Merge pull request #497 from schorschinho/develop

Release Push v.2.4.0

GUI/Osprey.m

@@ -30,7 +30,7 @@
 logoFcn = @()imread('osprey.png', 'BackgroundColor', gui.colormap.Background);
 logoBanner = uiw.utility.loadIcon(logoFcn);
 % Here the intro banner is created
-gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.3.0','Date', 'June 24, 2022',...
+gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.4.0','Date', 'August 8, 2022',...
 'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
 'ContactInfo', '[email protected]','LogoCData', logoBanner);
 

GUI/osp_Toolbox_Check.m

@@ -32,7 +32,7 @@
 %       2020-05-15: First version of the code.
 %% % 1. SAVE OSPREY VERSION%%%
 %%% 1. SAVE OSPREY VERSION%%%
-OspreyVersion = 'Osprey 2.3.0';
+OspreyVersion = 'Osprey 2.4.0';
 fprintf(['Timestamp %s ' OspreyVersion '  ' Module '\n'], datestr(now,'mmmm dd, yyyy HH:MM:SS'));
 hasSPM = 1; % For the compiled GUI
 %% % 2. GET SPMPATH AND TOOLBOXES%%%

GUI/osp_onPrint.m

@@ -376,15 +376,15 @@ function osp_onPrint( ~, ~ ,gui)
                     waterFitRangeString = ['Fitting range: ' num2str(MRSCont.opts.fit.rangeWater(1)) ' to ' num2str(MRSCont.opts.fit.rangeWater(2)) ' ppm'];
                     % Where are the metabolite names stored?
                     if strcmp(gui.fit.Style, 'ref') || strcmp(gui.fit.Style, 'w')
-                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){1};
+                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){1};
                         basisSetNames = basisSet.name;
                         subSpecName = gui.fit.Style;
                     else if strcmp(gui.fit.Style, 'conc')
-                            basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){basis,1};
+                            basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){basis,1};
                             basisSetNames = basisSet.name;
                             subSpecName = basisSet.names{1};
                             else
-                            basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){basis,1,subspectrum};
+                            basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){basis,1,subspectrum};
                             basisSetNames = basisSet.name;
                             subSpecName = basisSet.names{1};
                         end

GUI/osp_updateFitWindow.m

@@ -78,13 +78,13 @@ function osp_updateFitWindow(gui)
                 waterFitRangeString = ['Fitting range: ' num2str(MRSCont.opts.fit.rangeWater(1)) ' to ' num2str(MRSCont.opts.fit.rangeWater(2)) ' ppm'];
                 % Where are the metabolite names stored?
                 if strcmp(gui.fit.Style, 'ref') || strcmp(gui.fit.Style, 'w')
-                    basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){1};
+                    basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){1};
                     basisSetNames = basisSet.name;
                 else if strcmp(gui.fit.Style, 'conc')
-                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){basis,1};
+                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){basis,1};
                         basisSetNames = basisSet.name;
                     else
-                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){basis,1,subspectrum};
+                        basisSet = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){basis,1,subspectrum};
                         basisSetNames = basisSet.name;
                     end
                 end

GUI/osp_updateLoadWindow.m

@@ -200,7 +200,11 @@ function osp_updateLoadWindow(gui)
                 set(ViewAxes.Children, 'Parent', gui.Plot.data{gui.load.Selected}.Children);
                 set(gui.Plot.data{gui.load.Selected}.Children.Title, 'String', ViewAxes.Title.String);
                 set(gui.Plot.data{gui.load.Selected}.Children, 'XLim',ViewAxes.XLim);
-                set(gui.upperBox.data.Info{gui.load.Selected},'Title', ['Actual file: ' MRSCont.files_ref{Exp,gui.controls.Selected}] );
+                if ~isempty(MRSCont.files_ref)
+                    set(gui.upperBox.data.Info{gui.load.Selected},'Title', ['Actual file: ' MRSCont.files_ref{Exp,gui.controls.Selected}] );
+                else
+                    set(gui.upperBox.data.Info{gui.load.Selected},'Title', ['Actual file: ' MRSCont.files{Exp,gui.controls.Selected}] );
+                end
             case 'MM reference'
                 if Exp > max(MRSCont.opts.MultipleSpectra.mm_ref)
                     Exp = 1;

GUI/osp_updateQuantifyWindow.m

@@ -25,7 +25,7 @@ function osp_updateQuantifyWindow(gui)
 %%% 1. INITIALIZE %%%
         MRSCont = getappdata(gui.figure,'MRSCont');  % Get MRSCont from hidden container in gui class
         gui.layout.EmptyQuantPlot = 0;
-        basisSet = MRSCont.fit.resBasisSet.metab.(['np_sw_' num2str(MRSCont.processed.metab{gui.controls.Selected}.sz(1)) '_' num2str(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth)]){gui.controls.act_z,1,gui.controls.act_y};
+        basisSet = MRSCont.fit.resBasisSet.metab.(['np_sw_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.sz(1))) '_' num2str(round(MRSCont.processed.metab{gui.controls.Selected}.spectralwidth))]){gui.controls.act_z,1,gui.controls.act_y};
         subSpecName = basisSet.names{1};
         if ~(isfield(MRSCont.flags,'isPRIAM') || isfield(MRSCont.flags,'isMRSI')) || ~(MRSCont.flags.isPRIAM || MRSCont.flags.isMRSI)
             gui.upperBox.quant.Info = gui.layout.(gui.layout.quantifyTabhandles{gui.quant.Selected.Model}).Children(2).Children(1);          

README.md

@@ -100,7 +100,11 @@ Should you publish material that made use of Osprey, please cite the following p
 
 This work has been supported by NIH grants R01 EB016089, P41 EB15909, P41 EB031771, R01 EB023963, and K99 AG062230.
 
-We wish to thank the following individuals for their contributions to the
+We wish to thank collaborators and partners for providing LCModel basis sets and control files. If you use these resources for your analysis of the following data types, please mention the respective individuals in your acknowledgements:
+- Siemens 7T STEAM (TE = 5 ms): Dr. Dinesh Deelchand (University of Minnesota)
+- Siemens 3T and 7T SPECIAL (TE = 8.5/9 ms): Dr. Ariane Fillmer (PTB Berlin)
+
+We also wish to thank the following individuals for their contributions to the
 development of Osprey and shared processing code:
 
 - Jamie Near (McGill University, Montreal)

ci/UnitTest.m

@@ -56,20 +56,6 @@
         rt{2} = table(results{2});
     end
 
-    dir = strrep(which(['ci' filesep 'job' sequence '.m']),['job' sequence '.m'],['rawdata_CI' filesep 'sub-01' filesep 'anat']);
-    delete(fullfile(dir,'c1sub-01_T1w.nii.gz'));
-    delete(fullfile(dir,'c2sub-01_T1w.nii.gz'));
-    delete(fullfile(dir,'c3sub-01_T1w.nii.gz'));
-    delete(fullfile(dir,'sub-01_T1w.nii'));
-    delete(fullfile(dir,'sub-01_T1w_seg8.mat'));
-
-    dir = strrep(which(['ci' filesep 'job' sequence '.m']),['job' sequence '.m'],['rawdata_CI' filesep 'sub-02' filesep 'anat']);
-    delete(fullfile(dir,'c1sub-02_T1w.nii.gz'));
-    delete(fullfile(dir,'c2sub-02_T1w.nii.gz'));
-    delete(fullfile(dir,'c3sub-02_T1w.nii.gz'));
-    delete(fullfile(dir,'sub-02_T1w.nii'));
-    delete(fullfile(dir,'sub-02_T1w_seg8.mat'));
-
     dir = strrep(which(['ci' filesep 'job' sequence '.m']),['job' sequence '.m'],'derivatives');
     rmdir(dir,'s')
 
@@ -82,13 +68,6 @@
         results{2} = runtests('Osprey_Plot_GUI_test.m');
         rt{2} = table(results{2});
 
-        dir = strrep(which(['ci' filesep 'job' sequence '.m']),['job' sequence '.m'],['rawdata_CI' filesep 'sub-01' filesep 'anat']);
-        delete(fullfile(dir,'c1sub-01_T1w.nii.gz'));
-        delete(fullfile(dir,'c2sub-01_T1w.nii.gz'));
-        delete(fullfile(dir,'c3sub-01_T1w.nii.gz'));
-        delete(fullfile(dir,'sub-01_T1w.nii'));
-        delete(fullfile(dir,'sub-01_T1w_seg8.mat'));
-
         dir = strrep(which(['ci' filesep 'job' sequence '.m']),['job' sequence '.m'],'derivatives');
         rmdir(dir,'s')
     end

ci/azure-pipelines-develop-pull.yml

@@ -1,5 +1,5 @@
 # Pull request CI pipeline for Osprey
-# Triggers for each pull request into the develop branch
+# Triggers for each pull request into the develop branch 
 # Starts with a quick Single Subject PRESS test
 # If the first stage is successful a Full PRESS job is triggered
 

coreg/OspreyCoreg.m

@@ -38,6 +38,17 @@
 % Checking for version, toolbox, and previously run modules
 [~,MRSCont.ver.CheckOsp ] = osp_CheckRunPreviousModule(MRSCont, 'OspreyCoreg');
 
+%Do some check on the naming convention first to avoid overwriting the
+%output due to non BIDS conform data names
+SameName = 0;
+if MRSCont.nDatasets(1) > 1
+    specFile = MRSCont.files{1};
+    specFile2 = MRSCont.files{2};
+    [~, SpecName, ~]  = fileparts(specFile);
+    [~, SpecName2, ~]  = fileparts(specFile2);
+    SameName = strcmp(SpecName,SpecName2);
+end
+MRSCont.coreg.SameName = SameName;
 
 % Set up saving location
 saveDestination = fullfile(MRSCont.outputFolder, 'VoxelMasks'); %CWDJ - Address in future update
@@ -55,14 +66,20 @@
 for kk = 1:MRSCont.nDatasets(1)
      [~] = printLog('OspreyCoreg',kk,1,MRSCont.nDatasets,progressText,MRSCont.flags.isGUI ,MRSCont.flags.isMRSI);  
     if ~(MRSCont.flags.didCoreg == 1 && MRSCont.flags.speedUp && isfield(MRSCont, 'coreg') && (kk > length(MRSCont.coreg.vol_image))) || ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)
+
+        if SameName
+            [PreFix] = osp_generate_SubjectAndSessionPrefix(MRSCont.files{kk},kk);
+        else
+            PreFix = '';
+        end
 
         % Get the input file name
         [~,filename,~]   = fileparts(MRSCont.files{kk});
         % Get the nii file name
         [~,~,T1ext]   = fileparts(MRSCont.files_nii{kk});
 
         %<source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>][_desc-<label>]_mask.nii.gz
-        saveName = [osp_RemoveSuffix(filename),'_space-scanner']; %CWDJ Check space.
+        saveName = [PreFix '_' filename '_space-scanner']; %CWDJ Check space.
 
         % Generate file name for the voxel mask NIfTI file to be saved under
         maskFile            = fullfile(saveDestination, [saveName '_mask.nii']);

coreg/coreg_ge_nifti.m

@@ -41,10 +41,10 @@
 
 %%% 2. PREPARE THE MRS VOXEL COORDINATES %%%
 % Convert from RAS to LPS
-VoxOffs  = geom.pos .* [-1 1 1];
-tlhc_LPS = geom.rot.tlhc .* [-1 1 1];
-trhc_LPS = geom.rot.trhc .* [-1 1 1];
-brhc_LPS = geom.rot.brhc .* [-1 1 1];
+VoxOffs  = geom.pos .* [1 1 1];
+tlhc_LPS = geom.rot.tlhc .* [1 1 1];
+trhc_LPS = geom.rot.trhc .* [1 1 1];
+brhc_LPS = geom.rot.brhc .* [1 1 1];
 
 e1_SVS_n = trhc_LPS - tlhc_LPS;
 e1_SVS_n = e1_SVS_n ./ norm(e1_SVS_n);
@@ -132,7 +132,7 @@
 
 mask(mrs_box_ind) = 1;
 
-%mask = flip(mask,2);
+% mask = flip(mask,1);
 
 % Fill in the SPM volume header information
 vol_mask.fname   = maskFile;

exampledata/sdat/MEGA/jobSDAT_MEGA.m

@@ -254,7 +254,7 @@
         % (OPTIONAL)
         % Link to single NIfTI (*.nii) files for Siemens and Philips data
         % Link to DICOM (*.dcm) folders for GE data
-        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
+        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep subs(kk).name '_'  sess(ll).name '_T1w.nii.gz']};
 
         % External segmentation results
         % (OPTIONAL)

exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m

@@ -257,7 +257,7 @@
         % (OPTIONAL)
         % Link to single NIfTI (*.nii) files for Siemens and Philips data
         % Link to DICOM (*.dcm) folders for GE data
-        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
+        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep subs(kk).name '_'  sess(ll).name '_T1w.nii.gz']};
 
         % External segmentation results
         % (OPTIONAL)

exampledata/sdat/UnEdited/jobSDAT.m

@@ -240,7 +240,7 @@
         % (OPTIONAL)
         % Link to single NIfTI (*.nii) files for Siemens and Philips data
         % Link to DICOM (*.dcm) folders for GE data
-        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
+        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep subs(kk).name '_' sess(ll).name '_T1w.nii.gz']};
 
         % External segmentation results
         % (OPTIONAL)

exampledata/sdat/UnEdited/jobSDAT_LCModel.m

@@ -255,7 +255,7 @@
         % (OPTIONAL)
         % Link to single NIfTI (*.nii) files for Siemens and Philips data
         % Link to DICOM (*.dcm) folders for GE data
-        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep sess(ll).name '_T1w.nii.gz']};
+        files_nii(counter)  = {[sess(ll).folder filesep sess(ll).name filesep 'anat' filesep subs(kk).name filesep subs(kk).name '_' sess(ll).name '_T1w.nii.gz']};
 
         % External segmentation results
         % (OPTIONAL)