Commit d9dc97b0 authored by William Clarke's avatar William Clarke
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Documentation additions for revisions.

parent 87848dcd
......@@ -22,6 +22,7 @@ If this is your first experience with FSL-MRS, get started with the :ref:`Quick
processing
fitting
quantitation
macromolecules
simulation
visualisation
constants
......
.. _macromolecules:
Macromolecules
==============
It is recommended to use empirically derived macromolecular basis spectra for the fitting step. A measured MM spectrum described in JSON format can be added to the basis spectra by following the instructions on the :ref:`basis spectra simulation <sim_mm>` page.
A collection of MM basis spectra is available for a variety of field strengths, species and anatomies at `MRSHub <https://mrshub.org/datasets_mm/>`_.
In situations where an empirically measured macromolecular spectrum is not available FSL-MRS includes methods for quickly generating synthetic MM basis spectra. For details see `Synthetic MM`_. Both methods should not be used simultaneously.
For an in depth discussion of the effects of MM basis spectra choice on fitting performance see [CUDA12]_ and [GIAP19]_.
Synthetic MM
~~~~~~~~~~~~
Syntheic MM basis spectra may be added using the :code:`--add_MM` flag with :code:`fsl_mrs` or :code:`fsl_mrsi`. In the interactive environment the same can be achieved by calling the method :code:`add_MM_peaks` of :code:`fsl_mrs.core.MRS`.
By default this option will add the following basis spectra (in separate metabolite groups) to the basis sets.
.. csv-table::
:header: Peak name, Peak location(s) (ppm), Peak relative amplitude(s), Peak broadening (gamma/sigma)
:widths: 10, 10, 10, 10
MM09, 0.9, 3, 10/20
MM12, 1.2, 2, 10/20
MM14, 1.4, 2, 10/20
MM17, 1.7, 2, 10/20
MM21, "2.08, 2.25, 1.95, 3.0", "1.33, 0.22, 0.33, 0.4", 10/20
Additional peaks may be added int he interactive environment by calling :code:`add_MM_peaks` with optional arguments to override the defaults.
References
==========
.. [CUDA12] Cudalbu C, Mlynárik V, Gruetter R. Handling Macromolecule Signals in the Quantification of the Neurochemical Profile. Journal of Alzheimer’s Disease 2012;31:S101–S115 doi: 10.3233/JAD-2012-120100.
.. [GIAP19] Giapitzakis I-A, Borbath T, Murali‐Manohar S, Avdievich N, Henning A. Investigation of the influence of macromolecules and spline baseline in the fitting model of human brain spectra at 9.4T. Magnetic Resonance in Medicine 2019;81:746–758 doi: 10.1002/mrm.27467.
......@@ -74,11 +74,13 @@ glycine Gly
Metabolites to simulate can be specified on the command line using the :code:`–m` option with a list typed on the command line, with the :code:`–b` option specifying a text file with one metabolite listed per line, or the :code:`–s` option pointing to a spin system json file for custom spin systems.
It is **not recommended** to simulate and use all of the metabolites. A typical list to start with for short echo time spectroscopy might be
:
It is **not recommended** to simulate and use all of the metabolites. A typical list to start with for short echo time spectroscopy might be::
Ala, Asp, GPC, PCh, Cr, PCr, GABA, Glc, Gln, Glu, GSH, Ins, Lac, NAA, NAAG, PE, Tau
.. _sim_mm:
Including macromolecules in your basis set
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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