/MRS_MRI_libs

Contains libraries for reading, writing and analysing Magnetic Resonance Spectroscopy and Imaging (MRS & MRI) data.

Primary LanguageMATLABMIT LicenseMIT

MR_libs

Description

These are MATLAB libraries for post-processing, analysing and simulating Magnetic Resonance Spectroscopy and Imaging (MRS & MRI) data.

Configuration

Data files & header files are required to be added to MATLAB path.

File List

MRS_lib: contains functions for post-processing, analysing and simulating Magnetic Resonance Spectroscopy data

  • io/

    • mrs_readSPAR.m : reads .SPAR Philips MRS header file
    • mrs_readSDAT.m : reads .SDAT Philips MRS data file
    • mrs_readLIST.m : reads .list Philips MRS header file produced by delayed reconstruction
    • mrs_readDATA.m : reads .data Philips MRS data file produced by delayed reconstruction
    • mrs_readSIN.m : reads .sin Philips raw MRS header file
    • mrs_readRAW.m : reads .raw Philips raw MRS data file
    • mrs_readRDA.m : reads .RDA Siemens MRS file (header information and data)
    • mrs_readGEpfile.m : reads Pxxxx.7 GE MRS raw data file (header information and data)
    • mrs_readLcmodelBASIS.m : reads the LCModel input .basis file, which contains the basis set of model metabolite spectra
    • mrs_readLcmodelBasisRAW.m : reads th LCModel input .RAW file, which contains time domain data of one metabolite spectrum
    • mrs_readLcmodelTABLE.m : reads the metabolite absolute and relative concentration and their SDs from the LCModel output .table file
    • mrs_readLcmodelCOORD.m : reads the LCmodel output .coord file, which contains the coordinates of all curves on the one-page output
    • mrs_readLcmodelRAW.m : reads LCModel output .RAW file which contains time domain data of each metabolite spectrum
    • mrs_readJmruiTXT.m : reads .txt MRS data file from jMRUI
    • mrs_writeSDAT.m : writes MRS data to Philips .SDAT file
    • mrs_writeSPAR.m : writes MRS header information to Philips .SPAR file
    • mrs_editSPAR.m : edits Philips .SPAR file
    • mrs_writeLcmodelIN.m : writes .in file for creating a LCmodel baisis set
    • mrs_writeLcmodelBasisRAW.m : writes .RAW file, which contains time domain data of one metabolite spectrum

  • postprocess/

    • mrs_truncate.m : truncates points from the end of spectra
    • mrs_zerofill.m : fills zeros to the end of spectra
    • mrs_apod.m : applies line-broadening filter
    • mrs_fft.m : applies fourier transformation
    • mrs_ifft.m : applies inverse fourier transformation
    • mrs_rephase.m : rephases spectra with specified phase value
    • mrs_zeroPHC.m : applies automatic zero-order phase correction to a spectrum
    • mrs_manualzeroPHC.m : allows users to manually apply zero-order phase correction of a spectrum
    • mrs_firstPHC.m : applies automatic first-order phase correction to a spectrum
    • mrs_realign.m : aligns the target peaks in the spectra
    • mrs_average.m : calculates averaged data
    • mrs_lowpass.m : filters out high frequency components above specified frequency
    • mrs_highpass.m : filters out low frequency components below specified frequency

  • simulation/

    • mrs_PRESS.m : simulates signal acquired using Position Resolved Spectroscopy (PRESS)
    • mrs_STEAM.m : simulates signal acquired using Stimulated Echo Acquisition Mode (STEAM)
    • mrs_sLASER.m : simulates the signal acquired using semi-localised by adiabatic selective refocusing(sLASER) sequence
    • mrs_ISISscheme.m : demonstrates how Image Selective in vivo Spectroscopy (ISIS) works
    • mrs_simulateFID.m: simulates a Free Induction Decay (FID) or Half-Echo.

  • utils/

    • mrs_selectPeakrange.m : allows users to manually pick the peak range interactively
    • mrs_findPeak.m : locates the highest positive peak or lowest negative peak
    • mrs_fitPeak.m : fits a peak in the given range of a spectrum with a lorenztian curve
    • mrs_lorentzFit.m : fits data with a Lorenztian function by minimising the squared error
    • mrs_lorentzFun.m : defines the Lorentzian function
    • mrs_gaussianFit.m : fits data with a Gaussian function by minimising the squared error
    • mrs_gaussianFun.m : defines Gaussian function function
    • mrs_points2Hz.m : converts unit from points to Hz
    • mrs_points2ppm.m : converts unit from points to ppm
    • mrs_ppm2Hz.m : converts unit from ppm to Hz
    • mrs_plotSpectra.m : displays spectra
    • mrs_plotBASISspectra.m: displays spectra in LCmodel .basis file
    • mrs_viewCSI.m : displays a spectrum from a selected voxel
    • mrs_rot90.m : rotates the spectra images 90 degree clockwise
    • mrs_T1corr.m : applies T1 correction
    • mrs_T2corr.m : applies T2 correction
    • mrs_calFWHM.m : calculates the full width at haflf maximum height of the peak of interest
    • mrs_calTemp.m : calculates the temperature based on chemical shift difference of the water resonance and the temperature-independent reference resonance

  • voxel_planner/

    • create_stdMaskvoxel.m&.fig : allows you to plan MRS voxel size & location with a guid of MR structural images of a standard brain (MNI152_T1_1mm_brain.nii.gz) and functional region masks (HarvardOxford-cort-maxprob-thr0-1mm.nii.gz)

    Alt text

MRI_lib contains functions for post-processing, analysing and simulating Magnetic Resonance Imaging data

  • io/
    • mri_readHDR.m : reads .hdr MRI ANALYZE 7.5 header file
    • mri_readIMG.m : reads .img MRI ANALYZE 7.5 data file
    • mri_writeIMG.m : writes data to .img file
    • mri_readPAR.m : reads .PAR Philips MRI header file
    • mri_readREC.m : reads .REC Philips MRI data file
  • utils/
    • mri_IRcurve.m : calculates the inversion recovery (IR) curve
    • mri_absIRcurveFit.m : fits the data to absolute inversion recovery curve
    • mri_createSVOI.m : creates a mask for locating the spectroscopic VOI in MR images based on given information of MR images and MRS voxel.
    • mri_locateMask.m : creates a mask for locating the spectroscopic VOI in MR images based on Philips .PAR and .SPAR header files.
    • mri_dispSVOI.m : displays the spectroscopic VOI on top of MR images

NMR_lib: contains functions for NMR simulation

  • nmr_bloch.m : defines full Bloch equations in rotating frame
  • nmr_calT2star.m : calculates T2*
  • nmr_getGamma : returns gyromagnetic ratio value for different nuclei

Examples: contains example scripts. (Please email me if you want the data files)

  • example1.m : demonstrates how to use MR_libs to post-process MRS data.
  • example2.m : demonstrates how to use MR_libs to locate spectroscopic voxel in MR images.
  • example3.m : demonstrates how to use MR_libs to to simulate tye half-echo signal acquired using PRESS and STEAM sequences.respectively.
  • example4.m : demonstrates how to use MR_libs to do Bloch Equation simulation.
  • example5.m : demonstrates how to use MR_libs to simulate magnetisation profile produced by an RF pulse.
  • example6.m : demonstrates how to use MR_libs to estimate T1.
  • example7.m : demonstrates how to use MR_libs to displays a spectrum from a selected voxel (CSI data).
  • example8.m : demonstrates how to use MR_libs to create .RAW for a LCModel model spectrum, and create .in file for making a LCmodel basisset.

Acknowledgements

I would like to thank Professor Penny Gowland and Dr. Susan Francis for their supervision. I would also like to express my enormous thanks to Dr. Mary Stephensons and Dr. Emma Halls for their help and contributions.