Commit 0e8e692d authored by William Clarke's avatar William Clarke
Browse files

Results to spec doc, update changelog.

parent bb207649
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)
------------------------------
......
......@@ -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
......
......@@ -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
----
......
......@@ -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
---------------
......
......@@ -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']
......
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