We use Prisma Fit 3T Siemens MR scanner for our research. The hospital upgraded their syngo MR system E11 to XA30, after this upgrade MRS data format changed and we could not use LCModel. There is no CSA header in the new IMA format, and almost all scan parameters became private and hard to find, so LCModel software could not collect the necessary information. We tried to transfer spectral data of the new format into the old format, but it did not work. Is there anyone else who faces this problem, or do you have any suggestions?
Yes, the newer systems generate DICOM data with SOPClassUID of
1.2.840.10008.5.1.4.184.108.40.206 MR Spectroscopy Storage rather than the Siemens private
220.127.116.11.118.104.22.168. This is probably a good change for the long term as it brings various vendors into line with each other. However it is a pain when you’ve been used to the CSA headers. I have to admit I haven’t quite figured out the new structure as sometimes sequences seem to store pertinent information in
PerFrameFunctionalGroupsSequence and sometimes in
You can try spec2nii which should handle this new format and give you a NIfTI-MRS file. You can then write a small script to convert from the nifti format into the LCModel raw format (see here for NIfTI I/O examples). Someone was talking about making a LCModel wrapper which loads NIfTI-MRS but I can’t remember who.
Osprey can read NIfTI-MRS and call LCModel internally. @Helge has also added support for XA30 in Osprey this week, although it should be said this is a work in progress as we’re figuring the new parameter storage system out, as Will says.