Commit c84d1fe7 authored by William Clarke's avatar William Clarke
Browse files

Update documentation and FSL-MRS references in docs.

parent ac774d86
......@@ -162,6 +162,8 @@ Below are detailed explanations of some of the optional arguments in the wrapper
Group metaboites into sub-groups that get their own lineshape parameters (shift and broadening). This can either be a list of integers (one per metabolite) from 0 to the max number of groups minus one. Or it could be a list of metabolites to be grouped. E.g. using the flag :code:`--metab_groups Mac NAA+NAAG+Cr` then the Mac spectrum will have its own group, the NAA, NAAG, and Cr will be in a different group, and all other metabolites in a 3rd group. Other possibilities are combine_all and separate_all, where metabs are combined into a single group or separated into distinct groups respectively.
:code:`--add_MM`
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:`--add_MM_MEGA`
Add linked macromolecule peaks at 0.915 & 3.0 ppm (ratio of 3.75:2.0). This option is experimental!
:code:`--lorentzian`
By default the lineshape is a Voigt (lorentizian+gaussian). Use this flag to set to Lorentzian.
:code:`--ind_scale`
......
......@@ -18,4 +18,4 @@ Citing FSL-MRS
--------------
If you use FSL-MRS please cite:
Clarke WT, Stagg CJ, Jbabdi S. FSL-MRS: An end-to-end spectroscopy analysis package. MRM https://doi.org/10.1002/mrm.28630
\ No newline at end of file
Clarke WT, Stagg CJ, Jbabdi S. FSL-MRS: An end-to-end spectroscopy analysis package. Magnetic Resonance in Medicine 2021;85:2950–2964 doi: 10.1002/mrm.28630.
\ No newline at end of file
......@@ -75,7 +75,7 @@ def main():
fitting_args.add_argument('--add_MM', action="store_true",
help="include default macromolecule peaks")
fitting_args.add_argument('--add_MM_MEGA', action="store_true",
help="include default MEGA-PRESS macromolecule peaks")
help="include default MEGA-PRESS macromolecule peaks. This option is experimental!")
fitting_args.add_argument('--lorentzian', action="store_true",
help='Enable purely lorentzian broadening'
' (default is Voigt)')
......
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