FID-A simulations for LCModel

Analysis / Modeling Basis Sets
1

Hi,
I am trying to simulate a basis set with the ‘run_simSemiLASERShaped_fast’ script in FID-A. The result looks fine i.e. in MATLAB (see below). However, when I run makebasis to create LCModel’s file the peaks are shifted in ppm axis (both NAA and reference). I suppose that makebasis.in has a bug. Please let me know what You think:

 $seqpar
 seq='sLASER'
 echot=30.
 fwhmba=.013
 $end

 $nmall
 hzpppm=298.039
 deltat=.0002
 nunfil=4096
 filbas='test/test.basis'
 filps='test/test.ps'
 autosc=.false.
 autoph=.false.
 idbasi='my slaser 7t'
 $end

 
 $nmeach
 filraw='test/NAA.RAW'
 metabo='NAA'
 degzer=0.
 degppm=0.
 conc=1.
 ppmapp=2.4, 2.0
 ppmpk=0.
 $end

fida_naa
fida_naa2048×1536 36.5 KB

makebasis
makebasis1920×1484 125 KB

1 Like
2

ppmapp=2, 1 resolves the problem
Anyway, does anyone know hot to save the “PreviewData” window without access to LCModel’s GUI?

3

Hi bkossows,

I just wanted to say we have been there too! and applying some kind of shift is what we had to do as well.
I am not too sure if this is what you mean by the preview data but if you want to save the fit of all the metabolites you can add neach=99 to the control file.
Hope this is somewhat helpful!
Jess

4

I’m trying to use the same script mentioned originally in this thread (run_simSemiLASERShaped_fast), but for 3T Siemens sLASER data (TE=135ms), canned Siemens sequence (on XA30). New to simulations, but I assume the RF pulse file used in the script is not appropriate (script says "Varian RF pulse file). How do I get the proper RF pulse waveform file?