Merge pull request automaticanalysis#209 from tiborauer/master

DEBUGS

aa_engine/aas_getfiles_bystream_dep.m

@@ -1,6 +1,9 @@
 function fname = aas_getfiles_bystream_dep(aap,domain,indices,stream)
 % locate inputstream
 inputstreamindex = strcmp({aap.internal.inputstreamsources{aap.tasklist.currenttask.modulenumber}.stream.name},stream);
+if not(any(inputstreamindex))
+    inputstreamindex = cell2mat(cellfun(@(x) any(strcmp(strsplit(x,'.'),stream)),{aap.internal.inputstreamsources{aap.tasklist.currenttask.modulenumber}.stream.name},'UniformOutput',false));
+end
 
 % obnain source module number
 sourcenumber = aap.internal.inputstreamsources{aap.tasklist.currenttask.modulenumber}.stream(inputstreamindex).sourcenumber;

aa_modules/aamod_bet.m

@@ -44,20 +44,20 @@
         [pth nme ext]=fileparts(Simg);
 
         outStruct=fullfile(pth,['bet_' nme fslext]);
-
+
+        fslcommand = sprintf('bet %s %s -f %f -v',Simg,outStruct, ...
+                aap.tasklist.currenttask.settings.bet_f_parameter);
+
         if aap.tasklist.currenttask.settings.robust
-            % Run BET [-R Using robust setting to improve performance!]
             aas_log(aap,false,'1st BET pass (recursive) to find optimal centre of gravity and radius')
-            [junk, w]=aas_runfslcommand(aap, ...
-                sprintf('bet %s %s -f %f -v -R',Simg,outStruct, ...
-                aap.tasklist.currenttask.settings.bet_f_parameter));
-        else
-            aas_log(aap,false,'1st BET pass')
-            [junk, w]=aas_runfslcommand(aap, ...
-                sprintf('bet %s %s -f %f -v ',Simg,outStruct, ...
-                aap.tasklist.currenttask.settings.bet_f_parameter));
+            fslcommand = [fslcommand ' -R'];
+        else aap.tasklist.currenttask.settings.biasneck
+            aas_log(aap,false,'1st BET pass (using bias field and neck cleanup) to find optimal centre of gravity and radius')
+            fslcommand = [fslcommand ' -B'];
         end
 
+        [junk, w]=aas_runfslcommand(aap, fslcommand);
+
         aas_log(aap,false,sprintf('Bet output: %s',w));
 
         % This outputs last radius from recursive command...
@@ -151,7 +151,6 @@ function diag(aap,varargin)
 outstreams = aas_getstreams(aap,'output'); % 
 Simg = aas_getfiles_bystream(aap,aap.tasklist.currenttask.domain,[varargin{:}],inpstreams{1},'input');
 outStruct = aas_getfiles_bystream(aap,aap.tasklist.currenttask.domain,[varargin{:}],outstreams{1},'output');
-outMesh = aas_getfiles_bystream(aap,aap.tasklist.currenttask.domain,[varargin{:}],outstreams{3},'output');
 
 spm_check_registration(Simg)
 
@@ -165,6 +164,7 @@ function diag(aap,varargin)
 spm_orthviews('addcolouredimage',1,outStruct, [0.9 0.4 0.4])
 % Add mesh outlines, to see if BET has worked properly!
 if aap.tasklist.currenttask.settings.masks
+    outMesh = aas_getfiles_bystream(aap,aap.tasklist.currenttask.domain,[varargin{:}],outstreams{3},'output');
     for r = 1:size(outMesh,1)
         if strfind(outMesh(r,:), aas_getfslext(aap))
             indx = indx + 1;
@@ -181,4 +181,4 @@ function diag(aap,varargin)
 set(gcf,'PaperPositionMode','auto','Renderer','zbuffer');
 print('-djpeg','-r75',fullfile(aas_getpath_bydomain(aap,aap.tasklist.currenttask.domain,[varargin{:}]), ...
     ['diagnostic_' aap.tasklist.main.module(aap.tasklist.currenttask.modulenumber).name '_' aap.acq_details.subjects(varargin{1}).subjname '.jpg']));
-end
+end

aa_modules/aamod_bet.xml

@@ -22,8 +22,13 @@
 
             <!-- BET F parameter - from 0 to 1 (least to most agressive skull stripping -->
             <bet_f_parameter>0.5</bet_f_parameter>
+
+            <!-- The following parameters are mutually exclusive. Their existence will be tested sequentially in this order -->
             <!-- Robust bet (recursive BET)? 0 - NO; 1 - YES  -->
             <robust>1</robust>
+            <!-- Bias field and neck cleanup? 0 - NO; 1 - YES  -->
+            <biasneck>0</biasneck>
+
             <!-- Do we want to output the masks & meshes from BET? 0 - NO; 1 - YES 
             This might slightly increase the accuracy of BET -->
             <masks>1</masks>
@@ -42,4 +47,4 @@
 
         </currenttask>
     </tasklist>
-</aap>
+</aap>

aa_modules/aamod_firstlevel_contrasts.m

@@ -149,7 +149,7 @@
                             else
                                 sessweights = ones(1,numel(sessions));
                             end
-                            [junk, indsess] = intersect(sessnames,sessions);
+                            indsess = cellfun(@(x) find(strcmp(sessnames,x)), sessions);
                             sessforcon(indsess) = sessweights;
                         end
 

aa_modules/aamod_secondlevel_model.m

@@ -11,7 +11,38 @@
 
 switch task
     case 'report'
-        if ~exist(fullfile(aas_getstudypath(aap),['diagnostic_' aap.tasklist.main.module(aap.tasklist.currenttask.modulenumber).name '_design.jpg']),'file')
+        if numel(cellstr(spm_select('List',aas_getstudypath(aap),'^diagnostic.*'))) < 2 % two images expected
+            % group mask
+            for subj = 1:numel(aap.acq_details.subjects)
+                mask{subj} = aas_getfiles_bystream(aap,'subject',subj,'firstlevel_brainmask');
+            end
+            Vm = cell2mat(spm_vol(mask));
+            Ym = spm_read_vols(Vm);
+            Ys = sum(Ym,4);
+            Vs = Vm(1);
+            Vs.fname = fullfile(aas_getstudypath(aap),'groupmaps_summary.nii');
+            spm_write_vol(Vs,Ys)
+
+            so = slover;
+            so.figure = spm_figure('GetWin', 'SliceOverlay');
+
+            so.img.vol = spm_vol(fullfile(aap.directory_conventions.spmdir,aap.directory_conventions.T1template));
+            so.img.prop = 1;
+            so.transform = 'axial';
+            so = fill_defaults(so);
+            so.slices = -72:6:108;
+
+            so.img(2).vol = Vs;
+            so.img(2).type  = 'truecolour';
+            so.img(2).prop  = 0.33;
+            so.img(2).cmap  = hot;
+            so.img(2).range = [0 max(Ys(:))];
+            so.cbar = [so.cbar 2];
+
+            so = paint(so);
+            spm_print(fullfile(aas_getstudypath(aap),['diagnostic_' aap.tasklist.main.module(aap.tasklist.currenttask.modulenumber).name '_groupmasksummary.jpg']),so.figure,'jpg');
+
+            % design
             fSPM = aas_getfiles_bystream(aap,aap.tasklist.currenttask.outputstreams.stream{1}); fSPM = deblank(fSPM(1,:)); %all models are the same (number of inputs may vary)
             load(fSPM);            
             spm_DesRep('DesOrth',SPM.xX);

aa_modules/aamod_secondlevel_model.xml

@@ -11,6 +11,7 @@
             <permanenceofoutput>3</permanenceofoutput>
 
             <inputstreams>
+                <stream diagnostic="1">firstlevel_brainmask</stream>
                 <stream>firstlevel_spm</stream>
                 <stream>firstlevel_cons</stream>
             </inputstreams>