@@ -158,8 +158,10 @@ Below are detailed explanations of some of the optional arguments in the wrapper
Add macromolecule peaks at the following frequencies: 0.9, 1.2, 1.4, 1.7 ppm and a doublet at 2.08 & 3.0 ppm
:code:`--lorentzian`
By default the lineshape is a Voigt (lorentizian+gaussian). Use this flag to set to Lorentzian.
:code:`--ind_scale`
Allow independent scaling of specified basis spectra before fitting. For example this can be used to independently scale empirically measured macromolecules combined with simulated metabolite spectra.
:code:`--disable_MH_priors`
Disable the priors on the MH fitting. The priors are tuned for *in vivo* human brain spectroscopy. Use this option if your spectra has significantly different line widths, phases or large shifts. E.g. in liquid phase phantom or (potentially) pre-clinical systems.
The wrapper scripts can also take a configuration file as an input. For example, say we have a text file called :code:`config.txt` which contains the below:
@@ -9,4 +9,10 @@ MRS specific questions may be better answered on the `MRSHub forums <https://for
1. Unable to find example data
If you installed FSL-MRS through conda the example data can be downloaded directly from the GitLab repository `folder <https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tree/master/example_usage>`_.
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2. Poor fits
Two problems are commonley diagnosed when poor fits are seen:
1) Basis spectra are inconsistently scaled. For example empirically derived macromolecular basis spectra can be orders of magnitude larger than the other basis spectra. Before fitting, fsl_mrs(i) scales the magnitude of the data and basis spectra to a known range. Relative scales are preserved within the basis spectra. To permit fsl_mrs(i) to apply different scales to individual basis spectra use the :code:`--ind_scale` option with a list of basis names.
2) The data might have parameters unlike a 7T or 3T human *in vivo* brain spectrum. I.e. the spectrum originates from a pre-clinical system or from phantom. In this case the MCMC priors which are suitable for *in vivo* human case can be disabled using the :code:`--disable_MH_priors` option.