Problem running LCModel on MRspa

Hi, I am using MRspa for data analysis. After processing and selecting the proper basis file from the LCModel’s website, two problems arise when I press “Run LCModel”. I don’t know if they are related or separate. Has anyone else encountered similar problems?

And if I press continue the error message in Matlab is

And as a separate question, where can I see the needed values for T2water(ms), T2metab(ms), CSFwatercontent(%), tissuewatercontent(%)? Or do these need separate measurements?

– Nella

Copying @Dinesh here. I generally would advise against using the default LCModel basis sets, they’re outdated and generic and therefore in all likelihood not particularly well suited for your sequence.

As for the other values, I’m not familiar with MRspa, but I’d assume that you need to look up literature values for the relaxation times (some inspiration here). I don’t know what exactly the other two mean (whether they mean fractional tissue volume or the water content in different tissues), so I’ll also leave that for Dinesh to answer.

Hi Nella,
The generic basis sets generally do NOT contain the B0 frequency, and here MRspa is checking that. If you click “Run LCmodel” again, then Ok (sometime twice), it will run LCmodel. It is a known bug.
You will need to determine the %tissue in your MRS voxel. As for the T2 values, you can take a look at literature based on the specific MRS sequence you used in vivo.