#Get timepoints for SUVR window
startTime = timePred[np.where(petPredD > 10)[0][0]]
endTime = startTime + args.window[0]
suvrTime = np.linspace(startTime, endTime, 100)
#Get new basis
suvrBasis = nagini.rSplineBasis(suvrTime, petKnots)
#Get fits at each voxel
voxX, _, _, _ = np.linalg.lstsq(petBasis, petMasked.T)
#Get predictions at each voxel
voxPred = np.dot(suvrBasis, voxX)
#Get WB suvr image
voxSum = np.sum(voxPred, axis=0)
voxSum = voxSum / np.mean(voxSum)
#Write out image
nagini.writeMaskedImage(voxSum, mask.shape, maskData, pet.affine, pet.header,
'%s_suvrSpline' % (args.out[0]))
#For comparision calculate non-smoothed SUVR
startFrame = np.where(petTime >= startTime)[0][0]
endFrame = np.where(petTime <= endTime)[0][-1]
petSum = np.sum(petMasked[:, startFrame:(endFrame + 1)], axis=1)
petSum = petSum / np.mean(petSum)
nagini.writeMaskedImage(petSum, mask.shape, maskData, pet.affine, pet.header,
'%s_suvr' % (args.out[0]))
pet.affine,
header=pet.header)
#Then do the writing
try:
outImg.to_filename('%s.nii.gz' % (pName))
except (IOError):
print 'ERROR: Cannot save image at %s.' % (pName)
sys.exit()
#Write out root mean square images
nib.Nifti1Image(roiParams[:, -1], affine=np.identity(4)).to_filename(
'%s_%s.nii.gz' % (args.out[0], paramNames[-1]))
if args.noVox != 1:
nagini.writeMaskedImage(voxParams[:, -1], maskData.shape, maskData,
pet.affine, pet.header,
'%s_%s' % (args.out[0], paramNames[-1]))
#Write out chosen arguments
nagini.writeArgs(args, args.out[0])
#Convergence output
try:
#Open file
cOut = open('%s_convergence.txt' % (args.out[0]), "w")
#Write out ROI data
cOut.write('%i of %i\n' % (roiC, nRoi))
#Write out voxel data if necessary
if args.noVox != 1:
#Calculate residual with delay
fitResid = voxTac - voxFitted
#Calculate normalized root mean square deviation
fitRmsd = np.sqrt(np.sum(np.power(fitResid,2))/voxTac.shape[0]) / np.mean(voxTac)
#Save residual
fitParams[voxIdx,-1] = fitRmsd
except(RuntimeError,ValueError):
noC += 1
#Warn user about lack of convergence
if noC > 0:
print('Warning: %i of %i voxels did not converge.'%(noC,nVox))
#############
###Output!###
#############
print('Writing out results...')
#Set names for model images
paramNames = ['gef','kOne','kTwo','kThree','kFour','cmrGlu','alphaOne','alphaTwo','betaOne','betaTwo','netEx','influx','DV','conc','delay','nRmsd']
#Do the writing. For now, doesn't write variance images.
for iIdx in range(fitParams.shape[1]-1):
nagini.writeMaskedImage(fitParams[:,iIdx],maskData.shape,maskData,pet.affine,pet.header,'%s_%s'%(args.out[0],paramNames[iIdx]))
nagini.writeMaskedImage(fitParams[:,-1],maskData.shape,maskData,pet.affine,pet.header,'%s_%s'%(args.out[0],paramNames[-1]))
nagini.writeArgs(args,args.out[0])
#Set names for model images
if args.poly is True:
paramNames = ['CBF']
fitParams = voxCbf[:, np.newaxis]
else:
paramNames = wbLabels
if args.fModel != 1:
paramNames.remove('Dispersion')
paramNames.remove('Delay')
paramNames.append('nRmsd')
#Output images
for iIdx in range(fitParams.shape[1]):
nagini.writeMaskedImage(fitParams[:, iIdx], brainData.shape, brainData,
pet.affine, pet.header,
'%s_%s' % (args.out[0], paramNames[iIdx]))
#Compute extraction if necessary
if args.ps is not None:
if args.poly is True:
voxEx = voxCbf / cbfMasked
else:
voxEx = 1.0 - np.exp(fitParams[:, 0] / -cbfMasked)
nagini.writeMaskedImage(voxEx, brainData.shape, brainData, pet.affine,
pet.header, '%s_extraction' % (args.out[0]))
#Compute PSw if we used polynomial regression method
if args.poly is True:
voxPSw = -cbfMasked * np.log(1.0 - voxEx)
nagini.writeMaskedImage(voxPSw, brainData.shape, brainData, pet.affine,
fitParams[voxIdx,4] = ((voxFit[0][0]*cbfMasked[voxIdx]*voxFit[0][2])/(voxFit[0][1]+voxFit[0][2]))*gluScale
#Save parameter variances. Use delta method to get cmrGlu and k1 variance
fitParams[voxIdx,5:8] = np.diag(voxFit[1])
fitParams[voxIdx,8] = voxFit[1][0][0] * np.power(cbfMasked[voxIdx],2)
gluGrad = np.array([(gluScale*cbfMasked[voxIdx]*voxFit[0][2])/(voxFit[0][1]+voxFit[0][2]),
(-1*voxFit[0][0]*voxFit[0][2]*gluScale*cbfMasked[voxIdx])/np.power(voxFit[0][1]+voxFit[0][2],2),
(voxFit[0][0]*voxFit[0][1]*gluScale*cbfMasked[voxIdx])/np.power(voxFit[0][1]+voxFit[0][2],2)])
fitParams[voxIdx,9] = np.dot(np.dot(gluGrad.T,voxFit[1]),gluGrad)
#Get normalized root mean square deviation
fitResid = voxTac - voxFunc(fitX,voxFit[0][0],voxFit[0][1],voxFit[0][2])
fitRmsd = np.sqrt(np.sum(np.power(fitResid,2))/voxTac.shape[0])
fitParams[voxIdx,10] = fitRmsd / np.mean(voxTac)
except(RuntimeError):
noC += 1
#Warn user about lack of convergence
if noC > 0:
print('Warning: %i of %i voxels did not converge.'%(noC,nVox))
#############
###Output!###
#############
print('Writing out results...')
#Write out two parameter model images
for iIdx in range(len(imgNames)):
nagini.writeMaskedImage(fitParams[:,iIdx],brain.shape,brainData,pet.affine,pet.header,'%s_%s'%(args.out[0],imgNames[iIdx]))
cbfMasked[voxIdx]) / np.power(voxFit[0][1] + voxFit[0][2], 2),
(voxFit[0][0] * voxFit[0][1] * gluScale * cbfMasked[voxIdx]) /
np.power(voxFit[0][1] + voxFit[0][2], 2)
])
fitParams[voxIdx, 9] = np.dot(np.dot(gluGrad.T, voxFit[1]),
gluGrad)
#Get normalized root mean square deviation
fitResid = voxTac - voxFunc(fitX, voxFit[0][0], voxFit[0][1],
voxFit[0][2])
fitRmsd = np.sqrt(np.sum(np.power(fitResid, 2)) / voxTac.shape[0])
fitParams[voxIdx, 10] = fitRmsd / np.mean(voxTac)
except (RuntimeError):
noC += 1
#Warn user about lack of convergence
if noC > 0:
print('Warning: %i of %i voxels did not converge.' % (noC, nVox))
#############
###Output!###
#############
print('Writing out results...')
#Write out two parameter model images
for iIdx in range(len(imgNames)):
nagini.writeMaskedImage(fitParams[:, iIdx], brain.shape, brainData,
pet.affine, pet.header,
'%s_%s' % (args.out[0], imgNames[iIdx]))
endTime = startTime + args.window[0] suvrTime = np.linspace(startTime,endTime,100) #Get new basis suvrBasis = nagini.rSplineBasis(suvrTime,petKnots) #Get fits at each voxel voxX,_,_,_ = np.linalg.lstsq(petBasis,petMasked.T) #Get predictions at each voxel voxPred = np.dot(suvrBasis,voxX) #Get WB suvr image voxSum = np.sum(voxPred,axis=0); voxSum = voxSum / np.mean(voxSum) #Write out image nagini.writeMaskedImage(voxSum,mask.shape,maskData,pet.affine,pet.header,'%s_suvrSpline'%(args.out[0])) #For comparision calculate non-smoothed SUVR startFrame = np.where(petTime>=startTime)[0][0] endFrame = np.where(petTime<=endTime)[0][-1] petSum = np.sum(petMasked[:,startFrame:(endFrame+1)],axis=1) petSum = petSum / np.mean(petSum) nagini.writeMaskedImage(petSum,mask.shape,maskData,pet.affine,pet.header,'%s_suvr'%(args.out[0]))
#Write out polynomial matrix
np.savetxt('%s_polyMat.txt'%(args.out[0]),np.hstack((polyX,cbfPred[:,np.newaxis])))
#Polynomial regression coefficients
coefOut = open('%s_polyCoef.txt'%(args.out[0]), "w")
coefOut.write(coefString)
coefOut.close()
except(IOError):
print 'ERROR: Cannot write in output directory. Exiting...'
sys.exit()
#Don't do voxelwise estimation if user says not to
if args.wbOnly == 1:
sys.exit()
#Integrate all the pet data
petInt = np.trapz(petMasked,petTime,axis=1)
#Get matrix for flow predictions
petMat = np.stack((petInt,np.power(petInt,2)),axis=1)
#Get flow predictions at each voxel
petFlow = petMat.dot(polyCoef)
#Write out fow image
nagini.writeMaskedImage(petFlow,brain.shape,brainData,pet.affine,pet.header,'%s_flow'%(args.out[0]))
#Don't do voxelwise estimation if user says not to if args.wbOnly == 1: sys.exit() #Integreate pet tacs voxInt = np.trapz(petMasked,petTime,axis=1) #Create arrays for results voxOef = np.zeros_like(cbfMasked) voxOxy = np.zeros_like(cbfMasked) voxResid = np.zeros_like(cbfMasked) #Loop through voxels for voxIdx in tqdm(range(cbfMasked.shape[0])): #Make regressors for voxel voxX = ((1 - (0.835*cbfMasked[voxIdx]/lmbda))*cbfMasked[voxIdx]*aifOxyInt) - \ (0.835*cbvMasked[voxIdx]*aifOxyInterp) voxY = petMasked[voxIdx,:] + (cbfMasked[voxIdx]/lmbda*voxInt[voxIdx]) - (cbvMasked[voxIdx]*aifOxyInterp) \ - (cbvMasked[voxIdx]*cbvMasked[voxIdx]/lmbda*aifOxyInt) - (cbfMasked[voxIdx]*aifWaterInt) #Run voxelwise regression voxOef[voxIdx],voxResid[voxIdx] = opt.nnls(voxX[:,np.newaxis],voxY) #Get CMRO2 voxOxy[voxIdx] = voxOef[voxIdx] * cbfMasked[voxIdx] * oxyScale #Write out images nagini.writeMaskedImage(voxOef,brain.shape,brainData,pet.affine,pet.header,'%s_oefnn'%(args.out[0])) nagini.writeMaskedImage(voxOxy,brain.shape,brainData,pet.affine,pet.header,'%s_cmrOxynn'%(args.out[0]))
#Create aif figure
try:
plt.clf()
fig = plt.figure(1)
plt.scatter(aifTime, aifC, s=40, c="black")
plt.plot(aifTime,
np.dot(aifBasis, aifCoefs),
linewidth=5,
label='Spline Fit')
plt.xlabel('Time (seconds)')
plt.ylabel('Counts')
plt.title('Arterial Sampled Input function')
plt.legend(loc='upper right')
plt.suptitle(args.out[0])
plt.savefig('%s_aifPlot.jpeg' % (args.out[0]), bbox_inches='tight')
except (RuntimeError, IOError):
print 'ERROR: Could not save figure. Moving on...'
#Don't do voxelwise estimation if user says not to
if args.wbOnly == 1:
nagini.writeArgs(args, args.out[0])
sys.exit()
#Calculate voxelwise CBV
cbvData = petMasked * cbvScale
#Write out CBV image
nagini.writeMaskedImage(cbvData, brainData.shape, brainData, pet.affine,
pet.header, '%s_cbv' % (args.out[0]))
nagini.writeArgs(args, args.out[0])
#Write out polynomial matrix
np.savetxt('%s_polyMat.txt' % (args.out[0]),
np.hstack((polyX, cbfPred[:, np.newaxis])))
#Polynomial regression coefficients
coefOut = open('%s_polyCoef.txt' % (args.out[0]), "w")
coefOut.write(coefString)
coefOut.close()
except (IOError):
print 'ERROR: Cannot write in output directory. Exiting...'
sys.exit()
#Don't do voxelwise estimation if user says not to
if args.wbOnly == 1:
sys.exit()
#Integrate all the pet data
petInt = np.trapz(petMasked, petTime, axis=1)
#Get matrix for flow predictions
petMat = np.stack((petInt, np.power(petInt, 2)), axis=1)
#Get flow predictions at each voxel
petFlow = petMat.dot(polyCoef)
#Write out fow image
nagini.writeMaskedImage(petFlow, brain.shape, brainData, pet.affine,
pet.header, '%s_flow' % (args.out[0]))
#Load image headers pet = nagini.loadHeader(args.pet[0]) brain = nagini.loadHeader(args.brain[0]) #Check to make sure image dimensions match if pet.shape[0:3] != brain.shape[0:3]: print 'ERROR: Image dimensions do not match. Please check data...' sys.exit() #Get the image data petData = pet.get_data() brainData = brain.get_data() #Load in the idaif. idaif = nagini.loadIdaif(args.idaif[0]) #Flatten the PET images and then mask petMasked = petData.flatten()[brainData.flatten()>0] ############ ###Output### ############ #Calculate CBV in mL/hG cbvData = (petMasked * 100.0 ) / (args.r*args.d*idaif) #Write out CBV image nagini.writeMaskedImage(cbvData,brain.shape,brainData,pet.affine,pet.header,'%s_cbv'%(args.out[0]))
sys.exit()
#Integreate pet tacs
voxInt = np.trapz(petMasked, petTime, axis=1)
#Create arrays for results
voxOef = np.zeros_like(cbfMasked)
voxOxy = np.zeros_like(cbfMasked)
voxResid = np.zeros_like(cbfMasked)
#Loop through voxels
for voxIdx in tqdm(range(cbfMasked.shape[0])):
#Make regressors for voxel
voxX = ((1 - (0.835*cbfMasked[voxIdx]/lmbda))*cbfMasked[voxIdx]*aifOxyInt) - \
(0.835*cbvMasked[voxIdx]*aifOxyInterp)
voxY = petMasked[voxIdx,:] + (cbfMasked[voxIdx]/lmbda*voxInt[voxIdx]) - (cbvMasked[voxIdx]*aifOxyInterp) \
- (cbvMasked[voxIdx]*cbvMasked[voxIdx]/lmbda*aifOxyInt) - (cbfMasked[voxIdx]*aifWaterInt)
#Run voxelwise regression
voxOef[voxIdx], voxResid[voxIdx] = opt.nnls(voxX[:, np.newaxis], voxY)
#Get CMRO2
voxOxy[voxIdx] = voxOef[voxIdx] * cbfMasked[voxIdx] * oxyScale
#Write out images
nagini.writeMaskedImage(voxOef, brain.shape, brainData, pet.affine, pet.header,
'%s_oefnn' % (args.out[0]))
nagini.writeMaskedImage(voxOxy, brain.shape, brainData, pet.affine, pet.header,
'%s_cmrOxynn' % (args.out[0]))