tiborauer · Jan 5, 2024 · Nov 3, 2023 · Nov 3, 2023 · Nov 3, 2023 · Nov 7, 2023
diff --git a/aa_engine/aas_firstlevel_model_prepare.m b/aa_engine/aas_firstlevel_model_prepare.m
@@ -120,26 +120,40 @@
 %%%%%%%%%%%%%%%%%%%
 clear SPM
 
-%% retrieve TR from DICOM header
-% TR is manually specified (not recommended as source of error)
+%% retrieve TR
+
+
 if isfield(aap.tasklist.currenttask.settings,'TR') && ...
         ~isempty(aap.tasklist.currenttask.settings.TR)
-    SPM.xY.RT =aap.tasklist.currenttask.settings.TR;
+
+    % TR is manually specified
+
+    SPM.xY.RT = aap.tasklist.currenttask.settings.TR;
+
 else
-    % Get TR from DICOM header checking they're the same for all sessions
+
+    % Get TR from header
+
     for sess=subjSessionI
-        try
-            DICOMHEADERS=load(aas_getfiles_bystream(aap,subj,sess,'epi_dicom_header'));
-        catch
-            DICOMHEADERS=load(aas_getfiles_bystream(aap,subj,sess,'epi_header')); % For backwards compatibility
+
+        if aas_isfile_bystream(aap,subj,sess,'epi_dicom_header') % epi 
+            DICOMHEADERS = load(aas_getfiles_bystream(aap,subj,sess,'epi_dicom_header'));
+
+        elseif aas_isfile_bystream(aap,subj,sess,'dot_header') % dot
+            DICOMHEADERS = load(aas_getfiles_bystream(aap,subj,sess,'dot_header')); 
+
+        elseif aas_isfile_bystream(aap,subj,sess,'epi_header') % backwards compatibility
+            DICOMHEADERS = load(aas_getfiles_bystream(aap,subj,sess,'epi_header')); 
+
+        else
+            aas_log(aap,true,sprintf('No header found for this data. Exiting...')); 
+
         end
+
         try
-            TR=DICOMHEADERS.DICOMHEADERS{1}.volumeTR;
+            TR = DICOMHEADERS.DICOMHEADERS{1}.volumeTR;
         catch
-        end
-        % [AVG] This is for backwards compatibility!
-        if ~exist('TR','var') || isempty(TR)
-            TR=DICOMHEADERS.DICOMHEADERS{1}.volumeTR;
+            aas_log(aap,true,sprintf('TR not found in header. Exiting...'));          
         end
 
         if (sess==subjSessionI(1))
@@ -149,7 +163,9 @@
                 aas_log(aap,true,sprintf('Session %d has different TR from earlier sessions, they can''t be in the same model.',sess));
             end
         end
+
     end
+
 end
 
 %% Set up basis functions

diff --git a/aa_engine/aas_renamestream.m b/aa_engine/aas_renamestream.m
@@ -11,7 +11,11 @@
 end
 
 if strcmp(type,'output')
-    aas_log(aap,false,sprintf('WARNING: Renaming output %s of %s to %s.\n  It might break dependency for the consecuting module(s).\n  Make sure that you know what you are doing!',origstream,stage,newstream));
+    if (isempty(newstream))
+        aas_log(aap,false,sprintf('WARNING: Removing output "%s" of "%s"\n Downstream modules that take "%s" as an input will be passed an alternate source.',origstream,stage,origstream));
+    else
+        aas_log(aap,false,sprintf('WARNING: Renaming output "%s" of "%s" to "%s".\n Downstream modules that take "%s" as an input may also need to rename the stream.',origstream,stage,origstream,newstream));
+    end
 end
 
 %% Locate STAGE

diff --git a/aa_modules/aamod_QA.m b/aa_modules/aamod_QA.m
@@ -0,0 +1,257 @@
+function [aap,resp] = aamod_QA(aap, task)
+%
+% generate a QA summary of functional data
+%
+% Change History
+%
+% fall 2023 [MSJ] -- new
+%
+
+resp='';
+
+switch task
+
+    case 'report'
+
+    case 'doit'		
+
+
+        nvoxels = aap.tasklist.currenttask.settings.nvoxels;
+        carpetscale = aap.tasklist.currenttask.settings.carpetscale;
+
+        outlier_filter = aap.tasklist.currenttask.settings.outlier_filter;
+        outlier_threshold = aap.tasklist.currenttask.settings.outlier_threshold;
+
+        savedir = fullfile(aas_getstudypath(aap),'QA_images');
+        if ~exist(savedir,'dir');mkdir(savedir);end
+
+        [ ~,subindex_list ] = aas_getN_bydomain(aap,'subject');
+
+        summary_fname = fullfile(aas_getstudypath(aap),'data_summary.txt');
+
+        if exist(summary_fname,'file');delete(summary_fname);end
+
+        fid = fopen(summary_fname,'w'); % plaintext stats summary....
+
+        if (fid < 0)
+            aas_log(aap, true, 'Cannot open summary file for writing. Halting...');
+        end
+
+        group_outliers = []; % for group outlier plot...
+
+        for subject_index = subindex_list
+
+            [ ~,all_sess ] = aas_getN_bydomain(aap, 'session', subject_index);
+            session_list = intersect(all_sess, aap.acq_details.selected_sessions);           
+
+            for session_index = session_list        
+
+                data_instream_struct = aap.tasklist.currenttask.inputstreams(1).stream{1};
+                fname = aas_getfiles_bystream(aap, subject_index, session_index, data_instream_struct.CONTENT); 
+
+                header = spm_vol(fname);
+                data = spm_read_vols(header);
+
+                [ r,c,s,f ] = size(data);
+                data = reshape(data,r*c*s,f); % nvoxels x nframes
+
+                % stats
+
+                nancount = sum(isnan(data(:)));
+                zerocount = sum(data(:)==0);
+                voxsize = diag(header(1).mat);
+                voxsize = voxsize(1:3);
+
+                % swap nan for zeros -- so masking can strip nan
+
+                if (nancount > 0)
+                    data(isnan(data)) = 0;
+                end
+
+                datamax = max(data(:));
+                datamin = min(data(:));
+
+                % extract voxel subset for processing / plotting
+
+                selector = floor(linspace(1,r*c*s,nvoxels));
+                data = data(selector,:);
+
+                % we don't have a brainmask, so instead do a
+                % quick and dirty implicit mask: we assume any
+                % identically zero rows are outside of brain
+                % this results in a reasonably good selection
+                % especially if nvoxels is large-ish
+
+                data = data(all(data~=0,2),:);             
+
+                % style points - open window in center of display
+                % (this trick only works if not running cluster)
+
+                if (strcmp(aap.options.wheretoprocess, 'localsingle'))
+                    h = figure('Position',[0 0 1500 1000], 'Color', [1 1 1],'NumberTitle','off', 'Visible', 'off', 'MenuBar', 'none');
+                    movegui(h, 'center');
+                    set(h, 'Visible', 'on');
+                else
+                    h = figure('Position',[0 0 1500 1000],'Color', [1 1 1], 'NumberTitle','off','MenuBar','none');
+                end
+
+                subplot(3,3,[5 6 8 9]);
+
+                % joy plot
+
+                surf(data,log(abs(data)));
+                axis tight
+                xlabel('frame','FontSize',18);
+                ylabel('voxel','FontSize',18);
+                set(gca,'FontSize',18);
+                shading interp;
+                colormap gray;
+                cm = colormap;
+                colormap(cm.*cm.*cm); % suppresses midrange
+                view(-25,60);
+
+                % traditional carpet plot for comparison
+
+                subplot(3,3,[4 7]);
+                imagesc(data,[carpetscale(1)*max(data(:)) carpetscale(2)*max(data(:))]);
+                xlabel('frame','FontSize',14);
+                ylabel('voxel','FontSize',14);
+                title('grayplot','FontSize',14);
+
+                % sum over voxels plot and outliers
+
+                subplot(3,3,[1 2 3]);
+
+                sumovervoxels = sum(data,1,'omitnan');
+                plot(sumovervoxels,'k','LineWidth',2);
+                a = axis;
+                hold on;
+
+                switch outlier_filter
+
+                    case 'anymedian'
+
+                        outliers = isoutlier(data,'median',2, 'ThresholdFactor',outlier_threshold);
+                        outliers = any(outliers,1);
+
+                    case 'anymean'
+
+                        outliers = isoutlier(data,'mean',2, 'ThresholdFactor',outlier_threshold);
+                        outliers = any(outliers,1);
+
+                    case 'mediansum'
+
+                        outliers = isoutlier(sumovervoxels,'median', 'ThresholdFactor',outlier_threshold);                  
+
+                    case 'meansum'
+
+                        outliers = isoutlier(sumovervoxels,'mean', 'ThresholdFactor',outlier_threshold);
+
+                    case 'none'
+
+                        outliers = [];
+
+                end             
+
+                outlier_index = find(outliers);
+                if ~isempty(outlier_index)
+                    plot(outlier_index,0.5*(a(3)+a(4)),'r+','LineWidth',2,'MarkerSize',12);
+                end
+                axis tight;
+
+                % include stats in title
+
+                [~,n,~]=fileparts(fname);
+                n = strrep(n,'_','-');
+                titlestring = [n '   dim: ' num2str([r c s f]) '   voxsize: ' num2str(voxsize') '   max: ' num2str(datamax,3) ' min: ' num2str(datamin,3) '    nan: ' num2str(nancount) ' zeros: ' num2str(zerocount)];
+                title(titlestring,'FontSize',18);
+
+                if ~isempty(outlier_index)
+                    odescriptor = sprintf('outliers (%s > %g)', outlier_filter, outlier_threshold);
+                    legend({'sum over voxels', odescriptor},'FontSize',16);
+                else
+                    legend('sum over voxels','FontSize',16);
+                end
+                xlabel('frame','FontSize',18);
+                ylabel('intensity','FontSize',18);
+
+                fname_out = fullfile(savedir,sprintf('%s.jpg', n));
+
+                set(h,'Renderer','opengl');
+                set(findall(h,'Type','text'),'FontUnits','normalized');
+                h.InvertHardcopy = 'off'; % otherwise matlab changes our nice black bg to white
+                print(h, '-djpeg', '-r150', fname_out);
+
+                close(h);
+
+                % collect outliers for group outlier plot
+
+                if (isempty(group_outliers))
+                    group_outliers(1,:) = outliers;
+                else
+                    % must protect against unequal number-of-frames
+                    [~,ncols] = size(group_outliers);
+                    if (ncols < length(outliers))
+                        % this will zero extend ALL rows of group_outliers
+                        % to new width so we can add this data to bottom
+                        group_outliers(1,length(outliers)) = 0;
+                    end
+                    if (ncols > length(outliers))
+                        % this will extend current outliers to fit
+                        % group_outliers (we assume frame(1) are aligned)
+                        outliers(ncols) = 0;
+                    end
+                    group_outliers(end+1,:) = outliers;
+                end
+
+                % add stats to summary file
+
+                fprintf(fid,'%s    outliers: %d\n', titlestring, sum(outliers));
+
+            end % session
+
+        end % subject
+
+        fclose(fid); % summary_fname
+
+        % group outlier plot
+        % this is useful for detecting correlated artifacts across subjects
+
+        % get a little better appearance if we size the window to fit data
+
+        [nrows,ncols] = size(group_outliers);
+
+        if (strcmp(aap.options.wheretoprocess, 'localsingle'))
+            h2 = figure('Position',[0 0 6*ncols 20*nrows], 'Color', [1 1 1],'NumberTitle','off', 'Visible', 'off', 'MenuBar', 'none');
+            movegui(h2, 'center');
+            set(h2, 'Visible', 'on');
+        else
+            h2 = figure('Position',[0 0 6*ncols 20*nrows],'Color', [1 1 1], 'NumberTitle','off','MenuBar','none');
+        end
+
+        group_outliers(end+1,end+1) = 0; % pcolor needs a dummy row/col
+        pcolor(group_outliers);
+        title('Outliers','FontSize',16);
+        xlabel('frame','FontSize',14);
+        ylabel('subject','FontSize',14);
+        colormap gray;
+
+        fname_out = fullfile(aas_getstudypath(aap),'group_outliers.jpg');
+        set(h2,'Renderer','opengl');
+        set(findall(h2,'Type','text'),'FontUnits','normalized');
+        h2.InvertHardcopy = 'off';
+        print(h2, '-djpeg', '-r150', fname_out);
+        close(h2);
+
+        aap = aas_desc_outputs(aap, 'data_summary', summary_fname);
+
+        % done!
+
+    case 'checkrequirements'
+
+    otherwise
+
+        aas_log(aap,true,sprintf('Unknown task %s',task));
+
+end % switch
+end % function
diff --git a/aa_modules/aamod_QA.xml b/aa_modules/aamod_QA.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="utf-8"?>
+<aap>
+    <tasklist>
+        <currenttask domain='study' desc='make QA summary of functional data' modality='MRI'>
+
+            <!-- generate a collection of epi QA maps -->
+
+            <qsub>
+                <timeBase>1</timeBase>
+                <memoryBase>1</memoryBase>
+            </qsub>
+
+            <!-- number of voxels to include in QA plots -->
+
+            <!-- actual number will probably be less, as any NaN or -->
+            <!-- zero timeseries are asssumed outside brain and skipped -->
+
+            <nvoxels>1000</nvoxels>
+
+            <!-- min/max color scaling for the carpet plot -->
+
+            <carpetscale>[-2 0.8]</carpetscale>
+
+            <!-- outlier flagging -->
+
+            <outlier_filter options='anymedian|anymean|mediansum|meansum|none'>meansum</outlier_filter>
+            <outlier_threshold>3</outlier_threshold>
+
+            <inputstreams>
+                <stream isrenameable='1'>epi</stream>
+            </inputstreams>
+
+            <outputstreams>
+                <stream>QA_summary</stream>
+            </outputstreams>
+
+        </currenttask>
+    </tasklist>
+</aap>