Hello everyone, I acquired a sLASER sequence with a Siemens scanner. In FSL MRS a sequence to be simulated is described in a JSON format file. JSON format is needed to create a basis set (with fsl_mrs_sim), does anyone know how i can achieve this?
Thank you,
Arianna
Hi Arianna,
I’ve made a tutorial on how to do it as part of the FSL course: FSL-MRS Practical
However, it remains quite tricky if you are new to the field or MR physics. Precisely what sequence is it (i.e. is it a vendor sequence or something from a collaborator / your lab)? It might be that I have one already set up for it.
Exactly, we had found your tutorial, but as you say it’s quite tricky for us to follow. The sequence we used is a sequence set by us using the Siemens preset sequences for CSI (we don’t have the Minnesota c2p available). It is a sLASER with a TE=40 and TR=2000, acquired with a MAGNETOM Skyra scanner with standard gradients. I can’t find a way to make a baseset compatible with FSL, but only with LCModel (we simulated it with MRICloud). Can you help me?
Thanks again for your help!
If you’ve got an LCModel .basis file you can just convert that to the FSL format.
The documentation has some details Basis Spectra Manipulation — FSL-MRS 2.1.8 documentation, but in brief you can run basis_tools convert --remove_reference --hlsvd my_basis.basis my_fsl_formatted_basis.
@ariannapalumbo I just happen to have simulated Siemens CSI sLASER at TE = 135 ms for a collaborator the other week. Got pulses, timings and everything for TE = 40 ms too. These simulations are a substantial update in precision to what is on the MRSCloud simulation, but I haven’t found the time to push this update to the cloud version - please get in touch (goeltzs1 (-at-) jh (-dot-) edu) so I can get you the proper LCModel basis set you need that you can then convert over to FSL.
Cheers,
Georg