1 / 12

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

nolen
Télécharger la présentation

DEMRI (Dynamic Contrast Enhanced MRI)

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related