Siemens DICOM, rda, twix, XA and VE11

Paul · June 4, 2024, 3:34pm

Hi All,

I’m using a spectroscopy program that can only read the ‘older’ (VE11) Siemens DICOM format. However the scanners are being updates to XA, and now I’m unable to read in this new DICOM format.

I’ve tried tried saving files as ‘interoperability’. This does allow me to read in the images, but still not the spectroscopy DICOM files.

I also saw that a conversion script was shared on MRShub for rda format:

github.com

shui5/io_Siemens_XA2VE/blob/main/io_Siemens_XA2VE.m

%io_Siemens_XA2VE.m
%
%Steve C.N. Hui, Children's National Hospital, George Washington University 2023.
%
% USAGE:
% Run the script at the folder where the .rda data are stored.
% Require io_loadspec_rda from FID-A and io_writerda from Osprey
%
% DESCRIPTION:
% Takes Siemens MRS data acquired using XA20 or above and convert them into VE format that can be read by LCModel.
%
% INPUTS:
% .rda files acquired using XA software version
%
% OUTPUTS:
% .rda files that can be read by LCModel.
%
% file = 'NEURO.34.1.11914_Thala_288_ref.rda';
% rda_filename = fullfile(folder,file);
%  [in]=io_loadspec_rda(rda_filename);

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Is is also possible to convert the XA DICOM format to VE11? What actually is the difference between the .rda format and DICOM format? Is there a conversion program/script available to convert between these formats?

Thanks,
Paul

admin · June 5, 2024, 1:24pm

What software are you using to read the XA DICOM data?

RDA data generally contain the same raw MRS data as the MRS DICOMs, but far fewer header fields, so it’s not possible to convert RDA to DICOM. I’m sure it’s theoretically possible to do vice versa although I think that no one ever bothered.

Paul · June 12, 2024, 12:34pm

Hi,

We want to import it into the older Syngo (VE11c) software as we have as a standalone station with this. I know it’s time to move on from this software

I was thinking maybe it can import the .rda format. But I’m not managing to load the VE11c or XA60 .rda files with io_loadspec_rda.m (in order to convert it). I get the error:

Unable to perform assignment because the indices on the left side are not compatible with the size of
the right side.

Error in io_loadspec_rda (line 77)
rda.PositionVector(1) = str2num(value);

And if I just comment all the PositionVector cases, the next error occurs at fids = fids’;
Transpose on ND array is not defined. Use PERMUTE instead.
where the size of my csi fid is: 1 1024 16 16

Paul

hraum · June 18, 2024, 8:27am

Hi @Paul,
io_Siemens_XA2VE.m requires two scripts from Osprey. Have you the current version of Osprey?
In your script line 77 is “rda.PositionVector(1) = str2num(value)” and in the current version this is at line 101 (osprey/libraries/FID-A/inputOutput/io_loadspec_rda.m at develop · schorschinho/osprey · GitHub).
There is also an older discussion about this script (CoRegistration Error in Osprey with NIfTI), but I don’t know whether it’s suitable for the use at CSI data.

Best,
Heiner

peter · June 25, 2024, 4:21pm

Hi Paul, have you sorted this out yet? I have some Matlab code that I wrote/use in order to convert DICOMs (both VE11 and XA30) to .rda (essentially so I can use the data in LCModel, since LCModel doesn’t read XA* DICOMs properly). It’s not necessarily a “product” level code, but it seems to work, so if you still need help, I’m willing to share. I have used it for both SVS and CSI data.
Cheers,
Peter

Paul · June 28, 2024, 10:55am

Hi Peter,

I am definitely interested in obtaining your MATLAB code for this. We mostly are doing CSI, so this would come in very handy for us.

Paul

peter · June 28, 2024, 9:39pm

dcm2rdaXA30.m (4.8 KB)
Hi Paul,
the fairly rudimentary Matlab function that converts XA30 (presumably all XA, but only tested with our XA30 systems) DICOMs to “old style” rda is attached.
If this doesn’t help (sounds like you may actually need VE11C formatted DICOMs, not rda), it could be potentially used used to modify the function to read XA30 MRS DICOMs and then save DICOMs that VE11C can understand. I don’t have access to VE11C any more (sadly, XA platform sucks), so I’m not sure how helpful I might be designing/troubleshooting that, but keep us posted here…
Good luck,
Peter