%% generate .nrrd files % -----===== LOAD =====----- CDPpath = '\\Mpufs5\data_wnx1\_Data\CDP\CDP005\CDP005a\Formatted\'; PETin =am2mat([CDPpath 'frames\CDP005a_pet_fdg_FOV50_MBq_fr1.am']); CTin =am2mat([CDPpath 'CDP005a_ct_FOV50.am']); SEGin = nrrdread('C:\010-work\003_localGit\WiscPlan_v2\CDP_data\CDP5_SEG_FullResolution.nrrd'); DOGin = nrrdread('C:\010-work\003_localGit\WiscPlan_v2\CDP_data\CDP5_Doggo_FullResolution.nrrd'); % -----===== GENERATE =====----- CTimg=permute(imresize(CTin.data, 0.5), [2,1,3]); PETimg=permute(PETin.data, [2,1,3]); CTimg=imresize3(CTimg, size(PETimg)); % colorwash(CTimg, PETimg, [-500,500], [0,0.03]) % downsize Dfactor=2; % should be at least 2 CTimg2 = imresize(CTimg, 1/Dfactor); PETimg2 =imresize(PETimg, 1/Dfactor); voxel_size = PETin.voxel_size*Dfactor; ImStart = PETin.start; SEG = round(imresize(SEGin, 1/Dfactor)); DOG = round(imresize(DOGin, 1/Dfactor)); % virtual resize Rfactor = 1; voxel_size = voxel_size/Rfactor; ImStart = ImStart/Rfactor; % -----===== SAVE =====----- out_path='C:\010-work\003_localGit\WiscPlan_v2\CDP_data\'; filename=[out_path, 'CDP5_CT.nrrd']; matrix=single(CTimg2); pixelspacing=voxel_size; origin = ImStart; encoding = 'raw'; nrrdWriter(filename, matrix, pixelspacing, origin, encoding); out_path='C:\010-work\003_localGit\WiscPlan_v2\CDP_data\'; filename=[out_path, 'CDP5_PET.nrrd']; matrix=PETimg2; pixelspacing=voxel_size; origin = ImStart; encoding = 'raw'; nrrdWriter(filename, matrix, pixelspacing, origin, encoding); out_path='C:\010-work\003_localGit\WiscPlan_v2\CDP_data\'; filename=[out_path, 'CDP5_SEG.nrrd']; matrix=SEG; pixelspacing=voxel_size; origin = ImStart; encoding = 'raw'; nrrdWriter(filename, matrix, pixelspacing, origin, encoding); out_path='C:\010-work\003_localGit\WiscPlan_v2\CDP_data\'; filename=[out_path, 'CDP5_Doggo.nrrd']; matrix=DOG; pixelspacing=voxel_size; origin = ImStart; encoding = 'raw'; nrrdWriter(filename, matrix, pixelspacing, origin, encoding); % -----===== TEST =====----- % CTin=nrrdread('C:\010-work\003_localGit\WiscPlan_v2\CDP_data\CDP5_CT.nrrd'); % PETin=nrrdread('C:\010-work\003_localGit\WiscPlan_v2\CDP_data\CDP5_PET.nrrd'); % % colorwash(CTin, PETin, [-500,500], [0,0.03])