GLCM_analysis

GLCM_analysis/Zhang_feature.m

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+clc;clear all;close all;
+load D:\ZCL\课题-纹理特征\codes\codes\select_feature.mat;
+load D:\ZCL\课题-纹理特征\codes\codes\selectROI.mat;
+load D:\ZCL\课题-纹理特征\codes\codes\method.mat;
+path = 'D:\ZCL\课题-纹理特征\graymatrixdata\graymatrixdata\original_excel_data\NC';
+cd(path);
+method(4)={'Trace'};
+savemat = zeros(17,231);
+savemat(2:17,1)=1:16;
+num = 1;
+for i = 1:4
+    cd(char(method(i)));                  %进入第i个方法
+    for j = 1:23                    %23个区域
+        for k =1:10
+           %savemat(1,k*j+1)=char(select_feature(k));
+           savemat(2:17,num+1)=xlsread (char(strcat(roi(j),'.xlsx')),char(strcat(select_feature(k))),'A21:A36');
+           num=num+1;
+        end
+    end
+    save savemat
+    cd (path);                      %返回目录
+end

GLCM_analysis/codes/codes/AD_ROI.txt

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+Hippocampus 75 76 282 284
+splenium of corpus callosum 127 128
+Genu of corpus callosum left 123 124
+Parietal_R 24 28 30 32 34
+Temporal_L 35 37 39 41 43
+Occipital_L 51 53 55 57 59
+Occipital_R 52 54 56 58 60
+Insula_L 71
+Insula_R 72
+GP_L globus pallidus left 81
+Thalamus_L 83
+Thalamus_R 84
+FrontalLateralVentricle_L 171
+PosteriorLateralVentricle_L 173 174
+InferiorLateralVentricle_R 180
+FrontalLateralVentricle_R 176
+PosteriorLateralVentricle_R 178 179
+PeripheralFrontalWM_L 186 188 190 192 194 196 198 200 202 204 206 210
+PeripheralFrontalWM_R 187 189 191 193 195 197 199 201 203 205 207 211
+PeripheralParietalWM_L 155 208 212 214 216 218
+PeripheralParietalWM_R 156 209 213 215 217 219
+PeripheralTemporalWM_L 220 222 224 226 228 230
+ALIC 131 132
+PLIC 133 134
+Caud 77 78
+Thal 83 84
+Ventrical 171 172 173 174 175 176 177 178 179 180 181 285 286

GLCM_analysis/codes/codes/AD_T1_JHU_extractROI.m

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+clc;
+clear;
+[hdr,filetype,fileprefix,machine] = load_nii_hdr('E:\biomedical signal\0306_atlas_DICE\286L\a13_800001NC_286L.hdr');
+[seg,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+seg=double(seg);
+[a,b,c]=size(seg);
+slice=34;
+loc=find(seg==83|seg==84);
+volume=numel(loc);
+mask=zeros(a,b,c);
+mask(loc)=1;

GLCM_analysis/codes/codes/Analysis_seg.m

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+clc;
+clear;
+
+
+addpath('D:\JHU_AD\codes\functions');
+s01='800070';
+s02='061114';
+s1=['D:\JHU_AD\AD\',s01,'_',s02,'\T1_T2_DTI_ResampledImage_InSameSpace'];
+path0=strcat('D:\JHU_AD\AD\',s01,'_',s02,'\Result',s01,'\output\MNI_Shifted_Rotated_Axial_',s01,'_',s02,'_T1_brainmask_286Labels.hdr');
+path1=strcat(s1,'\affine_MD.hdr');
+path2=strcat(s1,'\affine_B0.hdr');
+path3=strcat(s1,'\affine_FA.hdr');
+path4=strcat(s1,'\affine_TRACE.hdr');
+
+
+source=('D:\JHU_AD\codes\ventricle2');
+destination=strcat('D:\JHU_AD\analysis\',s01,'AD\');
+
+
+[hdr,filetype,fileprefix,machine] = load_nii_hdr(path0);
+[seg,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+[hdr,filetype,fileprefix,machine] = load_nii_hdr(path1);
+[MD,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+[hdr,filetype,fileprefix,machine] = load_nii_hdr(path2);
+[B0,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+[hdr,filetype,fileprefix,machine] = load_nii_hdr(path3);
+[FA,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+[hdr,filetype,fileprefix,machine] = load_nii_hdr(path4);
+[TRACE,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+seg=double(seg);
+MD=double(MD);
+B0=double(B0);
+FA=double(FA);
+TRACE=double(TRACE);
+[a,b,c]=size(seg);
+slice=34;
+
+loc=find(seg>=171 & seg<=181|seg==285|seg==286);
+
+mkdir('D:\JHU_AD\codes\ventricle2');
+cd('D:\JHU_AD\codes\ventricle2');
+
+volume=numel(loc);
+save volume volume;
+mask=zeros(a,b,c);
+mask(loc)=1;
+
+
+M_target1=mask.*B0;
+B0_data=nonzeros(M_target1);
+save B0_data B0_data;
+
+M_target2=mask.*FA;
+FA_data=nonzeros(M_target2);
+save FA_data FA_data;
+
+M_target3=mask.*TRACE;
+TRACE_data=nonzeros(M_target3);
+save TRACE_data TRACE_data;
+
+M_target4=mask.*MD;
+MD_data=nonzeros(M_target4);
+save MD_data MD_data;
+
+figure(1);
+f_B0=plotGMM(B0_data);
+title('B0');
+print(1, '-dpng', 'B0'); 
+save f_B0 f_B0;
+
+
+figure(2);
+f_FA=plotGMM(FA_data);
+title('FA');
+print(2, '-dpng', 'FA'); 
+save f_FA f_FA;
+
+figure(3);
+f_TRACE=plotGMM(TRACE_data);
+title('TRACE');
+print(3 ,'-dpng', 'TRACE'); 
+save f_TRACE f_TRACE;
+
+figure(4);
+f_MD=plotGMM(MD_data);
+title('MD');
+print(4 ,'-dpng', 'MD'); 
+save f_MD f_MD;
+
+movefile(source,destination);
+
+% MEAN=mean(DATA);
+% VAR=var(DATA);
+
+% result=plotGMM(DATA);
+
+% DATA_DWI=zeros(volume,slice);
+% for i=2:slice
+% DATA_DWI(:,i)=nonzeros(mask.*DWI_4D(:,:,:,i));
+% 
+% M_DWI(i-1)=mean(mean(DATA_DWI(:,i)));
+% 
+% end
+% M_DWI=(M_DWI-min(M_DWI))/(max(M_DWI)-min(M_DWI));
+% figure;plot(M_DWI);
+% FP=zeros(slice,6);
+% for i=2:slice
+% DATA_DWI(:,i)=nonzeros(mask.*DWI_4D(:,:,:,i));
+% result=plotGMM(DATA_DWI(:,i));
+% FP(i,:)=[result.mu,result.sigma,result.phi];
+% end
+% FP1=FP(2:slice,:);
+% FP2=FP1(:);

GLCM_analysis/codes/codes/Excel2Excel.m

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+for i = 1:28;
+    for j = 1:4;
+        clc;
+        clearvars -except i j;
+        filespath_excel='I:\Data\AD';
+        filenames_excel=dir(filespath_excel);
+        filenames_excel=struct2cell(filenames_excel);
+        filenames_excel=filenames_excel(1,3:20)';
+        %roi_name = raw1;
+        peoplenum = filenames_excel(1:18,1);
+        load('I:\Data\codes\roi_name');
+        stat_header = load('I:\Data\codes\stat_header');
+        method = load('D:\Documents\MatlabCode\dtireference\method');
+        write_co = load('I:\Data\codes\write_co');
+
+        roi_load=char(roi_name(i));          %当前ROI的名称
+        destination=cell(28,1);
+        source = cell(4,1);
+
+        temp = method.method;
+        source{j,1} = strcat('I:\Data\graymatrixdata\NC\',temp{j,1},'\',roi_load,'.xlsx');     %读取目标excel文件
+        destination{i,1}=strcat('I:\Data\graymatrixdata\NC2\',temp{j,1},'\',roi_load,'.xlsx');
+        header = stat_header.txt1;
+        coordinate = write_co.write_co;
+        xlRange = 'B2:IA19';
+
+        %ans_Range = 'B2';
+        for sheet = 1:22;
+            aveSheet = sheet+1;
+            [num,txt,raw] = xlsread(source{j,1},aveSheet,xlRange);
+            %ans_Range = coordinate{sheet-1,1};
+            sheetname = header{sheet};
+            xlswrite(destination{i,1},num,sheetname,'B2');
+            xlswrite(destination{i,1},peoplenum,aveSheet,'A2');
+            for number = 1:18;
+                peopletemp = nanmean(num(number,:));
+                numbertemp = int2str(20+number);
+                location = strcat('A',numbertemp);
+                xlswrite(destination{i,1},peopletemp,aveSheet,location);
+            end
+        end
+
+    end
+    system('tskill excel');
+end

GLCM_analysis/codes/codes/ROI_analysis.m

@@ -0,0 +1,116 @@
+
+%for i=1:17;
+     i=5;
+        for j=1:27;
+        %  j=1;
+            clc;
+            clearvars -except i j;
+
+            addpath('K:\Data\JHU_AD\codes\functions');
+            load('K:\Data\JHU_AD\codes\num.mat');
+            load('K:\Data\JHU_AD\codes\roi_name');
+            filespath='K:\Data\JHU_AD\data\AD';
+            filenames=dir(filespath);
+            filenames=struct2cell(filenames);
+            filenames=filenames(1,3:18)';
+
+
+            roi_cur=char(roi_name(j));          %当前ROI的名称
+            roi_num=num(j,:)                    %当前ROI所对应的区域
+            roi_num(find(roi_num==0))=287;
+
+            file_cur=char(filenames(i,1));
+            display(file_cur);
+            s01=file_cur(1:6);
+            s02=file_cur(8:13);
+            s1=['K:\Data\JHU_AD\data\AD\',s01,'_',s02,'\T1_T2_DTI_ResampledImage_InSameSpace'];
+            path0=strcat('K:\Data\JHU_AD\data\AD\',s01,'_',s02,'\',s01,'\output\MNI_Shifted_Rotated_Axial_',s01,'_',s02,'_T1_brainmask_286Labels.hdr');
+            path1=strcat(s1,'\affine_MD.hdr');
+            path2=strcat(s1,'\affine_B0.hdr');
+            path3=strcat(s1,'\affine_FA.hdr');
+            path4=strcat(s1,'\affine_TRACE.hdr');
+
+
+            source=strcat('K:\Data\JHU_AD\codes\',roi_cur);
+            destination=strcat('K:\Data\JHU_AD\analysis\',s01,'NC\');
+
+
+            [hdr,filetype,fileprefix,machine] = load_nii_hdr(path0);
+            [seg,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+            [hdr,filetype,fileprefix,machine] = load_nii_hdr(path1);
+            [MD,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+            [hdr,filetype,fileprefix,machine] = load_nii_hdr(path2);
+            [B0,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+            [hdr,filetype,fileprefix,machine] = load_nii_hdr(path3);
+            [FA,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+            [hdr,filetype,fileprefix,machine] = load_nii_hdr(path4);
+            [TRACE,hdr] = load_nii_img(hdr,filetype,fileprefix,machine);
+            seg=double(seg);
+            MD=double(MD);
+            B0=double(B0);
+            TRACE=double(TRACE);
+            FA=double(FA);
+            [a,b,c]=size(seg);
+
+            %找到指定的ROI区域
+            loc=find(seg==roi_num(1)|seg==roi_num(2)|seg==roi_num(3)|seg==roi_num(4)|seg==roi_num(5)|seg==roi_num(6)|seg==roi_num(7)|seg==roi_num(8)|seg==roi_num(9)|seg==roi_num(10)|seg==roi_num(11)|seg==roi_num(12)|seg==roi_num(13));
+
+
+            mkdir(source);%创建新目录
+            cd(source);%进入新目录路径
+
+            volume=numel(loc);      %确定ROI区域的像素数
+            save volume volume;
+            mask=zeros(a,b,c);
+            mask(loc)=1;
+
+
+            M_target1=mask.*B0;
+            B0_data=nonzeros(M_target1);        %将掩膜叠加后把不为零的位置提取出来
+            save B0_data B0_data;
+
+            M_target3=mask.*TRACE;
+            TRACE_data=nonzeros(M_target3);
+            save TRACE_data TRACE_data;
+
+            M_target4=mask.*MD;
+            MD_data=nonzeros(M_target4);
+            save MD_data MD_data;
+
+            M_target2=mask.*FA;
+            FA_data=nonzeros(M_target2);
+            save FA_data FA_data;
+
+            figure(1);
+            f_B0=plotGMM(B0_data);
+            title('B0');
+            print(1, '-dpng', 'B0'); 
+            save f_B0 f_B0;
+
+            figure(2);
+            f_FA=plotGMM(FA_data);
+            title('FA');
+            print(2, '-dpng', 'FA'); 
+            save f_FA f_FA;
+
+            figure(3);
+            f_TRACE=plotGMM(TRACE_data);
+            title('TRACE');
+            print(3 ,'-dpng', 'TRACE'); 
+            save f_TRACE f_TRACE;
+
+            figure(4);
+            f_MD=plotGMM(MD_data);
+            title('MD');
+            print(4 ,'-dpng', 'MD'); 
+            save f_MD f_MD;
+
+            close Figure 1;
+            close Figure 2;
+            close Figure 3;
+            close Figure 4;
+
+            movefile(source,destination);
+
+        end
+ %   end

GLCM_analysis/codes/codes/all_ave.m

@@ -0,0 +1,25 @@
+%write the ave & std to the excel
+% ans_ave_AD = zeros(28,22);
+% ans_ave_NC = zeros(28,22);
+
+for j = 1:4;
+    for i = 1:28;
+        load('G:\Data\codes\roi_name.mat');
+        roi_load=char(roi_name(i));          
+        ans_ave_AD = 0;
+        ans_ave_NC = 0;
+        source=strcat('G:\Data\graymatrixdata\Bi_ave\Bi_',roi_load,'.xlsx');        
+        destination =strcat('G:\Data\graymatrixdata\all_average.xlsx');
+        readxlRange = 'B2:W37';
+        [num1,txt1,raw1] = xlsread(source,j+1,readxlRange);
+        for k = 1:22;
+            ans_ave_AD = mean(num1(1:18,k));
+            ans_ave_NC = mean(num1(19:36,k));
+            AD_range = strcat(char(k+65),int2str(2*i));
+            NC_range = strcat(char(k+65),int2str(2*i+1));
+            xlswrite(destination,ans_ave_AD,j,AD_range);
+            xlswrite(destination,ans_ave_NC,j,NC_range);
+        end     
+    end
+    system('tskill excel');
+end