first commit

Joint Fitting/batch_run.pro

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+pro batch_run
+
+;This file runs the script 'run_2cxm_phantom' in batch mode. It uses multithreading to access multiple cores to increase speed.
+
+!EXCEPT=0
+
+ mean_baseline = 163.0
+
+ COMMON S0_info, equal_and_free, unequal_and_free, equal_by_baseline
+ COMMON sigma_info, fixed_sigma, equal_sigma, known_sigma
+
+ ;parameters relating to how M0v and M0d are varied during fitting
+ equal_and_free = 1
+ unequal_and_free = 0
+ equal_by_baseline = 0
+
+ ;multithread indices. 6 jobs, sequential and joint estimation for 3 AIF conditions  
+ index = [1,2,3,4,5,6]
+
+ T1_dataType = 'vfa'; could adapt to fit to IR or SR T1 mapping data
+ model = 'XM'; could change to Tofts or E.Tofts 
+ n_repeats = 100; number of Monte Carlo repeats
+ n_vox_fit = 504; number of voxels to sample
+ snr_dyn = 5.0; required SNR of dynamic images 
+ snr_vfa = 11.2; required SNR of VFA images -> snr_dyn*sqrt(5) to account for 5 signal averages
+
+split_for,0,n_elements(index)-1,nsplit = 8,command = [$
+'tag = ""',$
+'a = run_2CXM_phantom(snr_dyn = snr_dyn, snr_vfa = snr_vfa, T1_dataType = T1_dataType,model = model,multithreadindex = index[i],n_repeats = n_repeats,n_vox_fit = n_vox_fit)'],$
+varnames=['snr_dyn','snr_vfa','T1_datatype','model','index','n_repeats','n_vox_fit']
+
+end

Joint Fitting/expconvolution.pro

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+function ExpConvolution, l, X
+
+  n = n_elements(X)/2
+
+  T = X[0:n-1] ; T is the first half go the X array, i.e. the time points
+
+  A = X[n:*]   ; A is the second half of the X array i.e. the concentration values at each time point ; units of mM
+
+
+  DT = T[1:n-1]-T[0:n-2] ; This is an array of dt between time points
+  DA = A[1:n-1]-A[0:n-2] ; this is an array of da between conc values
+
+  Z = l*DT ;Z is an array of K*dt
+
+  E = exp(-Z); E is an array of  exponentials [exp-lDT0, exp-lDT1 etc
+  E0 = 1-E ; E0 is an array [(1-exp-lDT0), (1-exp-lDT1)
+  E1 = Z-E0
+
+  Il = (A[0:n-2]*E0 + DA*E1/Z)/l
+
+  Y = fltarr(n) ; Y is a double precision array with every element set to 0.0
+
+  for i=0L,n-2 do Y[i+1] = E[i]*Y[i] + Il[i]
+
+  return, Y
+
+end

Joint Fitting/flash_func.pro

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+pro Flash_func,FA2,p,data
+
+ COMMON fit_params, TR,rad_dyn,rad_vfa,Inv_times,r,T10_v,S0d,S0v,baseline,n_timepoints,AIF,adj_AIF
+ COMMON S0_info, equal_and_free, unequal_and_free, equal_by_baseline
+
+  T1 = p[1]
+  E0 = exp(-TR/T1)
+  S0 = p[0]
+
+  data = S0*((sin(FA2)*(1-E0))/(1- cos(FA2)*E0)); FLASH EQUATION
+
+end