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• 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

====================================== History of inputs to 3dcalc ====== Input a:3dvolreg -prefix barr_vr.nii BARR.nii=== Input b:3dvolreg -prefix barr_vr.nii BARR.nii3dTstat -prefix barr_mean7.nii 'barr_vr.nii[0..6]'=== Input c:3dvolreg -prefix barr_vr.nii BARR.nii3dTstat -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.outOutput prefix: nl6.out

----- HISTORY -----

cd afni_src ; make model_demri_3.so ; mv model_demri_3.so ~/abin

setenv AFNI_MODEL_HELP_DEMRI_3setenv AFNI_MODEL_D3_R1 4.8setenv AFNI_MODEL_D3_RIB 1300mssetenv AFNI_MODEL_D3_RIT 800mssetenv AFNI_MODEL_D3_TR 7.6mssetenv AFNI_MODEL_D3_TF 20ssetenv AFNI_MODEL_D3_THETA 30setenv AFNI_MODEL_D3_MP_FILE barr_sagroionly.1Dsetenv AFNI_MODEL_D3_NFIRST 7setenv 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

3dNLfim parameters

Ktrans

Fit values

(Simplex and Powell)

Results

Results (cont.)

kep fpvve

•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

Discussion items: