Results to spec doc, update changelog.

CHANGELOG.rst

 This document contains the FSL-MRS release history in reverse chronological order.
 
-1.1.3 (TBC)
+1.1.3 (Tuesday 29th June 2021)
 ------------------------------
 - 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, differencing, conjugating, and adding to) basis sets.
 - Improved display of basis sets using mrs_tools or basis_tools.
 - Added 'default' MEGA-PRESS MM option to fsl_mrs and mrs class.
+- Preprocessing tools now add processing provenance information to NIfTI-MRS files.
 - Under the hood refactor of basis, MRS, and MRSI classes.
 - Updated density matrix simulator. Added some automatic testing.
+- Added documentation about the results_to_spectrum script.
 
 1.1.2 (Friday 16th April 2021)
 ------------------------------

README.md

@@ -57,7 +57,8 @@ After installation see the [quick start guide](https://open.win.ox.ac.uk/pages/f
 : Collection of tools for manipulating basis sets.
 - **svs_segment & mrsi_segment**
 : Run tissue segmentation for SVS/MRSI from T1 image.
-
+- **results_to_spectrum**
+: Generate spectrum representation of a fit from *fsl_mrs* results.
 ---
 
 ## Documentation

docs/user_docs/fitting.rst

@@ -41,7 +41,9 @@ Results from :code:`fsl_mrs` are stored in a single folder that contains the fol
 - CSV files summarising the metabolite concentrations (and uncertainties), fitted parameters, and some QC measures.
 - PNG files with summary of the fitting and (optionally) voxel location.
 
+A nifti file of the fitted spectrum, baseline, and individual metabolites can be generated using the :code:`results_to_spectrum` script. For example::
 
+    results_to_spectrum --export_baseline example_fit
 
 MRSI
 ----

docs/user_docs/visualisation.rst

@@ -10,7 +10,7 @@ There are 4 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) 
-#. FSLeyes (highly interactive)
+4. FSLeyes (highly interactive)
 
 1. Quick glance
 ---------------

fsl_mrs/scripts/results_to_spectrum

@@ -38,6 +38,10 @@ def main():
     from fsl_mrs.utils.baseline import prepare_baseline_regressor
     from fsl_mrs.core.nifti_mrs import gen_new_nifti_mrs
 
+    # output dir - make if it doesn't exist
+    if not args.output.exists():
+        args.output.mkdir(parents=True)
+
     # Read all_parameters.csv into pandas DF
     param_df = pd.read_csv(args.results_dir / 'all_parameters.csv')
 
@@ -51,17 +55,20 @@ def main():
 
     # Instantiate MRS object
     mrs = FID.mrs(basis=basis)
-    if orig_args['conjfid'] is not None:
-        if orig_args['conjfid']:
-            mrs.conj_FID = True
-        else:
-            mrs.check_FID(repair=True)
-
-    if orig_args['conjbasis'] is not None:
-        if orig_args['conjbasis']:
-            mrs.conj_Basis = True
-        else:
-            mrs.check_Basis(repair=True)
+    if orig_args['conjfid'] is None:
+        mrs.check_FID(repair=True)
+    elif orig_args['conjfid']:
+        mrs.conj_FID = True
+    else:
+        mrs.conj_FID = False
+
+    if orig_args['conjbasis'] is None:
+        mrs.check_Basis(repair=True)
+    elif orig_args['conjbasis']:
+        mrs.conj_Basis = True
+    else:
+        mrs.conj_Basis = False
+
     if not orig_args['no_rescale']:
         mrs.rescaleForFitting(ind_scaling=orig_args['ind_scale'])
     mrs.keep = orig_args['keep']