Values are derived from a survey of the literature. References listed below. Values for metabolites are derived from an average of NAA, Cr and Cho peaks.
@@ -168,6 +168,14 @@ Below are detailed explanations of some of the optional arguments in the wrapper
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. Priors can be fine tuned by altering the values in :code:`fsl_mrs.utils.constants`.
:code:`--internal_ref`
Set alternative metabolites for internal reference scaling (default is tCr = Cr + PCr). Multiple arguments can be specified for a combined internal reference.
:code:`--wref_metabolite`
Set alternative water scaling reference (default is Cr). Must be used if none of Cr, PCr and NAA are present in the basis set.
:code:`--ref_protons`
Number of protons that the water scaling reference is equivalent to (between defined integration limits). E.g. Cr is equivalent to 5 between 2 and 5 ppm. Only active when --wref_metabolite is used.
:code:`--ref_int_limits`
Integration limits for water scaling reference. Only active when --wref_metabolite is used.
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:
:code:`svs_segment` creates a small JSON file which can be passed to the fitting routines. :code:`mrsi_segment` creates NIfTI files of the fractional tissue volumes registered to the MRSI volume.
:code:`svs_segment` and :code:`mrsi_segment` both rely on fsl_anat to run FSL FAST tissue segmentation. If fsl_anat has already been run then the :code:`-t T1.nii.gz` can be substituted with :code:`-a T1.anat`.
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:code:`svs_segment` and :code:`mrsi_segment` both rely on fsl_anat to run FSL FAST tissue segmentation. If fsl_anat has already been run then the :code:`-t T1.nii.gz` can be substituted with :code:`-a T1.anat`.
Water Reference Scaling Model
-----------------------------
If provided with an unsuppressed water reference FSL-MRS can generate metabolite concentrations in units of molarity (moles of substance per unit-volume, mol/L), or molality (moles of substance per unit-weight, mol/kg). Scaling is performed alongside relaxation correction as described by equations 4 & 6 of [NEAR20]_.
Referencing to water is carried out by comparing the integrated water resonance in the unsuppressed water (between 1.65 and 7.65 ppm) to the integrated area of a reference metabolite. The raw unsuppressed signal is first fitted using to a simple model (a single peak with Voigt lineshape), and integration is carried out on the fitted data after residual phase has been removed. This is to ensure the corruption of the first few FID points doesn't result in integration of broad, negative-valued wings of the water peak. Similarly the integration of the reference metabolite is carried out on the scaled, broadened basis with the influence of phase and baseline removed.
The integrated areas are shown in the final plot of the html report if a reference dataset is provided.
References
----------
.. [NEAR20] `Near J et al. Preprocessing, analysis and quantification in single‐voxel magnetic resonance spectroscopy: experts' consensus recommendations. NMR in Biomed 2020. <https://pubmed.ncbi.nlm.nih.gov/32084297>`_
