Commit 1cb69f81 authored by William Clarke's avatar William Clarke
Browse files

update docs.

parent a5dd7d18
......@@ -167,7 +167,7 @@ Below are detailed explanations of some of the optional arguments in the wrapper
: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.
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`.
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:
......
......@@ -23,7 +23,7 @@ Troubleshooting hints
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.
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. Priors can be fine tuned by altering the values in :code:`fsl_mrs.utils.constants`.
3. Identifying the correct files for conversion
Raw data files, especially DICOM files can have obscure naming conventions. It can be difficult to determine which files should be converted for use in FSL-MRS. Tools such as gdcmdump from `GDCM <http://gdcm.sourceforge.net/>`_ can help in identifying the scans by giving you access to the DICOM headers.
......@@ -32,5 +32,6 @@ Troubleshooting hints
4. Data looks 'wrong' after conversion
If when using :code:`mrs_vis` you see no signal and just noise try conjugating the data using :code:`fsl_mrs_proc conj` or try expanding the ppm range plotted :code:`--ppmlim -10 10`. If you see a flat line, then conversion failed. The data might be corrupted - did the acquisition complete successfully?
.. image:: data/bad_data.png
:width: 600
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