Field Detail

• UI

  private ViewUserInterface UI

• volumes

  private double[][][][] volumes

• conc

  private double[][][][] conc

• AIFslice

  private double[][][] AIFslice

• srcImage

  private ModelImage srcImage

• nC

  private int nC

• nR

  private int nR

• nS

  private int nS

• nT

  private int nT

• extents2D

  private int[] extents2D

• extents3D

  private int[] extents3D

• extents4D

  private int[] extents4D

• resolutions3D

  float[] resolutions3D

• units3D

  int[] units3D

• resolutions4D

  float[] resolutions4D

• units4D

  int[] units4D

• length

  private int length

• volume

  private int volume

• time

  private double[] time

• te

  private double te

• tr

  private double tr

• display

  private int display

• waitbar

  private int waitbar

• mask_npixel

  private int mask_npixel

• options_conc

  private int options_conc

• S0_nSamplesMin

  private int S0_nSamplesMin

• S0_nSamplesMax

  private int S0_nSamplesMax

• S0_thresh

  private double S0_thresh

• aif_enable

  private int aif_enable

• aif_recirculation

  private int aif_recirculation

• aif_nSlice

  private int aif_nSlice

• aif_semiMajorAxis

  private double aif_semiMajorAxis

• aif_semiMinorAxis

  private double aif_semiMinorAxis

• aif_pArea

  private double aif_pArea

• aif_pTTP

  private double aif_pTTP

• aif_pReg

  private double aif_pReg

• aif_diffPeak

  private double aif_diffPeak

• aif_nVoxelMax

  private int aif_nVoxelMax

• aif_nVoxelMin

  private int aif_nVoxelMin

• qr_enable

  private int qr_enable

• qr_b

  private double qr_b

• qr_a

  private double qr_a

• qr_r

  private double qr_r

• deconv_SVD_threshold

  private double deconv_SVD_threshold

• deconv_SVD_residual

  private int deconv_SVD_residual

• deconv_cSVD_threshold

  private double deconv_cSVD_threshold

• deconv_cSVD_residual

  private int deconv_cSVD_residual

• deconv_oSVD_OIthres

  private double deconv_oSVD_OIthres

• deconv_oSVD_residual

  private int deconv_oSVD_residual

• deconv_SS_residual

  private int deconv_SS_residual

• deconv_method

  private java.lang.String[] deconv_method

• par_kh

  private double par_kh

• par_rho

  private double par_rho

• par_kvoi

  private double par_kvoi

• mask_data

  private byte[][][] mask_data

• mask_aif

  private byte[][][] mask_aif

• mask_aif_slice

  private byte[][] mask_aif_slice

• gauss2FittingObservations

  private int gauss2FittingObservations

• gauss2FittingData

  private double[] gauss2FittingData

• doCurveIntersect

  boolean doCurveIntersect

• x_out

  double[] x_out

• y_out

  double[] y_out

• x_loc

  double[] x_loc

• y_loc

  double[] y_loc

• readTestImage

  boolean readTestImage

• test2PerfectGaussians

  boolean test2PerfectGaussians

• GxData

  private double[] GxData

• GxxData

  private double[] GxxData

• sigmas

  private double[] sigmas

• firstGaussianMean

  double firstGaussianMean

• firstGaussianMeanBin

  int firstGaussianMeanBin

• firstGaussianAmplitude

  double firstGaussianAmplitude

• firstGaussianStandardDeviation

  double firstGaussianStandardDeviation

• c1

  double c1

• secondGaussianMeanBin

  int secondGaussianMeanBin

• secondGaussianAmplitude

  double secondGaussianAmplitude

• secondGaussianStandardDeviation

  double secondGaussianStandardDeviation

• secondGaussianMean

  double secondGaussianMean

• c2

  double c2

• minSum

  double minSum

• maxSum

  double maxSum

• outputFilePath

  private java.lang.String outputFilePath

• inputFileName

  private java.lang.String inputFileName

• outputPrefix

  private java.lang.String outputPrefix

• fileIO

  private FileIO fileIO

• saveFileFormat

  private int saveFileFormat

• doSaveAllOutputs

  private boolean doSaveAllOutputs

• S0map

  double[][][] S0map

• bolus

  int[] bolus

• equalTimeSpacing

  boolean equalTimeSpacing

• AIF_ROI

  byte[][] AIF_ROI

• AIF_ROI_x

  double[] AIF_ROI_x

• AIF_ROI_y

  double[] AIF_ROI_y

• AIF_conc

  double[] AIF_conc

• AIF_voxels

  int[][] AIF_voxels

• data_peak1

  double[] data_peak1

• weights_peak1

  double[] weights_peak1

• fitParameters_peak1

  double[] fitParameters_peak1

• cv_est_parGV_peak1

  double[] cv_est_parGV_peak1

• TR

  double TR

• Tmax

  double Tmax

• Tmin

  double Tmin

• TRfine

  double TRfine

• nTfine

  int nTfine

• tGrid

  double[] tGrid

• dati_peak2

  double[] dati_peak2

• weights_peak2

  double[] weights_peak2

• fitParameters_peak2

  double[] fitParameters_peak2

• cv_est_parGV_peak2

  double[] cv_est_parGV_peak2

• AIF_fit_weights

  double[] AIF_fit_weights

• AIF_fit_parameters

  double[] AIF_fit_parameters

• AIF_fit_cv_est_parGV

  double[] AIF_fit_cv_est_parGV

• AIF_fit_gv

  double[] AIF_fit_gv

• t0_init

  double t0_init

• alpha_init

  double alpha_init

• beta_init

  double beta_init

• A_init

  double A_init

• td_init

  double td_init

• K_init

  double K_init

• tao_init

  double tao_init

• gaussStandardDeviationCheck

  boolean gaussStandardDeviationCheck

• gauss1FittingCheck

  boolean gauss1FittingCheck

• gauss2FittingCheck

  boolean gauss2FittingCheck

• GVFittingCheck

  boolean GVFittingCheck

• GVRecirculationCheck

  boolean GVRecirculationCheck

• doAIFTransfer

  boolean doAIFTransfer

• errorInMaskRoutine

  boolean errorInMaskRoutine

• intensity

  double[] intensity

• probDouble

  double[] probDouble

• cbv

  double[][][] cbv

• cbv_lc

  double[][][] cbv_lc

• cbf_svd

  double[][][] cbf_svd

• cbf_svd_residual

  double[][][][] cbf_svd_residual

• cbf_csvd

  double[][][] cbf_csvd

• cbf_csvd_residual

  double[][][][] cbf_csvd_residual

• cbf_osvd

  double[][][] cbf_osvd

• cbf_osvd_OI

  double[][][] cbf_osvd_OI

• cbf_osvd_residual

  double[][][][] cbf_osvd_residual

• mtt_svd

  double[][][] mtt_svd

• mtt_csvd

  double[][][] mtt_csvd

• mtt_osvd

  double[][][] mtt_osvd

• ttp

  short[][][] ttp

• fwhm

  double[][][] fwhm

Constructor Detail

• DSC_MRI_toolbox

  public DSC_MRI_toolbox()

• DSC_MRI_toolbox

  public DSC_MRI_toolbox​(ModelImage srcImage,
                         java.lang.String outputFilePath,
                         double te,
                         double tr,
                         int aif_nSlice,
                         java.lang.String[] deconv_method)

• DSC_MRI_toolbox

  public DSC_MRI_toolbox​(double[][][][] volumes,
                         double te,
                         double tr,
                         int aif_nSlice,
                         java.lang.String outputFilePath)

Method Detail

• runAlgorithm

  public void runAlgorithm()

• getAIF_voxels

  public int[][] getAIF_voxels()

• DSC_mri_core

  public void DSC_mri_core()

• DSC_mri_mask

  public void DSC_mri_mask()

• backupSecondGaussianRoutine

  private void backupSecondGaussianRoutine()

• DSC_mri_conc

  public void DSC_mri_conc()

• DSC_mri_S0

  public void DSC_mri_S0()

• DSC_mri_aif

  public void DSC_mri_aif()

• DSC_mri_slice_selection_figure

  public int DSC_mri_slice_selection_figure()

• extractAIF

  public void extractAIF()

• DSC_mri_cbv

  public void DSC_mri_cbv()

• DSC_mri_cbv_lc

  public void DSC_mri_cbv_lc()

• DSC_mri_cbf

  public void DSC_mri_cbf()

• DSC_mri_SVD

  public void DSC_mri_SVD()

• DSC_mri_cSVD

  public void DSC_mri_cSVD()

• DSC_mri_oSVD

  public void DSC_mri_oSVD()

• DSC_mri_mtt

  public void DSC_mri_mtt()

• DSC_mri_ttp

  public void DSC_mri_ttp()

• DSC_mri_fwhm

  public void DSC_mri_fwhm()

• fwhm

  double fwhm​(double[] x,
              double[] yorg)

• vol2mat

  private double[][] vol2mat​(double[][][][] data,
                             byte[][][] selected)

• GVfunction

  private double[] GVfunction​(double[] p)

• fitGV_peak1

  private void fitGV_peak1​(double[] dati,
                           double[] orgWeights)

• fitGV_peak2

  private void fitGV_peak2​(double[] dati,
                           double[] weights)

• GVfunction_recirculation

  private double[] GVfunction_recirculation​(double[] p)

• GVfunction_peak1

  private double[] GVfunction_peak1​(double[] p)

• clusterHierarchical

  private void clusterHierarchical​(double[][] dati,
                                   int nCluster,
                                   double[][] centroidi)

• calculateREG

  private double[][] calculateREG​(byte[][] mask)

• cumtrapz

  private double[] cumtrapz​(double[] f)

• trapz

  private double trapz​(double[] f)

• trapz

  private double[][] trapz​(double[][][] f)

• saveImageFile

  private java.io.File saveImageFile​(ModelImage img,
                                     java.lang.String dir,
                                     java.lang.String fileBasename,
                                     int fileType)

• saveImageFile

  private java.io.File saveImageFile​(ModelImage img,
                                     java.lang.String dir,
                                     java.lang.String fileBasename,
                                     int fileType,
                                     boolean alwaysSave)

• calcZeroX

  public byte[] calcZeroX​(double[] buffer)

• edgeDetect

  public byte[] edgeDetect​(double[] secondDerivBuffer)

• makeGxxKernels1D

  private void makeGxxKernels1D()

  Creates Gaussian derivative kernels.

• makeGxKernels1D

  private void makeGxKernels1D()

• convolve

  private void convolve​(double[] imageBuffer,
                        double[] kernelBuffer,
                        double[] resultBuffer)

  Perform one-dimension convolution.

  Parameters:

  imageBuffer -

  kernelBuffer -

  resultBuffer - Problem is huge border effects. Convolution uses kernels of length going from 9 to 801 on buffer of length 100.

• curveIntersect

  public void curveIntersect​(double[] x,
                             double[] param)

• curveintersect_local

  public void curveintersect_local​(double[] x1,
                                   double[] y1,
                                   double[] x2,
                                   double[] y2)

• mminvinterp

  public void mminvinterp​(double[] x,
                          double[] y,
                          double yo)

• interp1

  public double[] interp1​(double[] x,
                          double[] y,
                          double[] x_loc)

• fitToExternalFunction

  public boolean fitToExternalFunction​(double[] x,
                                       double[] residuals,
                                       double[][] jacobian)

  Specified by:

  fitToExternalFunction in class CeresSolver