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DEMRI (Dynamic Contrast Enhanced MRI)

DEMRI (Dynamic Contrast Enhanced MRI). Kinetic modeling. ARN volume- registered. Rat brain. Steps. Volume register Identify sagittal sinus ROI can calculate Mp(0) for first few TRs, Mp(t) Calculate Cp(t), Gd concentration in plasma, with non-negative constraint

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DEMRI (Dynamic Contrast Enhanced MRI)

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  1. DEMRI (Dynamic Contrast Enhanced MRI) Kinetic modeling

  2. ARN volume- registered

  3. Rat brain

  4. Steps • Volume register • Identify sagittal sinus ROI can calculate Mp(0) for first few TRs, Mp(t) • Calculate Cp(t), Gd concentration in plasma, with non-negative constraint • 3dAutomask to limit voxels to brain or specify ROI • Also normalize to ratio of first few TRs and limit voxels of interest to those that change by at least 10% over the average of last five time points • May want to separate blood and tissue with two ROIs to use a single intrinsic relaxivity at a time (Gyrus Finder Plug-in?) • 3dNLfim - calculate fit of Ktrans, kep, fpv given Cp(t), R1,I, TR to the normalized m(C,T) • m = f(C,R1,I), C=f(Ct,fpv,Cp(t)), Ct=f(Cp(t), ktrans, kep or Ve) • final fit parameters = Ktrans, kep, fpv for each voxel

  5. ----- HISTORY ----- =================================== === History of inputs to 3dcalc === === Input a: 3dvolreg -prefix barr_vr.nii BARR.nii === Input b: 3dvolreg -prefix barr_vr.nii BARR.nii 3dTstat -prefix barr_mean7.nii 'barr_vr.nii[0..6]' === Input c: 3dvolreg -prefix barr_vr.nii BARR.nii 3dTstat -prefix barr_mean7.nii 'barr_vr.nii[0..6]' 3dAutomask -prefix barr_mask barr_mean7.nii =================================== 3dcalc -a barr_vr.nii -b barr_mean7.nii -c barr_mask+orig -prefix barr_norm7m.nii -datum float -expr 'a*c/b' 3dNLfim -input barr_norm7m.nii -signal demri_3 -ignore 0 -noise Zero -sconstr 0 0 0.05 -sconstr 1 0 0.05 -nabs -mask barr_mask+orig -nrand 10000 -nbest 10 -voxel_count -sfit barr_sfit6 -jobs 2 -progress 10000 -bucket 0 nl6.out Output prefix: nl6.out

  6. 3dNLfim parameters cd afni_src ; make model_demri_3.so ; mv model_demri_3.so ~/abin setenv AFNI_MODEL_HELP_DEMRI_3 setenv AFNI_MODEL_D3_R1 4.8 setenv AFNI_MODEL_D3_RIB 1300ms setenv AFNI_MODEL_D3_RIT 800ms setenv AFNI_MODEL_D3_TR 7.6ms setenv AFNI_MODEL_D3_TF 20s setenv AFNI_MODEL_D3_THETA 30 setenv AFNI_MODEL_D3_MP_FILE barr_sagroionly.1D setenv AFNI_MODEL_D3_NFIRST 7 setenv AFNI_MODEL_D3_DEBUG 1 3dNLfim -input barr_norm7m.nii \ -signal demri_3 \ -ignore 0 \ -noise Zero \ -sconstr 0 0 0.05 \ -sconstr 1 0 0.05 \ -nabs \ -mask barr_mask+orig \ -nrand 10000 \ -nbest 10 \ -voxel_count \ -sfit barr_sfit9 \ -jobs 2 \ -progress 10000 \ -bucket 0 nl9.out

  7. Results Fit values (Simplex and Powell) Ktrans

  8. Results (cont.) ve kep fpv

  9. Discussion items: • R1,i - function of fpv? • ve - limits, constraints on ktrans, kep • Powell optimization constraints • Mask voxel thresholds • Zero noise model speed • automatic sagittal sinus TAC versus manual, 3dROIstats

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