Adding NODDI model to gitlab

NODDI_Watson_diff/LegendreFunctions.h

+#define MACRO template <typename T> __device__ inline
+
+#define MN 7
+
+//legendre gaussian integrals, order 6
+MACRO void legendreGaussianIntegral(T x, T* L)
+{
+  if(x>(T)0.05){
+    //exact
+    T I[MN];
+    T sqrtx = sqrt_gpu(x);
+    I[0] = sqrt_gpu((T)MPI)*erff(sqrtx)/sqrtx;
+    T dx = (T)1.0/x;
+    T emx = -exp_gpu(-x);
+    for (int i=1;i<MN;i++){
+      I[i] = emx + ((i+1)-(T)1.5)*I[i-1];
+      I[i] = I[i]*dx;
+    }
+    
+    L[0] = I[0];
+	
+    L[1] = -(T)0.5*I[0] + (T)1.5*I[1];
+	
+    L[2] = (T)0.375*I[0] - (T)3.75*I[1] + (T)4.375*I[2];
+   
+    L[3] = -(T)0.3125*I[0] + (T)6.5625*I[1] - (T)19.6875*I[2] + (T)14.4375*I[3];
+	
+    L[4] = (T)0.2734375*I[0] - (T)9.84375*I[1] + (T)54.140625*I[2] - (T)93.84375*I[3] + (T)50.2734375*I[4];
+    
+    L[5] = -((T)63.0/(T)256.0)*I[0] + ((T)3465.0/(T)256.0)*I[1] - ((T)30030.0/(T)256.0)*I[2] + ((T)90090.0/(T)256.0)*I[3] - ((T)109395.0/(T)256.0)*I[4] + ((T)46189.0/(T)256.0)*I[5];
+    
+    L[6] = ((T)231.0/(T)1024.0)*I[0] - ((T)18018.0/(T)1024.0)*I[1] + ((T)225225.0/(T)1024.0)*I[2] - ((T)1021020.0/(T)1024.0)*I[3] + ((T)2078505.0/(T)1024.0)*I[4] - ((T)1939938.0/(T)1024.0)*I[5] + ((T)676039.0/(T)1024.0)*I[6];
+   
+  }else{
+    // x<=0.05, approx
+    // Computing the legendre gaussian integrals for small x
+    T x2=x*x;
+    T x3=x2*x;
+    T x4=x3*x;
+    T x5=x4*x;
+    T x6=x5*x;
+        
+    L[0] = (T)2.0 - (T)2.0*x/(T)3.0 + x2/(T)5.0 - x3/(T)21.0 + x4/(T)108.0;
+    
+    L[1] = -(T)4.0*x/(T)15.0 + (T)4.0*x2/(T)35.0 - (T)2.0*x3/(T)63.0 + (T)2.0*x4/(T)297.0;
+    
+    L[2] = (T)8.0*x2/(T)315.0 - (T)8.0*x3/(T)693.0 + (T)4.0*x4/(T)1287.0;
+	
+    L[3] = -(T)16.0*x3/(T)9009.0 + (T)16.0*x4/(T)19305.0;
+    
+    L[4] = (T)32.0*x4/(T)328185.0;
+    
+    L[5] = -(T)64.0*x5/(T)14549535.0;
+    
+    L[6] = (T)128.0*x6/(T)760543875.0;
+  }
+}
+
+
+MACRO T legendre_m0(int l, T x)
+{
+// From numerical recipes
+// Computes the associated Legendre polynomial P m0-l. 
+// 0 ≤ m ≤ l
+
+  T pmm=(T)1.0;
+  if(l==0){
+    return pmm;
+  }else{
+    T pmmp1=x;
+    T pll=(T)0.0;
+    if (l==1){
+      return pmmp1;
+    }else{
+      for(int ll=2;ll<=l;ll++){
+	pll=(x*((T)2.0*ll-(T)1.0)*pmmp1-(ll-(T)1.0)*pmm)/((T)ll);
+	pmm=pmmp1;
+	pmmp1=pll;
+      }
+      return pll;
+    }
+  }
+}
+    
+MACRO void computeSH_values(T xv, T* SH)
+{
+  SH[0] = sqrt_gpu(((T)1.0-(T)0.75)/(T)MPI);
+  SH[0]*= legendre_m0(0,xv); // l=0
+  
+  SH[1] = sqrt_gpu(((T)2.0-(T)0.75)/(T)MPI);
+  SH[1]*= legendre_m0(2,xv); // l=2
+
+  SH[2] = sqrt_gpu(((T)3.0-(T)0.75)/(T)MPI);
+  SH[2]*= legendre_m0(4,xv); // l=4
+
+  SH[3] = sqrt_gpu(((T)4.0-(T)0.75)/(T)MPI);
+  SH[3]*= legendre_m0(6,xv); // l=6
+
+  SH[4] = sqrt_gpu(((T)5.0-(T)0.75)/(T)MPI);
+  SH[4]*= legendre_m0(8,xv); // l=8
+
+  SH[5] = sqrt_gpu(((T)6.0-(T)0.75)/(T)MPI);
+  SH[5]*= legendre_m0(10,xv); // l=10
+
+  SH[6] = sqrt_gpu(((T)7.0-(T)0.75)/(T)MPI);
+  SH[6]*= legendre_m0(12,xv); // l=12
+}

NODDI_Watson_diff/NODDI_Watson_diff_finish.sh

+#!/bin/sh
+#
+#   Moises Hernandez-Fernandez - FMRIB Image Analysis Group
+#
+#   Copyright (C) 2004 University of Oxford
+#
+#   SHCOPYRIGHT
+
+Usage() {
+    echo ""
+    echo "Usage: NODDI_Watson_finish <subject_directory>"
+    echo ""
+    echo "expects to find all the estimatedParameters in subject directory"
+    echo ""
+    exit 1
+}
+
+[ "$1" = "" ] && Usage
+
+directory=$1
+cd ${directory}
+
+mv $directory/Param_0_samples.nii.gz $directory/fiso_samples.nii.gz
+mv $directory/Param_1_samples.nii.gz $directory/fintra_samples.nii.gz
+mv $directory/Param_2_samples.nii.gz $directory/kappa_samples.nii.gz
+
+# Change range???
+mv $directory/Param_3_samples.nii.gz $directory/th_samples.nii.gz
+mv $directory/Param_4_samples.nii.gz $directory/ph_samples.nii.gz
+
+Two_div_pi=0.636619772367581
+
+$FSLDIR/bin/fslmaths $directory/fiso_samples.nii.gz -Tmean $directory/mean_fiso
+$FSLDIR/bin/fslmaths $directory/fintra_samples.nii.gz -Tmean $directory/mean_fintra
+$FSLDIR/bin/fslmaths $directory/kappa_samples.nii.gz -Tmean $directory/mean_kappa
+$FSLDIR/bin/make_dyadic_vectors $directory/th_samples $directory/ph_samples $directory/nodif_brain_mask.nii.gz dyads1
+
+${FSLDIR}/bin/fslmaths $directory/mean_kappa -recip -atan -mul $Two_div_pi $directory/OD
+
+# For postmortem model have a 5th parameter (non-attenuating dot compartment)
+if [ -f $directory/Param_5_samples.nii.gz ]; then
+    mv $directory/Param_5_samples.nii.gz $directory/irFrac_samples.nii.gz
+    $FSLDIR/bin/fslmaths $directory/irFrac_samples.nii.gz -Tmean $directory/mean_irFrac.nii.gz
+fi

NODDI_Watson_diff/NODDI_Watson_finish.sh

+#!/bin/sh
+#
+#   Moises Hernandez-Fernandez - FMRIB Image Analysis Group
+#
+#   Copyright (C) 2004 University of Oxford
+#
+#   SHCOPYRIGHT
+
+Usage() {
+    echo ""
+    echo "Usage: NODDI_Watson_finish <subject_directory>"
+    echo ""
+    echo "expects to find all the estimatedParameters in subject directory"
+    echo ""
+    exit 1
+}
+
+[ "$1" = "" ] && Usage
+
+directory=$1
+cd ${directory}
+
+mv $directory/Param_0_samples.nii.gz $directory/fiso_samples.nii.gz
+mv $directory/Param_1_samples.nii.gz $directory/fintra_samples.nii.gz
+mv $directory/Param_2_samples.nii.gz $directory/kappa_samples.nii.gz
+
+# Change range???
+mv $directory/Param_3_samples.nii.gz $directory/th_samples.nii.gz
+mv $directory/Param_4_samples.nii.gz $directory/ph_samples.nii.gz
+
+Two_div_pi=0.636619772367581
+
+$FSLDIR/bin/fslmaths $directory/fiso_samples.nii.gz -Tmean $directory/mean_fiso
+$FSLDIR/bin/fslmaths $directory/fintra_samples.nii.gz -Tmean $directory/mean_fintra
+$FSLDIR/bin/fslmaths $directory/kappa_samples.nii.gz -Tmean $directory/mean_kappa
+$FSLDIR/bin/make_dyadic_vectors $directory/th_samples $directory/ph_samples $directory/nodif_brain_mask.nii.gz dyads1
+
+${FSLDIR}/bin/fslmaths $directory/mean_kappa -recip -atan -mul $Two_div_pi $directory/OD
+
+# For postmortem model have a 5th parameter (non-attenuating dot compartment)
+if [ -f $directory/Param_5_samples.nii.gz ]; then
+    mv $directory/Param_5_samples.nii.gz $directory/irFrac_samples.nii.gz
+    $FSLDIR/bin/fslmaths $directory/irFrac_samples.nii.gz -Tmean $directory/mean_irFrac.nii.gz
+fi

NODDI_Watson_diff/Pipeline_NODDI_Watson_diff.sh

+#!/bin/sh
+#
+#   Moises Hernandez-Fernandez - FMRIB Image Analysis Group
+#
+#   Copyright (C) 2004 University of Oxford
+#
+#   SHCOPYRIGHT
+#
+# Pipeline for fitting NODDI-Watson
+# Now with user specified dax and diso - Amy Howard Apr 2020 
+
+if [ "x$CUDIMOT" == "x" ]; then
+	echo ""
+	echo "Please, set enviroment variable CUDIMOT with the path where cuDIMOT is installed"
+	echo "The path must contain a bin directory with binary files, i.e. \$CUDIMOT/bin"
+	echo "For instance:   export CUDIMOT=/home/moises/CUDIMOT"
+	echo ""
+  exit 1
+fi
+
+bindir=${CUDIMOT}/bin
+
+make_absolute(){
+    dir=$1;
+    if [ -d ${dir} ]; then
+	OLDWD=`pwd`
+	cd ${dir}
+	dir_all=`pwd`
+	cd $OLDWD
+    else
+	dir_all=${dir}
+    fi
+    echo ${dir_all}
+}
+Usage() {
+    echo ""
+    echo "Usage: Pipeline_NODDI_Watson_diff.sh <subject_directory> [options]"
+    echo ""
+    echo "expects to find data and nodif_brain_mask in subject directory"
+    echo ""
+    echo "<options>:"
+    echo "--dax (axial diffusivity in m^2/s e.g. 0.0017)"
+    echo "--diso (isotropic diffusivity in m^2/s e.g. 0.003)"
+    echo "-Q (name of the GPU(s) queue, default cuda.q (defined in environment variable: FSLGECUDAQ)"
+    echo "-NJOBS (number of jobs to queue, the data is divided in NJOBS parts, usefull for a GPU cluster, default 4)"
+    echo "--runMCMC (if you want to run MCMC)"
+    echo "--rician (if you want to run rician noise modelling)"
+    echo "-b (burnin period, default 5000)"
+    echo "-j (number of jumps, default 1250)"
+    echo "-s (sample every, default 25)"
+    echo "--BIC_AIC (calculate BIC & AIC)"
+    echo ""
+    exit 1
+}
+
+[ "$1" = "" ] && Usage
+
+modelname=NODDI_Watson_diff
+step1=GridSeach
+step2=FitFractions
+
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib
+
+subjdir=`make_absolute $1`
+subjdir=`echo $subjdir | sed 's/\/$/$/g'`
+
+echo "---------------------------------------------------------------------------------"
+echo "------------------------------------ CUDIMOT ------------------------------------"
+echo "----------------------------- MODEL: $modelname -----------------------------"
+echo "---------------------------------------------------------------------------------"
+echo subjectdir is $subjdir
+
+start=`date +%s`
+
+#parse option arguments
+njobs=1
+burnin=1000
+njumps=1250
+sampleevery=25
+other=""
+queue=""
+lastStepModelOpts=" --getPredictedSignal"
+dax=0.0017
+diso=0.003
+
+shift
+while [ ! -z "$1" ]
+do
+  case "$1" in
+      --dax) dax=$2;shift;;
+      --diso) diso=$2;shift;;
+      -Q) queue="-q $2";shift;;
+      -NJOBS) njobs=$2;shift;;
+      -b) burnin=$2;shift;;
+      -j) njumps=$2;shift;;
+      -s) sampleevery=$2;shift;;
+      --runMCMC) lastStepModelOpts=$lastStepModelOpts" --runMCMC";;
+      --BIC_AIC) lastStepModelOpts=$lastStepModelOpts" --BIC_AIC";;
+      --rician) lastStepModelOpts=$lastStepModelOpts" --rician";;
+      #*) other=$other" "$1;;
+  esac
+  shift
+done
+
+#Set options
+opts="--bi=$burnin --nj=$njumps --se=$sampleevery"
+opts="$opts $other"
+
+if [ "x$SGE_ROOT" != "x" ]; then
+	queue="-q $FSLGECUDAQ"
+fi
+
+#check that all required files exist
+
+if [ ! -d $subjdir ]; then
+	echo "subject directory $1 not found"
+	exit 1
+fi
+
+if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
+	echo "${subjdir}/data not found"
+	exit 1
+fi
+
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
+	echo "${subjdir}/nodif_brain_mask not found"
+	exit 1
+fi
+
+if [ -e ${subjdir}.${modelname}/xfms/eye.mat ]; then
+	echo "${subjdir} has already been processed: ${subjdir}.${modelname}." 
+	echo "Delete or rename ${subjdir}.${modelname} before repeating the process."
+	exit 1
+fi
+
+echo Making output directory structure
+
+mkdir -p ${subjdir}.${modelname}/
+mkdir -p ${subjdir}.${modelname}/diff_parts
+mkdir -p ${subjdir}.${modelname}/logs
+mkdir -p ${subjdir}.${modelname}/Dtifit
+mkdir -p ${subjdir}.${modelname}/${step1}
+mkdir -p ${subjdir}.${modelname}/${step1}/diff_parts
+mkdir -p ${subjdir}.${modelname}/${step1}/logs
+mkdir -p ${subjdir}.${modelname}/${step2}
+mkdir -p ${subjdir}.${modelname}/${step2}/diff_parts
+mkdir -p ${subjdir}.${modelname}/${step2}/logs
+part=0
+
+echo Copying files to output directory
+
+${FSLDIR}/bin/imcp ${subjdir}/nodif_brain_mask ${subjdir}.${modelname}
+if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` = 1 ] ; then
+    ${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.${modelname}/nodif_brain
+fi
+
+# Specify Common Fixed Parameters
+CFP_file=$subjdir.${modelname}/CFP
+cp ${subjdir}/bvecs $subjdir.${modelname}
+cp ${subjdir}/bvals $subjdir.${modelname}
+echo  $subjdir.${modelname}/bvecs > $CFP_file
+echo  $subjdir.${modelname}/bvals >> $CFP_file
+N=`wc -w ${subjdir}/bvals | awk '{print $1;}'`
+for dparam in dax diso; do 
+    for file in $subjdir.${modelname}/$dparam $subjdir.${modelname}/ddtmp; do
+        if [ -f $file ]; then rm $file; fi
+    done
+    if [ "$dparam" == "dax" ]; then d=$dax; fi
+    if [ "$dparam" == "diso" ]; then d=$diso; fi
+    for ((i=1;i<=$N;i++)); do echo $d >> $subjdir.${modelname}/ddtmp; done
+    echo `cat $subjdir.${modelname}/ddtmp` >  $subjdir.${modelname}/$dparam    
+    echo  $subjdir.${modelname}/$dparam >> $CFP_file
+done
+rm $subjdir.${modelname}/ddtmp
+
+#Set more options
+opts=$opts" --data=${subjdir}/data --maskfile=$subjdir.${modelname}/nodif_brain_mask --forcedir --CFP=$CFP_file"
+
+# Calculate S0 with the mean of the volumes with bval<50
+bvals=`cat ${subjdir}/bvals`
+mkdir -p ${subjdir}.${modelname}/temporal
+pos=0
+for i in $bvals; do 
+    if [ $i -le 50 ]; then  
+       	fslroi ${subjdir}/data  ${subjdir}.${modelname}/temporal/volume_$pos $pos 1    
+    fi 
+    pos=$(($pos + 1))
+done
+fslmerge -t ${subjdir}.${modelname}/temporal/S0s ${subjdir}.${modelname}/temporal/volume*
+fslmaths ${subjdir}.${modelname}/temporal/S0s -Tmean ${subjdir}.${modelname}/S0
+rm -rf ${subjdir}.${modelname}/temporal
+
+# Specify Fixed parameters: S0
+FixPFile=${subjdir}.${modelname}/FixP
+echo ${subjdir}.${modelname}/S0 >> $FixPFile
+
+##############################################################################
+################################ First Dtifit  ###############################
+##############################################################################
+echo "Queue Dtifit"
+PathDTI=${subjdir}.${modelname}/Dtifit
+dtifit_command="${bindir}/Run_dtifit.sh ${subjdir} ${subjdir}.${modelname} ${bindir}"
+#SGE
+dtifitProcess=`${FSLDIR}/bin/fsl_sub $queue -l $PathDTI/logs -N dtifit $dtifit_command`
+
+##### Model Parameters: fiso, fintra, kappa, th, ph  ######
+#############################################################
+##################### Grid Search Step ######################
+#############################################################
+echo "Queue GridSearch process"
+PathStep1=$subjdir.${modelname}/${step1}
+
+# Create file to specify initialisation parameters (2 parameters: th,ph)
+InitializationFile=$PathStep1/InitializationParameters
+echo "" > $InitializationFile #fiso
+echo "" >> $InitializationFile #fintra
+echo "" >> $InitializationFile #kappa
+echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
+echo ${PathDTI}/dtifit_V1_ph.nii.gz >> $InitializationFile #ph
+
+# Do GridSearch (fiso,fintra,kappa)
+GridFile=$PathStep1/GridSearch
+echo "search[0]=(0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)" > $GridFile #fiso
+echo "search[1]=(0.0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0)" >> $GridFile #fintra
+echo "search[2]=(1,2,3,4,5,6,7,8)" >> $GridFile #kappa
+
+partsdir=$PathStep1/diff_parts
+outputdir=$PathStep1
+Step1Opts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --gridSearch=$GridFile --no_LevMar --init_params=$InitializationFile --fixed=3,4"
+
+postproc=`${bindir}/jobs_wrapper.sh $PathStep1 $dtifitProcess $modelname GS $njobs $Step1Opts`
+
+###############################################################
+##################### Fit only Fractions ######################
+###############################################################
+echo "Queue Fitting Fractions process"
+PathStep2=$subjdir.${modelname}/${step2}
+
+# Create file to specify initialisation parameters (2 parameters: fiso,fintra)
+InitializationFile=$PathStep2/InitializationParameters
+echo $PathStep1/Param_0_samples > $InitializationFile #fiso
+echo $PathStep1/Param_1_samples >> $InitializationFile #fintra
+echo $PathStep1/Param_2_samples >> $InitializationFile #kappa
+echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
+echo ${PathDTI}/dtifit_V1_ph.nii.gz >> $InitializationFile #ph
+
+partsdir=$PathStep2/diff_parts
+outputdir=$PathStep2
+Step2Opts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --init_params=$InitializationFile --fixed=2,3,4"
+
+postproc=`${bindir}/jobs_wrapper.sh $PathStep2 $postproc $modelname FitFractions $njobs $Step2Opts`
+
+######################################################################################
+######################### Fit all the parameters of the Model ########################
+######################################################################################
+echo "Queue Fitting process"
+
+# Create file to specify initialization parameters (5 parameters: fiso,fintra,kappa,th,ph)
+InitializationFile=$subjdir.${modelname}/InitializationParameters
+echo $PathStep2/Param_0_samples > $InitializationFile #fiso
+echo $PathStep2/Param_1_samples >> $InitializationFile #fintra
+echo ${PathStep1}/Param_2_samples >> $InitializationFile #kappa
+echo ${PathDTI}/dtifit_V1_th.nii.gz >> $InitializationFile #th
+echo ${PathDTI}/dtifit_V1_ph.nii.gz  >> $InitializationFile #ph
+
+partsdir=${subjdir}.${modelname}/diff_parts
+outputdir=${subjdir}.${modelname}
+ModelOpts=$opts" --outputdir=$outputdir --partsdir=$partsdir --FixP=$FixPFile --init_params=$InitializationFile $lastStepModelOpts"
+
+postproc=`${bindir}/jobs_wrapper.sh ${subjdir}.${modelname} $postproc $modelname FitProcess $njobs $ModelOpts`
+
+#########################################
+### Calculate Dispersion Index & dyads ###
+##########################################
+finish_command="/home/fs0/amyh/cudimot/mymodels/NODDI_Watson_diff/${modelname}_finish.sh ${subjdir}.${modelname}"
+#SGE
+finishProcess=`${FSLDIR}/bin/fsl_sub $queue -l ${subjdir}.${modelname}/logs -N ${modelname}_finish -j $postproc $finish_command`
+
+endt=`date +%s`
+runtime=$((endt-start))
+#echo Runtime $runtime
+echo Everything Queued

NODDI_Watson_diff/WatsonFunctions.h

+#define MACRO template <typename T> __device__ inline
+
+#define MPI 3.14159265358979323846
+#define M_SQRT_PI 1.772453850905516
+#define NMAX 6
+#define H 0.4
+#define A1 (2.0/3.0)
+#define A2 0.4
+#define A3 (2.0/7.0)
+
+
+MACRO T dawson(T x){  // From Numerical Recipes in C
+//Returns Dawson’s integral for any real x
+
+  int i,n0;
+  T d1,d2,e1,e2,sum,x2,xp,xx,ans;
+  T c[NMAX+1];
+  int init=0; // Flag is 0 if we need to initialize, else 1
+  if (init==0){
+    init=1;
+    for(i=0;i<NMAX;i++){
+      c[i]=((T)2.0*(i+1)-(T)1.0)*(T)H;
+      c[i]=exp_gpu(-c[i]*c[i]);
+    }
+  }
+  if(fabs_gpu(x) < (T)0.2){  // Use series expansion.
+    x2=x*x;
+    ans=x*((T)1.0-(T)A1*x2*((T)1.0-(T)A2*x2*((T)1.0-(T)A3*x2)));
+  }else{  // Use sampling theorem representation.
+    xx=fabs_gpu(x);
+    n0=2*(int)((T)0.5*xx/(T)H+(T)0.5);
+    xp=xx-n0*(T)H;
+    e1=exp_gpu((T)2.0*xp*(T)H);
+    e2=e1*e1;
+    d1=n0+1;
+    d2=d1-(T)2.0;
+    sum=0.0;
+    for (i=0;i<NMAX;i++,d1+=(T)2.0,d2-=(T)2.0,e1*=e2){
+      sum += c[i]*(e1/d1+(T)1.0/(d2*e1));
+    }
+    
+    //ans=(T)0.5641895835*SIGN(exp_gpu(-xp*xp),x)*sum; 
+    ans=exp_gpu(-xp*xp);
+    if(ans<0) ans=-ans; // magnitude
+    if(x<0) ans=-ans; // * sign(x)
+    ans=(T)0.5641895835*ans*sum; //Constant is 1/sqrt(pi)
+    
+  }
+  return ans;
+}
+
+MACRO void WatsonHinderedDiffusionCoeff(//input
+					T kappa,
+					// dPar is a constant
+					T dParallel,
+					T dPerp,
+					//output
+					T& dPar_equivalent,
+					T& dPerp_equivalent)
+{
+  T dParMdPerp = dParallel - dPerp;
+  if (kappa < (T)1e-5){
+    T dParP2dPerp = dParallel + (T)2.0*dPerp;
+    T k2 = kappa*kappa;
+
+    dPar_equivalent = dParP2dPerp/(T)3.0 
+      + (T)4.0*dParMdPerp*kappa/(T)45.0 
+      + (T)8.0*dParMdPerp*k2/(T)945.0;
+    
+    dPerp_equivalent = dParP2dPerp/(T)3.0 
+      - (T)2.0*dParMdPerp*kappa/(T)45.0 
+      - (T)4.0*dParMdPerp*k2/(T)945.0;
+
+  }else{
+    T sk;
+    T dawsonf;
+    //if(kapppa<0){
+    // never. kappa is always >=0
+    //}else{
+    sk = sqrt_gpu(kappa);
+    //dawsonf= (T)0.5*exp_gpu(-kappa)*sqrt_gpu(M_PI)*erfi_sk;
+    dawsonf=dawson(sk);
+    
+    T factor = sk/dawsonf;
+    
+    dPar_equivalent = (-dParMdPerp+(T)2.0*dPerp*kappa+dParMdPerp*factor) / ((T)2.0*kappa);
+    dPerp_equivalent = (dParMdPerp+(T)2.0*(dParallel+dPerp)*kappa-dParMdPerp*factor) / ((T)4.0*kappa);
+  }
+}
+
+MACRO void WatsonSHCoeff(T k, T* coeff)
+{
+  //commputes the spherical harmonic (SH) coefficients of the Watson's distribution with the concentration parameter k (kappa) and 12th order
+  
+  coeff[0]= (T)2.0*sqrt_gpu((T)MPI);
+  
+  if(k>30){
+    //very large kappa
+