DEBUGs

- Termination of the pipeline via aaq_qsubVeiwerClass is correctly detected by aaq_qsub and aa_doprocessing - aamod_fieldmapfromnifti now correctly outputs TEs from specified header - Reporting includes distributions of (both the first- and second-level) contrasts
automaticanalysis · Mar 18, 2016 · 4a61770 · 4a61770
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,8 @@
 ## 5.1.0 ##
 
+#### New general features ####
+  - [aa_export_toBIDS](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_toolbox/aa_export_toBIDS.m) export raw data from aa pipeline in BIDS format (limited functionality)
+
 #### New features for structural ####
   - automatic inputstream detection (and renaming) for aamod_roi_valid_structural
 
@@ -15,8 +18,10 @@
   - aas_log works with empty `aap`
   - [aas_runfslcommand](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aas_runfslcommand.m) and [aas_runFScommand](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aas_runFScommand.m) now pass run-time MATLAB path to in-shell MATLAB (if applicable)
   - [aa_provenance](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_toolbox/provenance/aa_provenance.m) now uses run-time dependency (see "New features ...")
-  - [QueueViewer](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aaq/QueueViewerClass.m) will not delete jobs finished with errors --> job folder will be kept for debugging and [aaq_qsubVeiwerClass](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aaq/aaq_qsubVeiwerClass.m) will not interfere with `aaq`
-  - Distributions of the contrasts are reported
+  - [QueueViewer](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aaq/QueueViewerClass.m) will not delete jobs finished with errors --> job folder will be kept for debugging
+  - Termination of the pipeline via [aaq_qsubVeiwerClass](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aaq/aaq_qsubVeiwerClass.m) is correctly detected by [aaq_qsub](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aaq/aaq_qsub.m) and [aa_doprocessing](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aa_doprocessing.m)
+  - [aamod_fieldmapfromnifti](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_modules/aamod_fieldmapfromnifti.xml) now correctly outputs TEs from specified header
+  - Reporting includes distributions of (both the first- and second-level) contrasts
   - [aamod_firstlevel_threshold](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_modules/aamod_firstlevel_threshold.xml) now correctly outputs coronal sections
   - [aamod_secondlevel_model](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_modules/aamod_secondlevel_model.xml) now correctly outputs for each firstlevel contrasts
   - [aas_add_meg_session](https://github.com/rhodricusack/automaticanalysis/blob/v5/aa_engine/aas_add_meg_session.m) now prevents adding the same session multiple times (e.g. when the function is called per subject)

diff --git a/aa_engine/aa_doprocessing.m b/aa_engine/aa_doprocessing.m
@@ -395,7 +395,7 @@
         if ~isempty(localtaskqueue.jobqueue), 
             localtaskqueue.runall(dontcloseexistingworkers, false); 
         end
-        if isfield(taskqueue,'killed') && taskqueue.killed, break; end
+        if isprop(taskqueue,'killed') && taskqueue.killed, break; end
     end
     % Wait until all the jobs have finished
     taskqueue.runall(dontcloseexistingworkers, true);
@@ -408,20 +408,22 @@
 % end
 % aas_log(aap,0,'Message deleted');
 
-if ismethod(taskqueue,'QVClose'), taskqueue.QVClose; end
-
-if ~isempty(aap.options.email)
-    % In case the server is broken...
-    try
-        aas_finishedMail(aap.options.email, aap.acq_details.root)
-    catch
+if ~isprop(taskqueue,'killed') || ~taskqueue.killed
+    if ismethod(taskqueue,'QVClose'), taskqueue.QVClose; end
+
+    if ~isempty(aap.options.email)
+        % In case the server is broken...
+        try
+            aas_finishedMail(aap.options.email, aap.acq_details.root)
+        catch
+        end
+    end
+
+    if isfield(aap.options,'garbagecollection') && aap.options.garbagecollection
+        aas_garbagecollection(aap,1)
     end
 end
 
-if isfield(aap.options,'garbagecollection') && aap.options.garbagecollection
-    aas_garbagecollection(aap,1)
-end
-
 aa_close;
 
 end

diff --git a/aa_engine/aaq/aaq_qsub.m b/aa_engine/aaq/aaq_qsub.m
@@ -81,7 +81,7 @@
                     JobID = obj.taskinqueue(ftmind);
                     Jobs = obj.scheduler.Jobs([obj.scheduler.Jobs.ID] == JobID);
                     if isempty(Jobs) % cleared by the GUI
-                        obj.QV.Hold = false;
+                        if obj.QV.isvalid, obj.QV.Hold = false; end
                         obj.killed = true;
                         return;
                     end
@@ -187,7 +187,7 @@
         end
 
         function obj = QVClose(obj)
-            if ~isempty(obj.QV)
+            if ~isempty(obj.QV) && obj.QV.isvalid
                 obj.QV.Close;
                 obj.QV.delete;
                 obj.QV = [];

diff --git a/aa_modules/aamod_fieldmapfromnifti.m b/aa_modules/aamod_fieldmapfromnifti.m
@@ -64,6 +64,8 @@
         for f = fieldnames(hdrfile)'
             if strfind(f{1},'Time'), dcmhdr{1}.(f{1}) = hdrfile.(f{1})*1000; end
         end
+        if isfield(dcmhdr{1},'RepetitionTime'), dcmhdr{1}.volumeTR = dcmhdr{1}.RepetitionTime/1000; end
+        if isfield(dcmhdr{1},'EchoTime1') && isfield(dcmhdr{1},'EchoTime2'), dcmhdr{1}.volumeTE = [dcmhdr{1}.EchoTime1 dcmhdr{1}.EchoTime2]/1000; end
 
         %% Output
         dcmhdrfn=fullfile(aas_getsesspath(aap,subj,sess),'fieldmap_dicom_header.mat');

diff --git a/aa_modules/aamod_firstlevel_contrasts.m b/aa_modules/aamod_firstlevel_contrasts.m
@@ -11,8 +11,8 @@
 
 switch task
     case 'report' % [TA]
-        if ~exist(fullfile(aas_getsubjpath(aap,subj),'diagnostic_aamod_firstlevel_contrast.jpg'),'file')
-            efficiency(aap,subj);
+        if isempty(spm_select('List',aas_getsubjpath(aap,subj),'^diagnostic_.*jpg'))
+            diag(aap,subj);
         end
         fdiag = dir(fullfile(aas_getsubjpath(aap,subj),'diagnostic_*.jpg'));
         for d = 1:numel(fdiag)
@@ -253,8 +253,8 @@
         SPM = spm_contrasts(SPM);
 
         % Efficiency based on Rik Henson's script [TA]
-        if settings.estimateefficiency
-            efficiency(aap, subj, SPM); 
+        if settings.estimateefficiency && strcmp(aap.options.wheretoprocess,'localsingle')
+            diag(aap, subj, SPM); 
         end
 
         % Describe outputs
@@ -282,15 +282,6 @@
         end
         cd (cwd);
 
-        %% DIAGNOSTICS (check distribution of T-values in contrasts)
-        cons = SPM.xCon; cons = cons([cons.STAT]=='T');
-        for c = cons
-            h = img2hist(fullfile(SPM.swd, c.Vspm.fname), [], strrep(c.name,' ',''), 0.1);
-            print(h,'-djpeg','-r150', fullfile(aas_getsubjpath(aap,subj), ...
-                ['diagnostic_aamod_firstlevel_contrast_dist_' strrep(c.name,' ','') '.jpg']));
-            close(h);
-        end
-
     case 'checkrequirements'
 
     otherwise
@@ -299,7 +290,7 @@
 end
 end
 
-function h = efficiency(aap,subj,SPM)
+function h = diag(aap,subj,SPM)
 % Based on Rik Henson's script
 
 % Note this calculation of efficiency takes the 'filtered and whitened'
@@ -311,6 +302,17 @@
 if nargin < 3 % SPM is not passed (e.g. reporting)
     load(aas_getfiles_bystream(aap,subj,'firstlevel_spm'));
 end
+
+% distribution
+cons = SPM.xCon; cons = cons([cons.STAT]=='T');
+for c = cons
+    h = img2hist(fullfile(SPM.swd, c.Vspm.fname), [], strrep(c.name,' ',''), 0.1);
+    print(h,'-djpeg','-r150', fullfile(aas_getsubjpath(aap,subj), ...
+        ['diagnostic_aamod_firstlevel_contrast_dist_' strrep(c.name,' ','') '.jpg']));
+    close(h);
+end
+
+% efficiency
 X = SPM.xX.xKXs.X;
 iXX=inv(X'*X);
 

diff --git a/aa_modules/aamod_meg_average.xml b/aa_modules/aamod_meg_average.xml
@@ -9,7 +9,7 @@
             </qsub>
 
             <robust>0</robust>
-            <conditionorder desc='Condition labels sperated with ":"'></conditionorder>
+            <conditionorder desc='Condition labels separated with ":"'></conditionorder>
 
             <inputstreams>
                 <stream>meg</stream>

diff --git a/aa_modules/aamod_secondlevel_contrasts.m b/aa_modules/aamod_secondlevel_contrasts.m
@@ -9,6 +9,9 @@
 
 switch task
     case 'report'
+        if isempty(spm_select('List',aas_getstudypath(aap),'^diagnostic_aamod_secondlevel_contrast.*jpg'))
+            diag(aap);
+        end
         fdiag = dir(fullfile(aas_getstudypath(aap),'diagnostic_*.jpg'));
         for d = 1:numel(fdiag)
             aap = aas_report_add(aap,[],'<table><tr><td>');
@@ -57,16 +60,6 @@
             allCons{flc} = spm_select('FPList',SPM.swd,'^con_.*');
             allTs{flc} = spm_select('FPList',SPM.swd,'^spmT_.*');
             allFs{flc} = spm_select('FPList',SPM.swd,'^spmF_.*');
-
-            % Diagnostics (check distribution of T-values in contrasts)
-            cons = SPM.xCon; cons = cons([cons.STAT]=='T');
-            for c = cons
-                h = img2hist(fullfile(SPM.swd, c.Vspm.fname), [], strrep(c.name,' ',''), 1);
-                print(h,'-djpeg','-r150', fullfile(aas_getstudypath(aap), ...
-                    ['diagnostic_aamod_firstlevel_contrast_dist_' basename(SPM.swd) '_' strrep(c.name,' ','') '.jpg']));
-                close(h);
-            end
-
         end
 
         %% Describe outputs
@@ -82,4 +75,27 @@
         aas_log(aap,1,sprintf('Unknown task %s',task));
 
 end
+end
+
+function diag(aap,SPM)
+
+if nargin < 2 % SPM is not passed (e.g. reporting)
+    fnSPMs = aas_getfiles_bystream(aap,'secondlevel_spm');
+    for flc = 1:size(fnSPMs,1)
+        fnSPM = deblank(fnSPMs(flc,:));
+        loaded=load(fnSPM);
+        SPM(flc)=loaded.SPM;
+    end
+end
+
+for flc = 1:numel(SPM)
+    % distribution
+    cons = SPM(flc).xCon; cons = cons([cons.STAT]=='T');
+    for c = cons
+        h = img2hist(fullfile(SPM(flc).swd, c.Vspm.fname), [], strrep(c.name,' ',''), 1);
+        print(h,'-djpeg','-r150', fullfile(aas_getstudypath(aap), ...
+            ['diagnostic_aamod_secondlevel_contrast_dist_' basename(SPM(flc).swd) '_' strrep(c.name,' ','') '.jpg']));
+        close(h);
+    end
+end
 end
diff --git a/aa_toolbox/aa_convert_subjects.m b/aa_toolbox/aa_convert_subjects.m
@@ -0,0 +1,29 @@
+function aap = aa_convert_subjects(aap)
+aap0 = aarecipe('aap_parameters_defaults.xml','aap_tasklist_fmri.xml');
+fields=fieldnames(aap0.schema.acq_details.subjects);
+fields(strcmp(fields,'ATTRIBUTE')) = [];
+for field=fields'
+    newsubj.(field{1})={[]};
+end
+fields(strcmp(fields,'subjname')) = [];
+newsubj.subjname = '';
+
+newsubj(1:numel(aap.acq_details.subjects)) = newsubj;
+
+oldsubj = aap.acq_details.subjects;
+for s = 1:numel(oldsubj)
+    for field=fields'
+        if isfield(oldsubj(s),field{1})
+            newsubj(s).(field{1})={oldsubj(s).(field{1})};
+        else
+            newsubj(s).(field{1})={[]};
+        end
+    end
+end
+
+aap.acq_details.subjects = newsubj;
+aap.aap_beforeuserchanges.acq_details.subjects = newsubj;
+for s = 1:numel(aap.acq_details.subjects)
+    aap = aamod_evaluatesubjectnames(aap,'doit',s);
+end
+aap.internal.aap_initial.acq_details.subjects = aap.acq_details.subjects;