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. 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 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. - 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. - Improved display of basis sets using mrs_tools or basis_tools.
- Added 'default' MEGA-PRESS MM option to fsl_mrs and mrs class. - 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. - Under the hood refactor of basis, MRS, and MRSI classes.
- Updated density matrix simulator. Added some automatic testing. - Updated density matrix simulator. Added some automatic testing.
- Added documentation about the results_to_spectrum script.
1.1.2 (Friday 16th April 2021) 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 ...@@ -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. : Collection of tools for manipulating basis sets.
- **svs_segment & mrsi_segment** - **svs_segment & mrsi_segment**
: Run tissue segmentation for SVS/MRSI from T1 image. : Run tissue segmentation for SVS/MRSI from T1 image.
- **results_to_spectrum**
: Generate spectrum representation of a fit from *fsl_mrs* results.
--- ---
## Documentation ## Documentation
......
...@@ -41,7 +41,9 @@ Results from :code:`fsl_mrs` are stored in a single folder that contains the fol ...@@ -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. - 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. - 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 MRSI
---- ----
......
...@@ -10,7 +10,7 @@ There are 4 ways of visualising/interacting with MRS data in FSL-MRS: ...@@ -10,7 +10,7 @@ There are 4 ways of visualising/interacting with MRS data in FSL-MRS:
1. Quick glance (human-readable, non-interactive) 1. Quick glance (human-readable, non-interactive)
2. CSV files (human- and machine-readable) 2. CSV files (human- and machine-readable)
3. HTML reports (fairly interactive) 3. HTML reports (fairly interactive)
#. FSLeyes (highly interactive) 4. FSLeyes (highly interactive)
1. Quick glance 1. Quick glance
--------------- ---------------
......
...@@ -38,6 +38,10 @@ def main(): ...@@ -38,6 +38,10 @@ def main():
from fsl_mrs.utils.baseline import prepare_baseline_regressor from fsl_mrs.utils.baseline import prepare_baseline_regressor
from fsl_mrs.core.nifti_mrs import gen_new_nifti_mrs 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 # Read all_parameters.csv into pandas DF
param_df = pd.read_csv(args.results_dir / 'all_parameters.csv') param_df = pd.read_csv(args.results_dir / 'all_parameters.csv')
...@@ -51,17 +55,20 @@ def main(): ...@@ -51,17 +55,20 @@ def main():
# Instantiate MRS object # Instantiate MRS object
mrs = FID.mrs(basis=basis) mrs = FID.mrs(basis=basis)
if orig_args['conjfid'] is not None: if orig_args['conjfid'] is None:
if orig_args['conjfid']: mrs.check_FID(repair=True)
mrs.conj_FID = True elif orig_args['conjfid']:
else: mrs.conj_FID = True
mrs.check_FID(repair=True) else:
mrs.conj_FID = False
if orig_args['conjbasis'] is not None:
if orig_args['conjbasis']: if orig_args['conjbasis'] is None:
mrs.conj_Basis = True mrs.check_Basis(repair=True)
else: elif orig_args['conjbasis']:
mrs.check_Basis(repair=True) mrs.conj_Basis = True
else:
mrs.conj_Basis = False
if not orig_args['no_rescale']: if not orig_args['no_rescale']:
mrs.rescaleForFitting(ind_scaling=orig_args['ind_scale']) mrs.rescaleForFitting(ind_scaling=orig_args['ind_scale'])
mrs.keep = orig_args['keep'] mrs.keep = orig_args['keep']
......
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