From ce40224a5cdd8de931ef41c70a56cfad12aa4159 Mon Sep 17 00:00:00 2001 From: scott Date: Thu, 4 May 2017 12:33:02 +0200 Subject: [PATCH] touch --- getBP_VOI.m | 6 +++--- getVOIvals.m | 4 ++-- justForFun.m | 6 +++--- svca4_bpVoi.m | 4 ++-- svca4_calculate.m | 4 ++-- svca4_calculate_classes.m | 10 +++++----- svca4_extractRefGui.m | 14 +++++++------- svca4_imageTACGui.m | 4 ++-- svca4_iterateGui.m | 18 +++++++++--------- svca4_mainGui.m | 16 ++++++++-------- svca4_timeShiftGui.m | 6 +++--- svca4_voiTACGui.m | 6 +++--- unNormCLASSES.m | 4 ++-- 13 files changed, 51 insertions(+), 51 deletions(-) diff --git a/getBP_VOI.m b/getBP_VOI.m index d61b53f..62ad1eb 100644 --- a/getBP_VOI.m +++ b/getBP_VOI.m @@ -5,15 +5,15 @@ subj = subj(1:5); % should remove this hard coding!!! %%% load VOI image %%% - VOI_struct = load_untouch_nii([svca4.outputPath '/roiMasks/' subj '_thalamus.nii.gz']); + VOI_struct = load_nii([svca4.outputPath '/roiMasks/' subj '_thalamus.nii.gz']); VOI = single(VOI_struct.img); indVOI = find(VOI==1); - BPc_struct = load_untouch_nii([svca4.outputPath '/petData_quantif/interfile_' subj '_pet_flip_CEREBa2_BPnd_SRTM2.nii']); + BPc_struct = load_nii([svca4.outputPath '/petData_quantif/interfile_' subj '_pet_flip_CEREBa2_BPnd_SRTM2.nii']); BPc = single(BPc_struct.img); thalBPc(s) = mean(BPc(indVOI)); - BPs_struct = load_untouch_nii([svca4.outputPath '/petData_quantif/interfile_' subj '_pet_flip_SVCAa2_BPnd_SRTM2.nii']); + BPs_struct = load_nii([svca4.outputPath '/petData_quantif/interfile_' subj '_pet_flip_SVCAa2_BPnd_SRTM2.nii']); BPs = single(BPs_struct.img); thalBPs(s) = mean(BPs(indVOI)); end diff --git a/getVOIvals.m b/getVOIvals.m index fe062e2..4c21eac 100644 --- a/getVOIvals.m +++ b/getVOIvals.m @@ -8,7 +8,7 @@ subj = subj(1:5); % should remove this hard coding!!! %%% load PET image %%% - PET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{s})); + PET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{s})); PET = single(PET_struct.img); svca4.Res = PET_struct.hdr.dime.pixdim([2 4 3]); % xDim = size(PET,1); @@ -16,7 +16,7 @@ zDim = size(PET,3); %%% load VOI image %%% - VOI_struct = load_untouch_nii([svca4.outputPath '/roiMasks/' subj '_thalamus.nii.gz']); + VOI_struct = load_nii([svca4.outputPath '/roiMasks/' subj '_thalamus.nii.gz']); VOI = single(VOI_struct.img); indVOI = find(VOI==1); diff --git a/justForFun.m b/justForFun.m index 9b2b024..e5c222c 100644 --- a/justForFun.m +++ b/justForFun.m @@ -18,16 +18,16 @@ subj = pet_files(s).name(1:6); %%% load pet image %%% - PET_struct = load_untouch_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/data_pet/' pet_files(s).name]); + PET_struct = load_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/data_pet/' pet_files(s).name]); PET = single(PET_struct.img); %%% load brain mask %%% - % BRAIN_struct = load_untouch_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/roiMasks/' brain_files(s).name]); + % BRAIN_struct = load_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/roiMasks/' brain_files(s).name]); % BRAIN = single(BRAIN_struct.img); % indBRAIN = find(BRAIN==1); %%% load Grey mask %%% - GM_struct = load_untouch_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/gmwm/' gmwm_files(s).name]); + GM_struct = load_nii(['/Users/scott/Dropbox/Experiments/nideco/NIDECO/svca4_avc/gmwm/' gmwm_files(s).name]); GM = single(GM_struct.img); indGM = find(GM==1); diff --git a/svca4_bpVoi.m b/svca4_bpVoi.m index 9c7877c..9f5d94f 100644 --- a/svca4_bpVoi.m +++ b/svca4_bpVoi.m @@ -15,11 +15,11 @@ bpf = bp_list{ind}; %%% load all BP image %%% - BP_struct = load_untouch_nii([bp_dir bpf]); + BP_struct = load_nii([bp_dir bpf]); BP = single(BP_struct.img); %%% load all VOIs %%% - VOI_struct = load_untouch_nii([svca4.SUBJECTS_DIR filesep subj filesep 'label' filesep subj '_AparcAseg_in_PET.nii.gz']); + VOI_struct = load_nii([svca4.SUBJECTS_DIR filesep subj filesep 'label' filesep subj '_AparcAseg_in_PET.nii.gz']); VOI = single(VOI_struct.img); VOInums = unique(VOI); VOInums = VOInums(VOInums > 0); diff --git a/svca4_calculate.m b/svca4_calculate.m index d3c245c..14f5121 100644 --- a/svca4_calculate.m +++ b/svca4_calculate.m @@ -16,11 +16,11 @@ CLASS(isnan(CLASS)) = 0; % this might not be the best way but if we don't do it the regression doesn't work. %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{targetID})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{targetID})); MASK = single(MASK_struct.img); %%% load target image %%% - TARGET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{targetID})); + TARGET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{targetID})); TARGET = single(TARGET_struct.img); % svca4.Res = TARGET_struct.hdr.dime.pixdim([2 4 3]); xDim = size(TARGET,1); diff --git a/svca4_calculate_classes.m b/svca4_calculate_classes.m index ffbaddd..5c80eb9 100644 --- a/svca4_calculate_classes.m +++ b/svca4_calculate_classes.m @@ -35,12 +35,12 @@ svca4.PET_durations = svca4.PET_standardDurations; %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); MASK = single(MASK_struct.img); %clear MASK_struct %%% load PET image %%% - PET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); + PET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); PET = single(PET_struct.img); svca4.Res = PET_struct.hdr.dime.pixdim([2 4 3]); % xDim = size(PET,1); @@ -66,7 +66,7 @@ if isBLOOD if isfield(svca4,'BANANA_list') BANANA_fname = fullfile(svca4.BANANA_dir, svca4.BANANA_list{fi}); - BANANA_struct = load_untouch_nii(BANANA_fname); + BANANA_struct = load_nii(BANANA_fname); BANANA = single(BANANA_struct.img); clear BANANA_struct BM4D = repmat(BANANA, [1 1 1 numel(svca4.BLOOD_frames)]); firstFrames = PET_norm(:,:,:,svca4.BLOOD_frames).*single(BM4D); @@ -92,7 +92,7 @@ isGMWM = any(svca4.GMWM_sel==fi); if isGMWM SEG_fname = fullfile(svca4.SEG_dir, svca4.SEG_list{fi}); - SEG_struct = load_untouch_nii(SEG_fname); + SEG_struct = load_nii(SEG_fname); GM = single(SEG_struct.img).*MASK; clear SEG_struct; WM = GM; WM(WM~=2) = 0; WM(WM==2)=1; GM(GM~=1) = 0; @@ -124,7 +124,7 @@ isINF = any(svca4.TSPO_sel==fi); if isINF INF_fname = fullfile(svca4.INF_dir, svca4.INF_list{fi}); - INF_struct = load_untouch_nii(INF_fname); + INF_struct = load_nii(INF_fname); INF = single(INF_struct.img); clear INF_struct; % it's not here we want to dilate! % if svca4.TSPODilateParameter diff --git a/svca4_extractRefGui.m b/svca4_extractRefGui.m index b07f482..6bb7f01 100644 --- a/svca4_extractRefGui.m +++ b/svca4_extractRefGui.m @@ -101,21 +101,21 @@ function extract_Callback(hObject, eventdata, handles) % load the brain mask mname = fullfile(svca4.MASK_dir,svca4.MASK_list{inds(s)}); - MASK_struct = load_untouch_nii(mname); + MASK_struct = load_nii(mname); MASK = single(MASK_struct.img); clear MASK_struct if handles.remCereb.Value == 1 CB = fullfile(svca4.outputPath, 'roiMasks', [svca4.Names{inds(s)} '_' 'cerebellum_grey.nii.gz']); % load the brain mask - CB_struct = load_untouch_nii(CB); + CB_struct = load_nii(CB); CB_mask = single(CB_struct.img); clear CB_struct MASK = MASK-CB_mask; end pname = fullfile(svca4.PET_dir,svca4.PET_list{inds(s)}); - PET_struct = load_untouch_nii(pname); + PET_struct = load_nii(pname); PET = single(PET_struct.img); xDim = size(PET,1); yDim = size(PET,2); @@ -127,28 +127,28 @@ function extract_Callback(hObject, eventdata, handles) fname = sprintf('%s/weights/%s_GRAY_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, ifeedback); else fname = sprintf('%s/weights/%s_GRAY_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, q*100,ifeedback); end - GRAY = load_untouch_nii(fname); + GRAY = load_nii(fname); GRAY = GRAY.img; if ifeedback == 0 fname = sprintf('%s/weights/%s_WHITE_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, ifeedback); else fname = sprintf('%s/weights/%s_WHITE_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, q*100,ifeedback); end - WHITE = load_untouch_nii(fname); + WHITE = load_nii(fname); WHITE = WHITE.img; if ifeedback == 0 fname = sprintf('%s/weights/%s_BLOOD_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, ifeedback); else fname = sprintf('%s/weights/%s_BLOOD_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, q*100,ifeedback); end - BLOOD = load_untouch_nii(fname); + BLOOD = load_nii(fname); BLOOD = BLOOD.img; if ifeedback == 0 fname = sprintf('%s/weights/%s_TSPO_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, ifeedback); else fname = sprintf('%s/weights/%s_TSPO_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{inds(s)}, q*100,ifeedback); end - TSPO = load_untouch_nii(fname); + TSPO = load_nii(fname); TSPO = TSPO.img; % ---------------------------------------- diff --git a/svca4_imageTACGui.m b/svca4_imageTACGui.m index 78e68e0..46174ed 100644 --- a/svca4_imageTACGui.m +++ b/svca4_imageTACGui.m @@ -88,11 +88,11 @@ function create_Callback(hObject, eventdata, handles) %handles.petF{1} %handles.imageF{1} %%% load PET image %%% -PET_struct = load_untouch_nii(handles.petF{1}); +PET_struct = load_nii(handles.petF{1}); PET = single(PET_struct.img); %%% load mask %%% -MASK_struct = load_untouch_nii(handles.imageF{1}); +MASK_struct = load_nii(handles.imageF{1}); MASK = single(MASK_struct.img); %%% if the image is not binary threshold at 95% %%% diff --git a/svca4_iterateGui.m b/svca4_iterateGui.m index f9ba087..a87f75e 100644 --- a/svca4_iterateGui.m +++ b/svca4_iterateGui.m @@ -109,12 +109,12 @@ function iterate_Callback(hObject, eventdata, handles) for fi=svca4.classIDs % for each target subject %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); MASK = single(MASK_struct.img); clear MASK_struct %%% load PET image %%% - PET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); + PET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); PET = single(PET_struct.img); svca4.Res = PET_struct.hdr.dime.pixdim([2 4 3]); % xDim = size(PET,1); @@ -141,7 +141,7 @@ function iterate_Callback(hObject, eventdata, handles) fname = sprintf('%s/weights/%s_BLOOD_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, ifeedback); else fname = sprintf('%s/weights/%s_BLOOD_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, q*100,ifeedback); end - BLOOD = load_untouch_nii(fname); + BLOOD = load_nii(fname); BLOOD = BLOOD.img; BLOOD = BLOOD.*MASK; quant_BLOOD = quantile(BLOOD(BLOOD~=0),q); @@ -169,7 +169,7 @@ function iterate_Callback(hObject, eventdata, handles) fname = sprintf('%s/weights/%s_GRAY_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, ifeedback); else fname = sprintf('%s/weights/%s_GRAY_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, q*100,ifeedback); end - GRAY = load_untouch_nii(fname); + GRAY = load_nii(fname); GRAY = GRAY.img; GRAY = GRAY.*MASK; quant_GRAY = quantile(GRAY(GRAY~=0),q); @@ -180,7 +180,7 @@ function iterate_Callback(hObject, eventdata, handles) fname = sprintf('%s/weights/%s_WHITE_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, ifeedback); else fname = sprintf('%s/weights/%s_WHITE_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, q*100,ifeedback); end - WHITE = load_untouch_nii(fname); + WHITE = load_nii(fname); WHITE = WHITE.img; WHITE = WHITE.*MASK; quant_WHITE = quantile(WHITE(WHITE~=0),q); @@ -204,7 +204,7 @@ function iterate_Callback(hObject, eventdata, handles) fname = sprintf('%s/weights/%s_TSPO_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, ifeedback); else fname = sprintf('%s/weights/%s_TSPO_q%d_it%.2d.nii', svca4.outputPath, svca4.Names{fi}, q*100,ifeedback); end - TSPO = load_untouch_nii(fname); + TSPO = load_nii(fname); TSPO = TSPO.img; TSPO = TSPO.*MASK; quant_TSPO = quantile(TSPO(TSPO~=0),q); @@ -253,12 +253,12 @@ function iterate_Callback(hObject, eventdata, handles) CLASS(isnan(CLASS)) = 0; % this might not be the best approach but the regression cannot have NaNs %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); MASK = single(MASK_struct.img); clear MASK_struct %%% load target image %%% - TARGET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); + TARGET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); TARGET = single(TARGET_struct.img); xDim = size(TARGET,1); yDim = size(TARGET,2); @@ -304,7 +304,7 @@ function iterate_Callback(hObject, eventdata, handles) %%% Save parametric maps %%% % NB: there is a L/R flip for the data needed but I'm not sure it % always will be!!! - OUT_struct = load_untouch_nii(sprintf('%s/%s', svca4.MRI_dir, svca4.MRI_list{fi})); + OUT_struct = load_nii(sprintf('%s/%s', svca4.MRI_dir, svca4.MRI_list{fi})); OUT_struct.img = []; fprintf('* Saving parametric maps for Target %d ...\n',fi); diff --git a/svca4_mainGui.m b/svca4_mainGui.m index 9dc2665..d145af2 100644 --- a/svca4_mainGui.m +++ b/svca4_mainGui.m @@ -66,14 +66,14 @@ function flip_Callback(hObject, eventdata, handles) [files, filepath] = uigetfile({'.nii','.nii.gz'},'Multiselect','on'); if size(files,1) == 1 pname = fullfile(filepath,files); - PET_struct = load_untouch_nii(pname); + PET_struct = load_nii(pname); PET_struct.img = flip(PET_struct.img,4); fname = [pname(1:end-4) '_flip.nii']; save_untouch_nii(PET_struct, fname); elseif size(files,1) > 1 for s = 1:length(files) pname = fullfile(filepath,files(s)); - PET_struct = load_untouch_nii(pname); + PET_struct = load_nii(pname); PET_struct.img = flip(PET_struct.img,4); fname = [pname(1:end-4) '_flipTime.nii']; save_untouch_nii(PET_struct, fname); @@ -175,12 +175,12 @@ function cereb_ref_Callback(hObject, eventdata, handles) CB = fullfile(svca4.outputPath, 'roiMasks', [svca4.Names{s} '_' 'cerebellum_grey.nii.gz']); % load the brain mask - CB_struct = load_untouch_nii(CB); + CB_struct = load_nii(CB); CB_mask = single(CB_struct.img); clear CB_struct pname = fullfile(svca4.PET_dir,svca4.PET_list{s}); - PET_struct = load_untouch_nii(pname); + PET_struct = load_nii(pname); PET = single(PET_struct.img); xDim = size(PET,1); yDim = size(PET,2); @@ -302,11 +302,11 @@ function bp_voi_Callback(hObject, eventdata, handles) bpf = bp_list{ind}; %%% load all BP image %%% - BP_struct = load_untouch_nii(bpf); + BP_struct = load_nii(bpf); BP = single(BP_struct.img); %%% load all VOIs %%% - VOI_struct = load_untouch_nii([svca4.SUBJECTS_DIR filesep subj filesep 'label' filesep subj '_AparcAseg_in_PET.nii.gz']); + VOI_struct = load_nii([svca4.SUBJECTS_DIR filesep subj filesep 'label' filesep subj '_AparcAseg_in_PET.nii.gz']); VOI = single(VOI_struct.img); VOInums = unique(VOI); VOInums = VOInums(VOInums > 0); @@ -343,9 +343,9 @@ function copy_header_Callback(hObject, eventdata, handles) change_files = uipickfiles('FilterSpec',[svca4.outputPath],'Prompt','Select all images to change their header.'); end - orig = load_untouch_nii(ref_file{1}); + orig = load_nii(ref_file{1}); for i = 1:length(change_files) - change = load_untouch_nii(change_files{i}); + change = load_nii(change_files{i}); out = orig; out.img = change.img; save_untouch_nii(out,change_files{i}) diff --git a/svca4_timeShiftGui.m b/svca4_timeShiftGui.m index 8014596..cbd837d 100644 --- a/svca4_timeShiftGui.m +++ b/svca4_timeShiftGui.m @@ -103,12 +103,12 @@ function shift_Callback(hObject, eventdata, handles) % load the brain mask mname = fullfile(svca4.MASK_dir,svca4.MASK_list{inds(s)}); - MASK_struct = load_untouch_nii(mname); + MASK_struct = load_nii(mname); MASK = single(MASK_struct.img); clear MASK_struct pname = fullfile(svca4.PET_dir,svca4.PET_list{inds(s)}); - PET_struct = load_untouch_nii(pname); + PET_struct = load_nii(pname); PET = single(PET_struct.img); xDim = size(PET,1); yDim = size(PET,2); @@ -133,7 +133,7 @@ function shift_Callback(hObject, eventdata, handles) % load the blood mask bname = fullfile(svca4.BANANA_dir, svca4.BANANA_list{inds(s)}); - BANANA_struct = load_untouch_nii(bname); + BANANA_struct = load_nii(bname); BANANA = single(BANANA_struct.img); BM4D = single(repmat(BANANA, [1 1 1 numel(svca4.BLOOD_frames)])); clear BANANA_struct diff --git a/svca4_voiTACGui.m b/svca4_voiTACGui.m index 4f95e02..d5c2c82 100644 --- a/svca4_voiTACGui.m +++ b/svca4_voiTACGui.m @@ -144,7 +144,7 @@ function create_TAC_Callback(hObject, eventdata, handles) for s = 1:length(handles.subs.Value) % loop on subjects %%% load segmentation image %%% - SEG_struct = load_untouch_nii(fullfile(svca4.SUBJECTS_DIR, subj{s}, 'label', [subj{s} '_AparcAseg_in_PET.nii.gz'])); + SEG_struct = load_nii(fullfile(svca4.SUBJECTS_DIR, subj{s}, 'label', [subj{s} '_AparcAseg_in_PET.nii.gz'])); SEG = single(SEG_struct.img); clear SEG_Struct indsVOI = ismember(SEG,voiNums); @@ -152,7 +152,7 @@ function create_TAC_Callback(hObject, eventdata, handles) %%% load PET image %%% tt = strfind(svca4.Names,subj{s}); Index = find(not(cellfun('isempty', tt))); - PET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{Index})); + PET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{Index})); PET = single(PET_struct.img); svca4.Res = PET_struct.hdr.dime.pixdim([2 4 3]); % xDim = size(PET,1); @@ -184,7 +184,7 @@ function create_TAC_Callback(hObject, eventdata, handles) %%%% end %%%% case 1 %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{s})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{s})); MASK = single(MASK_struct.img); clear MASK_struct diff --git a/unNormCLASSES.m b/unNormCLASSES.m index 3a26f53..ab0c98b 100644 --- a/unNormCLASSES.m +++ b/unNormCLASSES.m @@ -5,12 +5,12 @@ for fi = 1:numel(svca4.PET_list) %%% load brain mask %%% - MASK_struct = load_untouch_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); + MASK_struct = load_nii(fullfile(svca4.MASK_dir, svca4.MASK_list{fi})); MASK = single(MASK_struct.img); %clear MASK_struct %%% load PET image %%% - PET_struct = load_untouch_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); + PET_struct = load_nii(fullfile(svca4.PET_dir, svca4.PET_list{fi})); PET = single(PET_struct.img); svca4.Res = PET_struct.hdr.dime.pixdim([2 4 3]); % xDim = size(PET,1);