Commit 7d69da61 authored by William Clarke's avatar William Clarke
Browse files

Add fsl_mrs_summarise documentation. Add dash to requirements.

parent d8d2b204
Pipeline #14862 passed with stages
in 30 minutes and 29 seconds
......@@ -3,13 +3,17 @@ This document contains the FSL-MRS release history in reverse chronological orde
2.0.0 (WIP)
-----------
**Major rework of basis and fitting script interaction. First release of dynamic MRS fitting.**
*Static fitting*
- Default macromolecules are now added through basis_tools script rather than fitting. Fitting does not alter basis at run time now.
- Fixed bug in calculation of concentration covariances. New MC tests included.
- Better covariance estimation for parameters with small values (< machine epsilon)
- Better and faster covariance estimation.
*Dynamic fitting*
- Saved dynamic results now contain free parameter covariances.
- New documentation for dynamic fitting
- New fmrs_stats module and script for higher-level GLM analysis.
*Other new features*
- Experimental SVS results dashboard - view the results of multiple SVS fits together in a single summary.
- New documentation for dynamic fitting and all new features.
1.1.14 (Wednesday 29th June)
----------------------------
......
......@@ -5,12 +5,13 @@ Reports and Visualisation
Data and analysis results can be viewed in a number of ways in FSL-MRS, and at all stages of processing.
There are 4 ways of visualising/interacting with MRS data in FSL-MRS:
There are five ways of visualising/interacting with MRS data in FSL-MRS:
1. Quick glance (human-readable, non-interactive)
2. CSV files (human- and machine-readable)
3. HTML reports (fairly interactive)
4. FSLeyes (highly interactive)
5. SVS results dashboard (interactive)
1. Quick glance
---------------
......@@ -96,3 +97,30 @@ Now to make the power-spectrum display nicely, we need to change the x-axis scal
.. image:: data/fsleyes.png
:width: 700
5. SVS results dashboard
------------------------
**Warning: experimental / new feature**
The results from multiple single voxel (SVS) fits can be viewed on a single webpage by using the `fsl_mrs_summarise` command. For example:
.. code-block::
fsl_mrs_summarise results_dir/
Where :code:`results_dir/` contains sub-directories of results generated by the :code:`fsl_mrs` command.
.. image:: data/fsl_mrs_summarise_0.png
:width: 700
This generates an interactive `Dash` app that displays metabolite concentrations, uncertainties, and QC parameters (SNR and linewidths). Sumamry statistics are given in table form below.
By selecting one of the plotted datasets, the data + fit is displayed lower in the page.
.. image:: data/fsl_mrs_summarise_1.png
:width: 700
.. image:: data/fsl_mrs_summarise_2.png
:width: 700
The single dataset + fit is displayed next to the mean (±1SD) data and fit.
\ No newline at end of file
......@@ -11,3 +11,4 @@ fslpy>=3.9.0
pillow
spec2nii>=0.3.0
dill
dash
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment