# LWFIT
LWFIT code for GABA quantification from MEGA-PRESS magnetic resonance spectra. It is
based on a peak integration approach in the frequency domain to estimate the
concentration of the metabolites.
The code requires matlab to run. It was originally developed using matlab 2017b and
has also been tested with Matlab R2021a (9.10.0.1602886) under Linux. To use the code,
start with the Matlab live scripts Notebook-XX.mlx which show how to use the individual
functions. Further details are in the comments of the relevant functions.
LWFIT aligns the edit-off and difference spectra so that the main NAA peak is
precisely at 2.01 ppm and then calculates the areas for
* NAA: 1.91 - 2.11 ppm, difference,
* Cr: 2.90 - 3.10 ppm, edit-off,
* GABA: 2.90 - 3.12 ppm, difference,
* Glu and Gln, GLX1: 2.25 - 2.45 ppm, difference,
* and GLX2: 3.65 - 3.85 ppm, difference.
It uses the real frequency-domain spectra and numerically integrates the peaks
using piecewise-linear functions over the indicated fixed ppm ranges, selected to
minimise contamination from other signals. Lorentzian, Gaussian and spline fitting
and several baseline fitting and filtering methods were explored but initial testing
indicated that numerical integration with minimal pre-processing yielded the most
accurate estimation results of the methods considered. While more aggressive noise
filters aesthetically improve the quality of the spectra, their application tends to
exacerbate underestimation of GABA, especially for weak signals, suggesting that
filtering eliminates some of the GABA signal present in the data. So we only
perform zero-filling (4096 points) and a frequency shift to align the NAA peak.
The code has been used in the following paper and more details are available there:
CW Jenkins, M Chandler, FC Langbein, SM Shermer. **Benchmarking GABA Quantification:
A Ground Truth Data Set and Comparative Analysis of TARQUIN, LCModel, jMRUI and
Gannet.** [[arxiv:1909.02163]](https://arxiv.org/abs/1909.02163)
The analysis results of LWFIT used in that paper for a specific dataset, using
the Matlab live scripts above are in the wiki, with all results computed and also
converted to PDF.
## Locations
The code is developed and maintained on [qyber\\black](https://qyber.black)
at https://qyber.black/mrs/code-lwfit
This code is mirrored at
* https://github.com/xis10z/Code-LWFIT
The mirrors are only for convenience, accessibility and backup.
## People
* [Sophie M Shermer](https://qyber.black/lw1660), [Physics](https://www.swansea.ac.uk/physics), [Swansea University](https://www.swansea.ac.uk/)
* [Christopher W Jenkins](https://qyber.black/chris), [Physics](https://www.swansea.ac.uk/physics) and [Centre for Nanohealth](https://www.swansea.ac.uk/nanohealth/facilities/) and [Clinical Imaging Unit](https://www.swansea.ac.uk/medicine/research/researchfacilities/jointclinicalresearchfacility/clinicalimagingfacility/), [Swansea University](https://www.swansea.ac.uk/); [Cardiff University Brain Research Imaging Centre (CUBRIC)](https://www.cardiff.ac.uk/cardiff-university-brain-research-imaging-centre)
* [Frank C Langbein](https://qyber.black/xis10z), [School of Computer Science and Informatics](https://www.cardiff.ac.uk/computer-science), [Cardiff University](https://www.cardiff.ac.uk/); [langbein.org](https://langbein.org/)
* [Max Chandler](https://qyber.black/max), [School of Computer Science and Informatics](https://www.cardiff.ac.uk/computer-science), [Cardiff University](https://www.cardiff.ac.uk/)
## Citation
SM Shermer, FC Langbein, CW Jenkins, M Chandler. **Code - LWFIT**. Version 1.0. _FigShare_, Software. May 2021.
[[DOI:10.6084/m9.figshare.14540757.v1]](https://doi.org/10.6084/m9.figshare.14540757.v1)
[[DEV:https://qyber.black/mrs/code-lwfit]](https://qyber.black/mrs/code-lwfit)
[[MIRROR:https://github.com/xis10z/Code-LWFIT/tree/v1.0]](https://github.com/xis10z/Code-LWFIT/tree/v1.0)
## License
Copyright (C) 2019-2021, Sophie M Shermer, Swansea University
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
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分段线性拟合matlab代码-Code-LWFIT:从MEGA-PRESS磁共振波谱(MRS)进行GABA定量
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分段线性拟合matlab代码伦敦自由贸易区 LWFIT代码用于根据MEGA-PRESS磁共振光谱对GABA进行定量。 它基于频域中的峰积分方法来估计代谢物的浓度。 该代码需要matlab才能运行。 它最初是使用matlab 2017b开发的,并且已经在Linux下通过Matlab R2021a(9.10.0.1602886)进行了测试。 要使用该代码,请先从Matlab实时脚本Notebook-XX.mlx开始,该脚本演示了如何使用各个功能。 有关详细信息,请参见相关功能的注释。 LWFIT校正编辑谱图和差异谱图,以使主NAA峰精确地位于2.01 ppm,然后计算出 NAA:1.91-2.11 ppm,差异, Chrome:2.90-3.10 ppm,脱模, GABA:2.90-3.12 ppm,差异, Glu和Gln,GLX1:2.25-2.45 ppm,差异, 和GLX2:3.65-3.85 ppm,差异。 它使用真实的频域频谱,并在指定的固定ppm范围内使用分段线性函数对峰进行数值积分,以最大程度地减少来自其他信号的污染。 探索了Lorentzian,Gaussian和样条曲线拟
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Code-LWFIT-master.zip (41个子文件)
Code-LWFIT-master
Notebook_E3.mlx 5KB
.gitignore 17B
GetSpectra.m 1KB
ApplyFilter.m 1017B
PlotSpectEDIT.m 8KB
WriteSeriesIMA.m 557B
Notebook_E4b.mlx 5KB
Notebook_E2.mlx 6KB
CombineSpectra_RAW.m 3KB
FitPeaks.m 2KB
ReadSpectIMA.m 2KB
PlotLineWidth.m 782B
RewriteIMA.m 2KB
ReadSpectRaw.m 1KB
LICENSE 34KB
Endian2Complex.m 474B
twix_map_obj.m 35KB
PlotMetaboliteAreasGLX.m 2KB
CompDiffSpect.m 336B
.github
mirror.sh 1KB
workflows
mirror-qyber-wiki.yml 322B
README.md 5KB
WriteSpecIMA.m 377B
CombineSpectra_RAW_EJA.m 1KB
FitLorentz.m 2KB
GetProtFromImageNew.m 757B
FitPeaks_WS_ON.m 2KB
ReadSpectIMA_SA.m 1KB
ReadRawDataSeries2.m 657B
Notebook_E1.mlx 4.97MB
Notebook_E4a.mlx 5KB
MakeTableLorentzFit.m 1001B
ReadDAT.m 25KB
CombineSpectra_SA.m 2KB
Notebook_E4d.mlx 5KB
GetRefData.m 6KB
Notebook_E4c.mlx 5KB
RewriteIMA_single.m 663B
ReadRawDataSeries.m 977B
CleanHeader2.m 2KB
PlotMetaboliteAreas.m 4KB
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