Hi, I would like to convert a basis generated with FSL-MRS (.JSON format) to a SPANT-compatible format, since I develop my MRS pipeline in R for statistical analysis.
Thanks in advance !
Hi Clement,
Happy to take a look. Could you send me what you have so far? I’m not familiar with the .JSON format for storing basis sets.
@wclarke is there a way to export basis sets as set of NIfTI MRS files? spant has two functions (read_basis_niidir and write_basis_niidir) for dealing with this storage method.
Martin
@martin Sorry there isn’t, given that the basis standard format never quite got there I didn;t get around to implementing it. The files are very simple, they are just a directory with a JSON for each metabolite storing the FID, there is a field for real and imaginary data, the dwell and the central frequency.
thanks @wclarke, I see examples at : William Clarke / WIN MRS Basis Sets · GitLab so shouldn’t take long to implement a reader…
We should probably revive the discussions we had with @Helge a while ago on a common basis set standard.
As an example, Will, how do you handle 2D-fitting a TE series (where you have different basis sets for each spectrum)? One folder per TE?
Yes, nothing clever, just a folder per echo time. Definitely up for resurrecting the standard format discussions.
I’m not 100% sold on the nifti solution, but maybe it’s the easiest.
Yes, happy to discuss/support something simple like “the folder of NIfTI files” format, as this likely to be fine for the vast majority of users.
Thank you for your answers. Actually, it wasn’t difficult to code. I had a problem with LCModel because the basis peaks were too narrow. Applying line broadening solved the numerical problem, but I’m not sure if it might introduce bias into the quantifications.