Update README

README.md

@@ -6,13 +6,18 @@
 FSL-MRS is a collection of python modules and wrapper scripts for pre-processing and model fitting of Magnetic Resonance Spectroscopy (MRS) data.
 
 ---
-
 ### Installation 
 
     git clone https://git.fmrib.ox.ac.uk/saad/fsl_mrs.git
     cd fsl_mrs
     pip install .
 
+#### Dependencies
+
+    pip install spec2nii
+
+After installation see the [quick start guide](https://users.fmrib.ox.ac.uk/~wclarke/fsl_mrs/userdoc/quick_start.html).
+
 ---
 
 ### Content
@@ -22,35 +27,45 @@ FSL-MRS is a collection of python modules and wrapper scripts for pre-processing
 - **fsl\_mrs**
 : fit a single spectrum 
 - **fsl\_mrsi**
-: fit a 4D volume of spectra 
-- **fsl\_mrs\_preproc**
+: fit a 3D volume of 1D spectra 
+- **fsl\_mrs\_proc**
 : pre-processing (coil combination, averaging, eddy-current correction) 
+- **fsl\_mrs\_preproc**
+: Pre-packaged processing for non-edited SVS. 
 - **fsl\_mrs\_sim**
-: simulate basis
+: simulate basis spectra
 - **mrs_vis**
-: quick visualisation of the spectrum
+: quick visualisation of the spectra or basis spectra
+- **svs_segment & mrsi_segment**
+: Run tissue segmentation for SVS/MRSI from T1 image.
 
 ---
 
-#### Usage
+### Usage
 
 For each of the wrapper scripts above, simply type `<name_of_script> --help` to get the usage.
 
+Example command-line usage is demonstrated in the packaged [Jupyter Notebook](https://git.fmrib.ox.ac.uk/saad/fsl_mrs/-/blob/master/example_usage/Example%20SVS%20processing%20-%20command-line.ipynb.).
+
+Documentation can be found online [here](https://users.fmrib.ox.ac.uk/~wclarke/fsl_mrs/userdoc/index.html).
 
-#### File types
+### File types
 
-FSL-MRS accepts FID data in NIFTI format. It can also read .RAW format (like LCModel). 
+FSL-MRS accepts FID data in NIfTI + JSON format. Some scripts can also read .RAW (LCModel) and text (jMRUI).
 
-#### Working in python
+Conversion to NIfTI is provided by [spec2nii](https://github.com/wexeee/spec2nii).
 
-If you don't want to use the wrapper scripts, you can use the python modules directly in your own python scripts/programs. Here are some examples below:
+### Working in python
 
-- Pre-processing
-- Model fitting - single voxel
-- Model fitting - MRSImaging
+If you don't want to use the wrapper scripts, you can use the python modules directly in your own python scripts/programs. Or in an interactive Python environment (see example [notebook](https://git.fmrib.ox.ac.uk/saad/fsl_mrs/-/blob/master/example_usage/Example%20SVS%20processing%20-%20interactive%20notebook.ipynb)) 
+
+---
 
+### Permissions and citations
 
+If you use FSL-MRS in your research please cite:
 
+Please see the LICENSE file for licensing information.