, however using NIfTI we cannot extract the stimulation coordinates from the Nexstim. We can only get this information from the regular dicoms.
Does anyone have a script or is familiar with this problem to help us find a workaround? We are hoping to just convert the enhanced dicoms to regular dicoms and use them that way with the Nexstim.
Thanks!
Meg
Command used (and if a helper script was used, a link to the helper script or the command generated):
Dear @meggon - not a direct answer to your question, but maybe helpful in the meantime: you can export the Dicoms in a compatibility mode from the scanner which gives you the old Dicom images. Would that work for you?
Hi @stebo85- thanks for your response! That is what we are doing moving forward. However, we can’t do that on our prior collected data because our scanner doesn’t save scans after a certain amount of time. I wish we could do that!
Are you using/can you use dcm2niix? We’re successfully using the April 2023 update version (Release version 11-April-2023 · rordenlab/dcm2niix · GitHub) with XA30 “enhanced” dicoms, but don’t do nexstim. The dcm2niix authors might be able to help you get the info you need out of the dicoms, if dcm2niix doesn’t already extract it.
In theory, theory and practice are the same. However, in practice they are different.
In theory, you can convert your enhanced DICOM to unenhanced DICOMs using gdcmtar
gdcmtar -U -i ~/in/in.dcm -o ~/out/out
In practice, I doubt this will work. My sense is that you may want to work with Nexstim to update their software. The Siemens XA DICOMs are vastly different from the classic Siemens VE DICOMs. Many details have changed (in particular, a lot of private tags no longer exist and crucial sequence details are stored in modern public tags).
Hi @jaetzel and @neurolabusc! Thanks so much for your insight and help. I really appreciate it. I’m going to try out both options ASAP. But, I agree @neurolabusc, that it most likely won’t work due to the differences between the Siemens updates.
I was in contact with Nexstim and it looks like this has been an ongoing issue. They said they will try to add in a solution to the next software update, but in the meantime, they urged me to try to get the original files from the scanner and export them as non-enhanced and to avoid converting any of the files.
