Commit 6b3c73c2 authored by William Clarke's avatar William Clarke
Browse files

Add documentation.

parent d769b18b
......@@ -3,6 +3,8 @@ This document contains the FSL-MRS release history in reverse chronological orde
1.1.3 (TBC)
------------------------------
- Added mrs_tools script. Replaces mrs_vis and mrs_info. Adds split/merge/reorder functionality.
- Added basis_tools script. Tools for manipulating (shifting, scaling converting, and adding to) basis sets.
- Under the hood refactor of basis, MRS and MRSI classes.
1.1.2 (Friday 16th April 2021)
------------------------------
......
......@@ -53,6 +53,8 @@ After installation see the [quick start guide](https://open.win.ox.ac.uk/pages/f
: simulate basis spectra
- **mrs_tools**
: Collection of tools for NIfTI-MRS. Includes quick visualisation and information.
- **basis_tools**
: Collection of tools for manipulating basis sets.
- **svs_segment & mrsi_segment**
: Run tissue segmentation for SVS/MRSI from T1 image.
......
.. _basis_tools:
Basis Spectra Manipulation
==========================
basis_tools
-----------
The :code:`basis_tools` script provides the user with tools for manipulating basis spectra in the FSL-MRS JSON format.
Provide one of the following subcommands with :code:`basis_tools` to convert, scale, add to or shift basis spectra.
info
****
| *Example* :code:`basis_tools info path/to/my/basis`
| Provides a short summary of the contents of the basis set.
vis
***
| *Example* :code:`basis_tools vis path/to/my/basis --ppmlim 0.2 4.2`
| Provides visualisation of the basis set.
convert
*******
| *Example* :code:`basis_tools convert path/to/my/lcmbasis.BASIS path/to/my/fslbasis`
| Convert LCModel (.Basis) or JMRUI format basis sets to FSL-MRS (.json) format.
add
***
| *Example* :code:`basis_tools add --scale --name my_new_basis my_new_basis.json path/to/my/fslbasis`
| Add a json formatted basis spectrum to an existing basis set.
shift
*****
| *Example* :code:`basis_tools shift path/to/my/fslbasis NAA 1.0 path/to/my/edited_fslbasis`
| Shift a basis spectrum on the chemical shift axis.
scale
*****
| *Example* :code:`basis_tools shift path/to/my/fslbasis NAA path/to/my/scaled_fslbasis`
| Rescale a basis spectrum to the mean of all other basis spectra (or to specified target :code:`--target_scale`.
\ No newline at end of file
......@@ -25,6 +25,7 @@ If this is your first experience with FSL-MRS, get started with the :ref:`Quick
quantitation
macromolecules
simulation
basis_tools
visualisation
constants
troubleshooting
......
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