Update installation documentation.

docs/user_docs/conda.rst

+.. _conda:
+:orphan:
+
+===========
+Conda Guide
+===========
+
+This is a short guide on setting up conda for the first time.
+
+1. Download and install a python 3.7 version of Miniconda from the `package website <https://docs.conda.io/en/latest/miniconda.html>`_.
+2. Create a conda enviroment.
+
+::
+
+    conda create --name fsl_mrs python=3.7
+
+3. Activate the enviroment.
+
+::
+
+    conda activate fsl_mrs
+
+4. Optionally install Jupyter notebooks. This is required to run the example Jupyter notebooks.
+
+::
+
+    conda install -c conda-forge notebook
+
+5. Follow the FSL-MRS & spec2nii install instructions on the :ref:`Installation 
+<install>` page.
+
+
+See the Conda `documentation <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_ for more information.
\ No newline at end of file

docs/user_docs/conf.py

@@ -37,6 +37,15 @@ rst_epilog = """
 
 .. |fslmrs_gitlab| replace:: FSL-MRS GitLab
 .. _fslmrs_gitlab: https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
+
+.. |fslmrs_github_tracker| replace:: FSL-MRS GitHub Issue Tracker
+.. _fslmrs_github_tracker: https://github.com/wexeee/fsl_mrs/issues
+
+.. |fslmrs_pkg_data| replace:: FSL-MRS example data
+.. _fslmrs_pkg_data: https://users.fmrib.ox.ac.uk/~wclarke/fsl_mrs/example_usage.zip
+
+.. |dev_email| replace:: developers
+.. _dev_email: mailto:william.clarke@ndcn.ox.ac.uk,saad@fmrib.ox.ac.uk
 """
 
 
@@ -67,4 +76,4 @@ html_theme = 'sphinx_rtd_theme'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
\ No newline at end of file
+html_static_path = []
\ No newline at end of file

docs/user_docs/fitting.rst

@@ -80,7 +80,9 @@ FSL-MRS can also be used in an interactive Python environment. The following is
 In an IPython or Jupyter Notebook environment, run the follwing (the example data resides in the main :code:`fsl_mrs` package folder):
 
 Loading and preparing the data:
+
 ::
+
     from fsl_mrs import MRS
 
     FID_file     = 'example_usage/example_data/metab.nii'
@@ -91,12 +93,16 @@ Loading and preparing the data:
     mrs.processForFitting()
 
 Fitting the model to the data:
+
 ::
+
     from fsl_mrs.utils import fitting
     results = fitting.fit_FSLModel(mrs)
 
 Visualising the fit:
+
 ::
+
     from fsl_mrs.utils import plotting
     plotting.plotly_fit(mrs,results)
 

docs/user_docs/install.rst

+.. _install:
+
 Installation Instructions
 =========================
 
-FSL-MRS can currently be installed using two methods.
+FSL-MRS can currently be installed using one of two methods.
 
-1. From GitLab
-~~~~~~~~~~~~~~
+Option 1: From GitLab
+~~~~~~~~~~~~~~~~~~~~~
 Download or clone from |fslmrs_gitlab|_. To get FSL-MRS with example data and example Jupyter notebooks, download the full package from gitlab. `Git LFS <https://git-lfs.github.com/>`_ must be installed to download package data.
 
 ::
@@ -13,10 +15,11 @@ Download or clone from |fslmrs_gitlab|_. To get FSL-MRS with example data and ex
     cd fsl_mrs
     pip install .
 
-2. From Conda
-~~~~~~~~~~~~~
+Option 2: From Conda
+~~~~~~~~~~~~~~~~~~~~
 
-The primary installation method is via *conda*. After installing conda and creating or activating a suitable `enviroment <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>`_ you can install FSL-MRS from the FSL conda channel.
+The primary installation method is via *conda*. After installing conda and creating or activating a suitable you can install FSL-MRS from the FSL conda channel. See our page on setting up a :ref:`conda enviroment 
+<conda>` for a step by step guide.
 
 ::
 
@@ -24,6 +27,11 @@ The primary installation method is via *conda*. After installing conda and creat
                   -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel/ \
                   fsl_mrs
 
+Example data with conda
+-----------------------
+Installation with conda is easy, but you won't get the packaged example data and notebooks. This can be downloaded separately here: |fslmrs_pkg_data|_.
+
+
 spec2nii
 ~~~~~~~~
 To convert data to NIfTI install the spec2nii program from conda.

docs/user_docs/seq_file_params.rst

 .. _seq_file_params:
+:orphan:
 Sequence description parameters
 ===============================
 

docs/user_docs/troubleshooting.rst

-Troubleshooting
-===============
+=============================
+Troubleshooting & Bug Reports
+=============================
 
 Troubleshooting hints and tips will be added here. If you are having a problem which cannot be solved by anything on this page, either try searching the `FSL
 mailing list <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=FSL>`_ archives to see if somebody else has had the same problem, or send a email to the mailing list.
 
 MRS specific questions may be better answered on the `MRSHub forums <https://forum.mrshub.org/>`_.
 
+Bug Reporting 
+=============
+
+Please report bugs on the public |fslmrs_github_tracker|_ or via email to the |dev_email|_.
+
+Troubleshooting hints
+=====================
 
 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>`_.