Hello, and thanks in advance for the help! We have MEGA-PRESS data that usually exported/processed in Osprey as twix files. However, there was a transfer issue for one participant and I had to convert their data from DICOM to nii.gz using spec2nii. I’m getting the following error when trying to load their data:
Array indices must be positive integers or logical values.
Error in osp_LoadNII (line 186)
raw.fids = reshape(raw.fids,[raw.sz(raw.dims.t) raw.sz(raw.dims.averages)/2 2]);
Error in OspreyLoad (line 256)
[MRSCont] = osp_LoadNII(MRSCont);
Error in osp_onLoad (line 35)
MRSCont = OspreyLoad(MRSCont);
What sequence are you using to generate these data? To be fair, we haven’t done a whole lot of testing on non-conventional NIfTI-MRS data, so this will be a helpful case.
It could be helpful to see the shape it comes out of spec2nii - can you post the contents of the JSON sidecar file here? (You can generate that by specifying the -j flag when calling spec2nii; you should probably also anonymize the data before posting with the -v flag).
We are using a Siemens 3.0T Prismafit MR scanner with the GABA: SIEMENS WIP MEGA-PRESS sequence: Edit ON(OFF)= 1.90 (7.46) ppm; TR=2000 ms, TE= 68 ms; number of averages= 160. I’m including screenshots of the json files below for the non-water and water suppressed files. Let me know if more info would be helpful!
Thanks! Can you also simply load the file with the io_loadspec_niimrs function, i.e. out = io_loadspec_niimrs(filename) and post the values of out.dims and out.sz here?
