diff --git a/snmFigs.m b/snmFigs.m
new file mode 100644
index 0000000..f120b1f
--- /dev/null
+++ b/snmFigs.m
@@ -0,0 +1,585 @@
+%% SNM Talk:
+close all
+avc = '/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_snm_avc/';
+thal = '/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_snm_thal/';
+
+close all
+hf = figure;
+xSi = 10;
+ySi = 7;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 10;
+mSize = 2;
+lWidth = 1.5;
+
+% ax1
+% do avc mean
+load([avc 'svca4_snm_avc.mat'])
+plot(svca4.PET_standardEndTimes,nanmean(squeeze(svca4.classes_it00(svca4.GMWM_sel,1,:))),'-d','LineWidth',lWidth,'color', [0.9290    0.6940    0.1250]); hold on
+plot(svca4.PET_standardEndTimes,nanmean(squeeze(svca4.classes_it00(svca4.GMWM_sel,2,:))),'-s','LineWidth',lWidth,'MarkerFaceColor',[0    0.4470    0.7410],'color', [0    0.4470    0.7410])
+plot(svca4.PET_standardEndTimes,nanmean(squeeze(svca4.classes_it00(svca4.BLOOD_sel,3,:))),'-x','LineWidth',lWidth,'color', [0.8500    0.150    0.0980])
+plot(svca4.PET_standardEndTimes,nanmean(squeeze(svca4.classes_it00(svca4.TSPO_sel,4,:))),'-^','LineWidth',lWidth,'MarkerFaceColor',[0.4940    0.1840    0.5560],'color', [0.4940    0.1840    0.5560])
+
+% do thal
+load([thal 'svca4_snm_thal.mat'])
+plot(svca4.PET_standardEndTimes,nanmean(squeeze(svca4.classes_it00(svca4.TSPO_sel,4,:))),'-o','LineWidth',lWidth,'MarkerFaceColor',[0.4660    0.6740    0.1880],'color', [0.4660    0.6740    0.1880])
+ylim([-1 8])
+xlim([0 3600])
+
+set(findall(gcf,'type','line'),'MarkerSize',mSize)
+hl = legend('Grey','White','Blood','HSB-Stroke','HSB-Thalamus');
+set(hl,'box','off')
+
+xlabel('Time after injection (sec)')
+ylabel('normalized Bq/cc')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+set(gca,'box','off')
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/classes.png')
+
+%%
+close all
+meanTACs = '/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/';
+avc = '/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/';
+thal = '/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_thals/';
+
+cereb = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/mean_CB_GM.txt');
+thal = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/thal_mean_svcaRef_G0.00W1.00B1.00T1.00.txt');
+thal_q = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/thal_q_mean_svcaRef_G0.05W0.05B0.05T0.05.txt');
+avc = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/avc_mean_svcaRef_G0.00W1.00B1.00T1.00.txt');
+avc_q = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/avc_q_mean_svcaRef_G0.05W0.05B0.05T0.05.txt');
+noCB_thal_q = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/thal_q_mean_noCB_svcaRef_G0.05W0.05B0.05T0.05.txt');
+noCB_avc_q = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/avc_q_mean_noCB_svcaRef_G0.05W0.05B0.05T0.05.txt');
+noCB_thal = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/thal_mean_noCB_svcaRef_G0.00W1.00B1.00T1.00.txt');
+noCB_avc = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/FigureTACs/avc_mean_noCB_svcaRef_G0.00W1.00B1.00T1.00.txt');
+
+close all
+hf = figure;
+xSi = 10;
+ySi = 7;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 10;
+mSize = 2;
+lWidth = 1.5;
+
+plot(cereb.end_seconds_,cereb.TAC_1_1_,'LineWidth',lWidth,'color',[0.4660    0.6740    0.1880]);hold on
+plot(thal.end_seconds_,thal.TAC_1_1_,'LineWidth',lWidth,'color',[0    0.4470    0.7410]);hold on
+plot(avc.end_seconds_,avc.TAC_1_1_,'LineWidth',lWidth,'color',[0.9290    0.6940    0.1250]);hold on
+
+xlim([0 3600])
+
+xlabel('Time after injection (sec)')
+ylabel('Bq/cc')
+set(gca,'box','off')
+
+hh = legend('Cerebellum','svca_HSB-thalamus','svca_HSB-stroke');
+set(hh,'box','off','Interpreter', 'none','Location','south')
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/thalVavc.png')
+
+%% with the no CB as well
+close all
+hf = figure;
+xSi = 10;
+ySi = 7;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 10;
+mSize = 2;
+lWidth = 1.5;
+
+plot(cereb.end_seconds_,cereb.TAC_1_1_,'LineWidth',lWidth,'color',[0.4660    0.6740    0.1880]);hold on
+plot(thal.end_seconds_,thal.TAC_1_1_,'LineWidth',lWidth,'color',[0    0.4470    0.7410]);hold on
+plot(noCB_thal.end_seconds_,noCB_thal.TAC_1_1_,'--','LineWidth',lWidth,'color',[0    0.4470    0.7410]);hold on
+
+plot(avc.end_seconds_,avc.TAC_1_1_,'LineWidth',lWidth,'color',[0.9290    0.6940    0.1250]);hold on
+plot(noCB_avc.end_seconds_,noCB_avc.TAC_1_1_,'--','LineWidth',lWidth,'color',[0.9290    0.6940    0.1250]);hold on
+
+xlim([0 3600])
+
+xlabel('Time after injection (sec)')
+ylabel('Bq/cc')
+set(gca,'box','off')
+
+hh = legend('Cerebellum','svca_HSB-thalamus','svca_HSB-thalamus_noCerebellum','svca_HSB-stroke','svca_HSB-stroke_noCerebellum');
+set(hh,'box','off','Interpreter', 'none','Location','south')
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/cbVnocb.png')
+
+%% with quantiles
+close all
+hf = figure;
+xSi = 10;
+ySi = 8;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 10;
+mSize = 2;
+lWidth = 1.5;
+
+plot(cereb.end_seconds_,cereb.TAC_1_1_,'LineWidth',lWidth,'color',[0.4660    0.6740    0.1880]);hold on
+plot(thal.end_seconds_,thal.TAC_1_1_,'LineWidth',lWidth,'color',[0    0.4470    0.7410]);hold on
+plot(thal_q.end_seconds_,thal_q.TAC_1_1_,'--','LineWidth',lWidth,'color',[0    0.4470    0.7410]);hold on
+
+plot(avc.end_seconds_,avc.TAC_1_1_,'LineWidth',lWidth,'color',[0.9290    0.6940    0.1250]);hold on
+plot(avc_q.end_seconds_,avc_q.TAC_1_1_,'--','LineWidth',lWidth,'color',[0.9290    0.6940    0.1250]);hold on
+
+xlim([0 3600])
+
+xlabel('Time after injection (sec)')
+ylabel('Bq/cc')
+set(gca,'box','off')
+
+hh = legend('Cerebellum','svca_HSB-thalamus','svca_HSB-thalamus_quantiles','svca_HSB-stroke','svca_HSB-stroke_quantiles');
+set(hh,'box','off','Interpreter', 'none','Location','south')
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/quantiles.png')
+
+
+%%
+% define the lobes
+%%%% Compare noCB to CB models %%%
+cd('/Users/scott/Dropbox/Experiments/nideco/NIDECO/quantification')
+% load stroke HSB model with and without CB
+stroke = load('svca_strokeSRTM2.mat','bpTable');
+stroke_nC = load('svca_stroke_noCBSRTM2.mat','bpTable');
+stroke_q = load('svca_stroke_qSRTM2.mat','bpTable');
+cereb = load('cerebellumSRTM2.mat','bpTable');
+clear bpTable
+
+% load thalamus HSB model with and without CB
+thal = load('svca_thalamusSRTM2.mat','bpTable');
+thal_nC = load('svca_thalamus_noCBSRTM2.mat','bpTable');
+clear bpTable
+
+lobes.stroke = svca4_lobeBP(stroke.bpTable);
+lobes.stroke_nC = svca4_lobeBP(stroke_nC.bpTable);
+lobes.stroke_q = svca4_lobeBP(stroke_q.bpTable);
+lobes.thal = svca4_lobeBP(thal.bpTable);
+lobes.thal_nC = svca4_lobeBP(thal_nC.bpTable);
+lobes.cereb = svca4_lobeBP(cereb.bpTable);
+
+
+%%% average across hemisphere and get correlation between with and without CB
+%%% HSB-stroke %%%
+% for stroke_thal
+stroke.thalamus = mean([stroke.bpTable.Left_Thalamus_Proper stroke.bpTable.Right_Thalamus_Proper],2);
+stroke_nC.thalamus = mean([stroke_nC.bpTable.Left_Thalamus_Proper stroke_nC.bpTable.Right_Thalamus_Proper],2);
+[R.stroke.thal,P.stroke.thal,RL.stroke.thal,RU.stroke.thal] = corrcoef(stroke.thalamus,stroke_nC.thalamus);
+% for stroke_putamen
+stroke.putamen = mean([stroke.bpTable.Left_Putamen stroke.bpTable.Right_Putamen],2);
+stroke_nC.putamen = mean([stroke_nC.bpTable.Left_Putamen stroke_nC.bpTable.Right_Putamen],2);
+[R.stroke.putamen,P.stroke.putamen,RL.stroke.putamen,RU.stroke.putamen] = corrcoef(stroke.putamen,stroke_nC.putamen);
+% for stroke_caudate
+stroke.caudate = mean([stroke.bpTable.Left_Caudate stroke.bpTable.Right_Caudate],2);
+stroke_nC.caudate = mean([stroke_nC.bpTable.Left_Caudate stroke_nC.bpTable.Right_Caudate],2);
+[R.stroke.caudate,P.stroke.caudate,RL.stroke.caudate,RU.stroke.caudate] = corrcoef(stroke.caudate,stroke_nC.caudate);
+% for stroke_hippo
+stroke.hippo = mean([stroke.bpTable.Left_Hippocampus stroke.bpTable.Right_Hippocampus],2);
+stroke_nC.hippo = mean([stroke_nC.bpTable.Left_Hippocampus stroke_nC.bpTable.Right_Hippocampus],2);
+[R.stroke.hippo,P.stroke.hippo,RL.stroke.hippo,RU.stroke.hippo] = corrcoef(stroke.hippo,stroke_nC.hippo);
+% for stroke_whiteMatter
+stroke.white = mean([stroke.bpTable.Left_Cerebral_White_Matter stroke.bpTable.Right_Cerebral_White_Matter],2);
+stroke_nC.white = mean([stroke_nC.bpTable.Left_Cerebral_White_Matter stroke_nC.bpTable.Right_Cerebral_White_Matter],2);
+[R.stroke.white,P.stroke.white,RL.stroke.white,RU.stroke.white] = corrcoef(stroke.white,stroke_nC.white);
+% for stroke_cerebellum
+stroke.cerebellum = mean([stroke.bpTable.Left_Cerebellum_Cortex stroke.bpTable.Right_Cerebellum_Cortex],2);
+stroke_nC.cerebellum = mean([stroke_nC.bpTable.Left_Cerebellum_Cortex stroke_nC.bpTable.Right_Cerebellum_Cortex],2);
+[R.stroke.cerebellum,P.stroke.cerebellum,RL.stroke.cerebellum,RU.stroke.cerebellum] = corrcoef(stroke.cerebellum,stroke_nC.cerebellum);
+
+[R.stroke.frontal,P.stroke.frontal,RL.stroke.frontal,RU.stroke.frontal] = corrcoef(lobes.stroke.frontal,lobes.stroke_nC.frontal);
+[R.stroke.parietal,P.stroke.parietal,RL.stroke.parietal,RU.stroke.parietal] = corrcoef(lobes.stroke.parietal,lobes.stroke_nC.parietal);
+[R.stroke.temporal,P.stroke.temporal,RL.stroke.temporal,RU.stroke.temporal] = corrcoef(lobes.stroke.temporal,lobes.stroke_nC.temporal);
+[R.stroke.occipital,P.stroke.occipital,RL.stroke.occipital,RU.stroke.occipital] = corrcoef(lobes.stroke.occipital,lobes.stroke_nC.occipital);
+
+%%% HSB-thalamus %%%
+% for thal_thal
+thal.thalamus = mean([thal.bpTable.Left_Thalamus_Proper thal.bpTable.Right_Thalamus_Proper],2);
+thal_nC.thalamus = mean([thal_nC.bpTable.Left_Thalamus_Proper thal_nC.bpTable.Right_Thalamus_Proper],2);
+[R.thal.thal,P.thal.thal,RL.thal.thal,RU.thal.thal] = corrcoef(thal.thalamus,thal_nC.thalamus);
+% for thal_putamen
+thal.putamen = mean([thal.bpTable.Left_Putamen thal.bpTable.Right_Putamen],2);
+thal_nC.putamen = mean([thal_nC.bpTable.Left_Putamen thal_nC.bpTable.Right_Putamen],2);
+[R.thal.putamen,P.thal.putamen,RL.thal.putamen,RU.thal.putamen] = corrcoef(thal.putamen,thal_nC.putamen);
+% for thal_caudate
+thal.caudate = mean([thal.bpTable.Left_Caudate thal.bpTable.Right_Caudate],2);
+thal_nC.caudate = mean([thal_nC.bpTable.Left_Caudate thal_nC.bpTable.Right_Caudate],2);
+[R.thal.caudate,P.thal.caudate,RL.thal.caudate,RU.thal.caudate] = corrcoef(thal.caudate,thal_nC.caudate);
+% for thal_hippo
+thal.hippo = mean([thal.bpTable.Left_Hippocampus thal.bpTable.Right_Hippocampus],2);
+thal_nC.hippo = mean([thal_nC.bpTable.Left_Hippocampus thal_nC.bpTable.Right_Hippocampus],2);
+[R.thal.hippo,P.thal.hippo,RL.thal.hippo,RU.thal.hippo] = corrcoef(thal.hippo,thal_nC.hippo);
+% for thal_whiteMatter
+thal.white = mean([thal.bpTable.Left_Cerebral_White_Matter thal.bpTable.Right_Cerebral_White_Matter],2);
+thal_nC.white = mean([thal_nC.bpTable.Left_Cerebral_White_Matter thal_nC.bpTable.Right_Cerebral_White_Matter],2);
+[R.thal.white,P.thal.white,RL.thal.white,RU.thal.white] = corrcoef(thal.white,thal_nC.white);
+% for thal_cerebellum
+thal.cerebellum = mean([thal.bpTable.Left_Cerebellum_Cortex thal.bpTable.Right_Cerebellum_Cortex],2);
+thal_nC.cerebellum = mean([thal_nC.bpTable.Left_Cerebellum_Cortex thal_nC.bpTable.Right_Cerebellum_Cortex],2);
+[R.thal.cerebellum,P.thal.cerebellum,RL.thal.cerebellum,RU.thal.cerebellum] = corrcoef(thal.cerebellum,thal_nC.cerebellum);
+
+[R.thal.frontal,P.thal.frontal,RL.thal.frontal,RU.thal.frontal] = corrcoef(lobes.thal.frontal,lobes.thal_nC.frontal);
+[R.thal.parietal,P.thal.parietal,RL.thal.parietal,RU.thal.parietal] = corrcoef(lobes.thal.parietal,lobes.thal_nC.parietal);
+[R.thal.temporal,P.thal.temporal,RL.thal.temporal,RU.thal.temporal] = corrcoef(lobes.thal.temporal,lobes.thal_nC.temporal);
+[R.thal.occipital,P.thal.occipital,RL.thal.occipital,RU.thal.occipital] = corrcoef(lobes.thal.occipital,lobes.thal_nC.occipital);
+
+% thal vs avc
+[R.avcVsthal.thal,P.avcVsthal.thal,RL.avcVsthal.thal,RU.avcVsthal.thal] = corrcoef(stroke.thalamus,thal.thalamus);
+
+cereb.thalamus = mean([cereb.bpTable.Left_Thalamus_Proper cereb.bpTable.Right_Thalamus_Proper],2);
+cereb.putamen = mean([cereb.bpTable.Left_Putamen cereb.bpTable.Right_Putamen],2);
+cereb.hippo = mean([cereb.bpTable.Left_Hippocampus cereb.bpTable.Right_Hippocampus],2);
+cereb.caudate = mean([cereb.bpTable.Left_Caudate cereb.bpTable.Right_Caudate],2);
+
+
+%%
+close all
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(stroke.thalamus(1:8),thal.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke.thalamus(9:10),thal.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+ylabel('BP for HSB-thalamus')
+xlabel('BP for HSB-stroke')
+title('Thalamus')
+[r,p] = corrcoef(stroke.thalamus,thal.thalamus);
+text(.04,.92,'r = .98, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.stroke.temporal(1:8),lobes.thal.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.stroke.temporal(9:10),lobes.thal.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-stroke')
+title('Temporal')
+[r,p] = corrcoef(lobes.stroke.temporal,lobes.thal.temporal);
+text(.04,.55,'r = .94, p = .0001')
+
+subplot(1,3,3)
+plot(stroke.putamen(1:8),thal.putamen(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke.putamen(9:10),thal.putamen(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-stroke')
+title('Putamen')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+[r,p] = corrcoef(stroke.putamen,thal.putamen);
+
+text(.04,.55,'r = .87, p = .0001')
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_thalVSavc.png')
+
+%% cereb no cereb
+close all
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(stroke_nC.thalamus(1:8),stroke.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke_nC.thalamus(9:10),stroke.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+ylabel('BP for HSB-stroke_noCerebellum','Interpreter','none')
+title('Thalamus')
+[r,p] = corrcoef(stroke.thalamus,stroke_nC.thalamus);
+text(.04,.92,'r = .99, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.stroke_nC.temporal(1:8),lobes.stroke.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.stroke_nC.temporal(9:10),lobes.stroke.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+%ylabel('BP for HSB-stroke_noCerebellum','Interpreter','none')
+title('Temporal')
+[r,p] = corrcoef(lobes.stroke.temporal,lobes.stroke_nC.temporal);
+text(.04,.92,'r = .99, p = .0001')
+
+subplot(1,3,3)
+plot(stroke_nC.putamen(1:8),stroke.putamen(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke_nC.putamen(9:10),stroke.putamen(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+%ylabel('BP for HSB-stroke_noCerebellum','Interpreter','none')
+title('Putamen')
+[r,p] = corrcoef(lobes.stroke.temporal,lobes.stroke_nC.temporal);
+text(.04,.92,'r = .99, p = .0001')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_cbVnocb.png')
+
+%% cereb no cereb thal
+close all
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(thal_nC.thalamus(1:8),thal.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(thal_nC.thalamus(9:10),thal.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-thalamus')
+ylabel('BP for HSB-thalamus_noCerebellum','Interpreter','none')
+title('Thalamus')
+[r,p] = corrcoef(thal_nC.thalamus,thal.thalamus);
+text(.04,.92,'r = .99, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.thal_nC.temporal(1:8),lobes.thal.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.thal_nC.temporal(9:10),lobes.thal.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-thalamus')
+%ylabel('BP for HSB-stroke_noCerebellum','Interpreter','none')
+title('Temporal')
+[r,p] = corrcoef(lobes.thal.temporal,lobes.thal_nC.temporal);
+text(.04,.92,'r = .99, p = .0001')
+
+subplot(1,3,3)
+plot(thal_nC.putamen(1:8),thal.putamen(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(thal_nC.putamen(9:10),thal.putamen(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-thalamus')
+%ylabel('BP for HSB-stroke_noCerebellum','Interpreter','none')
+title('Putamen')
+[r,p] = corrcoef(lobes.thal_nC.temporal,lobes.thal.temporal);
+text(.04,.92,'r = .99, p = .0001')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_cbVnocbTHAL.png')
+
+%% quant no quant
+close all
+
+stroke_q.thalamus= mean([stroke_q.bpTable.Left_Thalamus_Proper stroke_q.bpTable.Right_Thalamus_Proper],2);
+stroke_q.putamen = mean([stroke_q.bpTable.Left_Putamen stroke_q.bpTable.Right_Putamen],2);
+
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(stroke_q.thalamus(1:8),stroke.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke_q.thalamus(9:10),stroke.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+ylabel('BP for HSB-stroke_quantiles','Interpreter','none')
+title('Thalamus')
+[r,p] = corrcoef(stroke.thalamus,stroke_q.thalamus);
+text(.04,.92,'r = .97, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.stroke_q.temporal(1:8),lobes.stroke.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.stroke_q.temporal(9:10),lobes.stroke.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+ylabel('BP for HSB-stroke_quantiles','Interpreter','none')
+title('Temporal')
+[r,p] = corrcoef(lobes.stroke.temporal,lobes.stroke_q.temporal);
+text(.04,.92,'r = .85, p = .0015')
+
+subplot(1,3,3)
+plot(stroke_q.putamen(1:8),stroke.putamen(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke_q.putamen(9:10),stroke.putamen(9:10),'k+','markersize',mSize); hold on
+axis([0 1 0 1])
+xlabel('BP for HSB-Stroke')
+ylabel('BP for HSB-stroke_quantiles','Interpreter','none')
+title('Putamen')
+[r,p] = corrcoef(stroke_q.putamen,stroke.putamen);
+text(.04,.92,'r = .48, p = .1')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_quants.png')
+
+%%
+close all
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(stroke.thalamus(1:8),cereb.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke.thalamus(9:10),cereb.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+ylabel('BP for Cerebellum')
+xlabel('BP for HSB-stroke')
+title('Thalamus')
+[r,p] = corrcoef(stroke.thalamus,cereb.thalamus);
+text(.04,.92,'r = .96, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.stroke.temporal(1:8),lobes.cereb.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.stroke.temporal(9:10),lobes.cereb.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-stroke')
+title('Temporal')
+[r,p] = corrcoef(lobes.stroke.temporal,lobes.cereb.temporal);
+text(.04,.55,'r = .94, p = .0001')
+
+subplot(1,3,3)
+plot(stroke.caudate(1:8),cereb.caudate(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(stroke.caudate(9:10),cereb.caudate(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-stroke')
+title('Putamen')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+[r,p] = corrcoef(stroke.caudate,cereb.caudate);
+
+text(.04,.275,'r = .93, p = .0001')
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_cerebVavc.png')
+
+%%
+close all
+% plot
+hf = figure;
+xSi = 15;
+ySi = 5;
+linWidth = 2;
+set(hf,'color','w',...
+    'PaperUnits','centimeters',...
+    'paperpositionmode','manual',...
+    'paperposition',[0 0 xSi ySi],...
+    'papersize',[xSi ySi])
+
+fSize = 6;
+mSize = 3.5;
+lWidth = 0.8;
+
+set(gcf,'color','w')
+subplot(1,3,1)
+plot(thal.thalamus(1:8),cereb.thalamus(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(thal.thalamus(9:10),cereb.thalamus(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+ylabel('BP for Cerebellum')
+xlabel('BP for HSB-thalamus')
+title('Thalamus')
+[r,p] = corrcoef(thal.thalamus,cereb.thalamus);
+text(.04,.92,'r = .96, p = .0001')
+
+subplot(1,3,2)
+plot(lobes.thal.temporal(1:8),lobes.cereb.temporal(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(lobes.thal.temporal(9:10),lobes.cereb.temporal(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-thalamus')
+title('Temporal')
+[r,p] = corrcoef(lobes.thal.temporal,lobes.cereb.temporal);
+text(.04,.275,'r = .94, p = .0001')
+
+subplot(1,3,3)
+plot(thal.putamen(1:8),cereb.putamen(1:8),'o','markersize',mSize,'MarkerFaceColor','b'); hold on
+set(gca,'ColorOrderIndex',1);
+plot(thal.putamen(9:10),cereb.putamen(9:10),'k+','markersize',mSize); hold on
+axis([0 max(axis) 0 max(axis)])
+%ylabel('HSB-thalamus')
+xlabel('BP for HSB-thalamus')
+title('Putamen')
+set(findall(gcf,'type','axes'),'FontSize',fSize)
+
+[r,p] = corrcoef(thal.putamen,cereb.putamen);
+
+text(.04,.275,'r = .72, p = .021')
+
+print(gcf,'-dpng', '-r1500','/Users/scott/GoogleDrive/pet_avc/snmmi_2017/snmTalk/BP_cerebVthal.png')
diff --git a/test.m b/test.m
new file mode 100644
index 0000000..3aed8e2
--- /dev/null
+++ b/test.m
@@ -0,0 +1,43 @@
+clear all
+close all
+clc
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+refTAC = readtable('/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_thals/TACs/02_02_CB_GM.txt');
+
+%pet = load_untouch_nii('/Users/scott/Dropbox/Experiments/nideco/NIDECO/data_pet/02_02_pet_flip.nii');
+pet = load_nii('/Users/scott/Dropbox/Experiments/nideco/NIDECO/data_pet/02_02_nifti_from_dicom_PMOD.nii');
+PET = pet.img;
+
+PET(10:20,10:20,10:20,:) = repmat(reshape(refTAC.TAC_kBq_cc_,1,1,1,31),11,11,11,1);
+pet.img = PET;
+save_nii(pet,'/Users/scott/Dropbox/Experiments/nideco/NIDECO/data_pet/02_02_nifti_from_dicom_PMOD_resaved.nii')
+
+
+pet_un = load_nii('/Users/scott/Dropbox/Experiments/nideco/NIDECO/data_pet/02_02_nifti_from_dicom_PMOD_resaved.nii');
+PET = single(pet.img);
+
+out = [refTAC.TAC_kBq_cc_...
+       refTAC.TAC_kBq_cc_.*pet_un.hdr.dime.scl_slope...
+       squeeze(pet_un.img(15,15,15,:))...
+       squeeze(pet_un.img(15,15,15,:)).*pet_un.hdr.dime.scl_slope]
+%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+scottWeights = load_untouch_nii('/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_thals_pmod/weights/01_08_GRAY_it00.nii');
+[im_TEP,TEPinfos]=gtiminterfileread('/Users/scott/Dropbox/Experiments/nideco/NIDECO/data_interfile/SVCA_map_grey_s01.hdr');
+
+close all
+figure; imagesc(squeeze(scottWeights.img(end:-1:1,end:-1:1,45)))
+figure; imagesc(squeeze(im_TEP(:,:,45)))
+
+sMean = mean(scottWeights.img(scottWeights.img ~= 0))
+sSTD = std(scottWeights.img(scottWeights.img ~= 0))
+
+cMean = mean(im_TEP(im_TEP ~= 0))
+cSTD = std(im_TEP(im_TEP ~= 0))
+
+diff = squeeze(scottWeights.img(end:-1:1,end:-1:1,:))-squeeze(im_TEP(:,:,:));
+
+[min(diff(:)) mean(diff(:)) max(diff(:)) std(diff(:))]
+
+[min(unique(squeeze(scottWeights.img(end:-1:1,end:-1:1,:))-squeeze(im_TEP(:,:,:)))) max(unique(squeeze(scottWeights.img(end:-1:1,end:-1:1,:))-squeeze(im_TEP(:,:,:))))]