Commit 0e71f3da authored by William Clarke's avatar William Clarke
Browse files

Update docs and changelog. Options added to MRSI.

parent e5d4cd8c
This document contains the FSL-MRS release history in reverse chronological order.
1.0.1 (Friday 19th June 2020)
- Output folder in fsl_mrs_proc will now be created if it does not exist.
- fsl_mrs_proc now handles data with a singleton coil dimension correctly.
- --ind_scale and --disable_MH_priors options added to fsl_mrs and fsl_mrsi.
1.0.0 (Wednesday 17th June 2020)
......@@ -25,7 +25,7 @@ copyright = f'{date.year}, Will Clarke & Saad Jbabdi, University of Oxford, Oxfo
author = 'William Clarke'
# The full version, including alpha/beta/rc tags
version = '1.0.0'
version = '1.0.1'
release = version
# From PM's fsleyes doc
......@@ -158,8 +158,10 @@ Below are detailed explanations of some of the optional arguments in the wrapper
Add macromolecule peaks at the following frequencies: 0.9, 1.2, 1.4, 1.7 ppm and a doublet at 2.08 & 3.0 ppm
By default the lineshape is a Voigt (lorentizian+gaussian). Use this flag to set to Lorentzian.
Allow independent scaling of specified basis spectra before fitting. For example this can be used to independently scale empirically measured macromolecules combined with simulated metabolite spectra.
Disable the priors on the MH fitting. The priors are tuned for *in vivo* human brain spectroscopy. Use this option if your spectra has significantly different line widths, phases or large shifts. E.g. in liquid phase phantom or (potentially) pre-clinical systems.
The wrapper scripts can also take a configuration file as an input. For example, say we have a text file called :code:`config.txt` which contains the below:
......@@ -9,4 +9,10 @@ MRS specific questions may be better answered on the `MRSHub forums <https://for
1. Unable to find example data
If you installed FSL-MRS through conda the example data can be downloaded directly from the GitLab repository `folder <>`_.
\ No newline at end of file
2. Poor fits
Two problems are commonley diagnosed when poor fits are seen:
1) Basis spectra are inconsistently scaled. For example empirically derived macromolecular basis spectra can be orders of magnitude larger than the other basis spectra. Before fitting, fsl_mrs(i) scales the magnitude of the data and basis spectra to a known range. Relative scales are preserved within the basis spectra. To permit fsl_mrs(i) to apply different scales to individual basis spectra use the :code:`--ind_scale` option with a list of basis names.
2) The data might have parameters unlike a 7T or 3T human *in vivo* brain spectrum. I.e. the spectrum originates from a pre-clinical system or from phantom. In this case the MCMC priors which are suitable for *in vivo* human case can be disabled using the :code:`--disable_MH_priors` option.
\ No newline at end of file
......@@ -10,10 +10,9 @@
import numpy as np
from fsl_mrs.core import MRS
from fsl_mrs.utils import mrs_io,plotting,fitting,misc
from fsl_mrs.utils import mrs_io, misc
import matplotlib.pyplot as plt
import nibabel as nib
import os.path as op
from fsl_mrs.utils.mrs_io.fsl_io import saveNIFTI
class MRSI(object):
......@@ -67,6 +66,7 @@ class MRSI(object):
self.rescale = False
self.keep = None
self.ignore = None
self.ind_scaling = None
self._store_scalings = None
......@@ -165,7 +165,7 @@ class MRSI(object):
if self.rescale:
def plot(self,mask=True,ppmlim=(0.2,4.2)):
if mask:
......@@ -73,6 +73,12 @@ def main():
fitting_args.add_argument('--lorentzian', action="store_true",
help="Enable purely lorentzian broadening"
" (default is Voigt)")
fitting_args.add_argument('--ind_scale', default=None, type=str,
help='List of basis spectra to scale'
' independently of other basis spectra.')
fitting_args.add_argument('--disable_MH_priors', action="store_true",
help="Disable MH priors.")
optional.add_argument('--TE', type=float, default=None, metavar='TE',
......@@ -195,6 +201,9 @@ def main():
Fitargs['model'] = 'voigt'
if args.disable_MH_priors:
Fitargs['disable_mh_priors'] = True
# Echo time
if args.TE is not None:
echotime = args.TE*1E-3
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