Moved installable items to menu.

connectomics/mapper/connectome.sh

@@ -115,33 +115,33 @@ if [ -z $filename ]
                     then # split jobs for fMRI and dMRI
                     cmd="/autofs/cluster/nimlab/connectomes/software/lead_dbs/connectomics/mapper/run_cs_conseed.sh /usr/pubsw/common/matlab/8.6 1 0 /autofs/cluster/nimlab/connectomes/ $line $command $writesingle $outputfolder $maskname"
                     echo $cmd
-                    pbsubmit -q highio -l vmem=20gb -c "$cmd"
+                    pbsubmit -q highio -l vmem=30gb -c "$cmd"
                     cmd="/autofs/cluster/nimlab/connectomes/software/lead_dbs/connectomics/mapper/run_cs_conseed.sh /usr/pubsw/common/matlab/8.6 0 1 /autofs/cluster/nimlab/connectomes/ $line $command $writesingle $outputfolder $maskname"
                     echo $cmd
-                    pbsubmit -q highio -l vmem=20gb -c "$cmd"
+                    pbsubmit -q highio -l vmem=30gb -c "$cmd"
                 else
                 cmd="/autofs/cluster/nimlab/connectomes/software/lead_dbs/connectomics/mapper/run_cs_conseed.sh /usr/pubsw/common/matlab/8.6 $dofMRI $dodMRI /autofs/cluster/nimlab/connectomes/ $line $command $writesingle $outputfolder $maskname"
                 echo $cmd
-                pbsubmit -q highio -c "$cmd"
-            fi
+                pbsubmit -q highio -l vmem=30gb highio -c "$cmd"
+                fi
             done < "$filename"
         else
             if [ $doboth == 1 ]
                 then # split jobs for fMRI and dMRI
                     cmd="/autofs/cluster/nimlab/connectomes/software/lead_dbs/connectomics/mapper/run_cs_conseed.sh /usr/pubsw/common/matlab/8.6 1 0 /autofs/cluster/nimlab/connectomes/ $filename $command $writesingle $outputfolder $maskname"
                     echo $cmd
-                    pbsubmit -q highio -l vmem=20gb -c "$cmd"
+                    pbsubmit -q highio -l vmem=30gb -c "$cmd"
                     cmd="/autofs/cluster/nimlab/connectomes/software/lead_dbs/connectomics/mapper/run_cs_conseed.sh /usr/pubsw/common/matlab/8.6 0 1 /autofs/cluster/nimlab/connectomes/ $filename $command $writesingle $outputfolder $maskname"
                     echo $cmd
-                    pbsubmit -q highio -l vmem=20gb -c "$cmd"
+                    pbsubmit -q highio -l vmem=30gb -c "$cmd"
             else
                 echo $cmd
-                pbsubmit -q highio -l vmem=20gb -c "$cmd"
+                pbsubmit -q highio -l vmem=30gb -c "$cmd"
             fi
         fi
 
     else
-        # submit to actual script:
+        # run actual script:
         echo $cmd
         $cmd
     fi

ea_checkinstall.m

@@ -1,51 +1,71 @@
-function success=ea_checkinstall(cmd,force)
+function [success,commands]=ea_checkinstall(cmd,force)
 success=1;
 earoot=ea_getearoot;
 if ~exist('force','var')
     force=0;
 end
 switch cmd
+    case 'list' % simply return list of installable datasets
+        success={'Big Brain 100um subcortical (Amunts 2013)','Lead-DBS Macaque Toolbox','Structural group connectome (Horn 2013)'};
+        commands={'bigbrain','macaque','groupconnectome2013'};
     case 'bigbrain'
-        if ~exist([earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii'],'file') || force
-            disp('BigBrain not installed. Downloading...')
-            try
-            websave([earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii.gz'],'http://www.lead-dbs.org/release/data/bigbrain_2015_100um_bb.nii.gz');
-            gunzip([earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii.gz']);
-            catch
-                success=0;
-            end
-            try delete([earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii.gz']); end
-            try delete([earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii.gz.html']); end
+        checkf=[earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii'];
+        force=ea_alreadyinstalled(checkf);
+        if ~exist(checkf,'file') || force
+            success=ea_downloadasset('Bigbrain 100um subcortical',...
+                [earoot,'templates',filesep,'bigbrain_2015_100um_bb.nii.gz'],...
+                'http://www.lead-dbs.org/release/data/bigbrain_2015_100um_bb.nii.gz');
         else
             disp('BigBrain is installed.')
         end
     case 'macaque'
-        if ~exist([earoot,'toolbox',filesep,'macaque'],'file') || force
-            disp('Macaque toolbox not installed. Downloading...')
-            try
-            websave([earoot,'toolbox',filesep,'macaque.zip'],'http://www.lead-dbs.org/release/download.php?id=macaque');
-            unzip([earoot,'toolbox',filesep,'macaque.zip']);
-            catch
-                success=0;
-            end
-            try delete([earoot,'toolbox',filesep,'macaque.zip']); end
-            try delete([earoot,'toolbox',filesep,'macaque.zip.html']); end
+        checkf=[earoot,'toolbox',filesep,'macaque'];
+        force=ea_alreadyinstalled(checkf);
+        if ~exist(checkf,'file') || force
+            success=ea_downloadasset('Lead-DBS Macaque toolbox',...
+                [earoot,'toolbox',filesep,'macaque.zip'],...
+                'http://www.lead-dbs.org/release/download.php?id=macaque');
         else
             disp('Macaque toolbox is installed.')
         end
     case 'groupconnectome2013'
-        if ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) full.mat'],'file') || force
-            try
-            websave([ea_getconnectomebase('dmri'),'groupconnectome2013.zip'],'http://www.lead-dbs.org/release/download.php?id=group');
-            unzip([ea_getconnectomebase('dmri'),'groupconnectome2013.zip']);
-            catch
-                success=0;
-            end
-            try delete([ea_getconnectomebase('dmri'),'groupconnectome2013.zip']); end
-            try delete([ea_getconnectomebase('dmri'),'groupconnectome2013.zip.html']); end    
+        checkf=[ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) full.mat'];
+        force=ea_alreadyinstalled(checkf);
+        if ~exist(checkf,'file') || force
+            success=ea_downloadasset('structural group connectome (Horn 2013)',...
+                [ea_getconnectomebase('dmri'),'groupconnectome2013.zip'],...
+                'http://www.lead-dbs.org/release/download.php?id=group');
         else
             disp('Group Connectome (Horn 2013) is installed.')
         end
     otherwise
         success=0;
+end
+
+
+function success=ea_downloadasset(assetname,destination,URL)
+success=1;
+disp(['Downloading ',assetname,'...'])
+try
+    websave(destination,URL);
+    unzip(destination);
+catch
+    success=0;
+end
+try delete(destination); end
+try delete([destination,'.html']); end
+
+
+function force=ea_alreadyinstalled(checkf)
+if ~exist(checkf,'file') % then file not there, should install anyways.
+    force=1;
+    return
+end
+choice = questdlg('This dataset seems already to be installed. Do you wish to re-download it?', ...
+    'Redownload Dataset?', ...
+    'Yes','No','No');
+if strcmp(choice,'Yes')
+    force=1;
+else
+    force=0;
 end

ea_corrplot.m

@@ -3,8 +3,16 @@
 
 
 X=varargin{1};
+try
 description=varargin{2};
+catch
+    description='';
+end
+try
 labels=varargin{3};
+catch
+    labels='';
+end
 if nargin==4
     handles=varargin{4};
 end

helpers/ea_menuinstall.m

@@ -0,0 +1,14 @@
+function ea_menuinstall(~,~,cmd,force)
+
+choice=questdlg(['Please confirm to start downloading dataset: ',cmd],'Download additional data','Proceed','Cancel','Proceed');
+
+if ~strcmp(choice,'Proceed')
+    return
+end
+
+success=ea_checkinstall(cmd,force);
+if ~success
+    errordlg([cmd,' dataset could not be installed.']);
+else
+    msgbox([cmd,' successfully installed.']);
+end

helpers/gui/ea_menu_initmenu.m

@@ -18,4 +18,12 @@ function ea_menu_initmenu(handles,cmd)
         ea_menu_addsubmit(handles);
         setappdata(handles.leadfigure,'menuprobe',1);
     end
+
+    % always add install addons
+    g = uimenu('Label','Install');
+    [list,commands]=ea_checkinstall('list');
+    for l=1:length(list)
+       uimenu(g,'Label',list{l},'Callback',{@ea_menuinstall,commands{l},0}); 
+    end
+
 end

lead.m

@@ -59,11 +59,7 @@ function lead_OpeningFcn(hObject, eventdata, handles, varargin)
 guidata(hObject, handles);
 
 earoot=ea_getearoot;
-if ~isdeployed
-    addpath(genpath(earoot));
-    rmpath(genpath([earoot,'.git']));
-    rmpath(genpath([earoot,'release']));
-end
+
 
 % check for commands first
 if nargin>3
@@ -103,7 +99,11 @@ function lead_OpeningFcn(hObject, eventdata, handles, varargin)
     end
 
 end
-
+if ~isdeployed
+    addpath(genpath(earoot));
+    rmpath(genpath([earoot,'.git']));
+    rmpath(genpath([earoot,'release']));
+end
 
 set(handles.leadfigure,'name','Welcome to the Lead Neuroimaging Suite');
 

lead_dbs.m

@@ -130,21 +130,7 @@ function lead_dbs_OpeningFcn(hObject, eventdata, handles, varargin)
 
 
 
-% check if group connectome files are present
-if ~exist([ea_getconnectomebase('dmri')],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) full.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 2.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 5.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 5.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 10.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 50.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 100.mat'],'file') || ...
-        ~exist([ea_getconnectomebase('dmri'),'Groupconnectome (Horn 2013) thinned out x 500.mat'],'file')
-    set(handles.dlgroupc,'Visible','on');
-    set(handles.dlgroupc,'BackgroundColor',[0.2,0.8,0.2]);
-else
-    set(handles.dlgroupc,'Visible','off');
-end
+
 
 
 %im = imread('bg_gui.png');
@@ -1122,19 +1108,7 @@ function viewmanual_Callback(hObject, eventdata, handles)
 web('http://www.lead-dbs.org/?page_id=71', '-browser')
 
 
-% --- Executes on button press in dlgroupc.
-function dlgroupc_Callback(hObject, eventdata, handles)
-% hObject    handle to dlgroupc (see GCBO)
-% eventdata  reserved - to be defined in a future version of MATLAB
-% handles    structure with handles and user data (see GUIDATA)
-choice = questdlg('Lead will download and install the Horn 2013 Group connectome files. This may take a while...', ...
-    'Start GC Download', ...
-    'OK','Cancel','OK');
-earoot=[ea_getearoot];
-if strcmp(choice,'OK')
-    disp('Downloading Horn 2013 Group Connectome');
-    success=ea_checkinstall('groupconnectome2013',force);
-end
+
 
 
 % --- Executes on selection change in vizspacepopup.

lead_group.m

@@ -2388,15 +2388,18 @@ function calcgroupconnectome_Callback(hObject, eventdata, handles)
 normalized_fibers_mm=[]; % combined connectome
 allidx=[];
 ea_dispercent(0,'Concatenating connectome');
+maxfibno=0;
 for sub=1:length(M.patient.list)
     ea_dispercent(sub/length(M.patient.list));
 
     [nfibs,idx]=ea_loadfibertracts([M.patient.list{sub},filesep,options.prefs.FTR_normalized]);
     idx=idx(1:20000); % only use first 20k fibers of each subject.
     sumidx=sum(idx);
     nfibs=nfibs(1:sumidx,:);
+    nfibs(:,4)=nfibs(:,4)+maxfibno; % add offset
     normalized_fibers_mm=[normalized_fibers_mm;nfibs];
     allidx=[allidx;idx];
+    maxfibno=max(normalized_fibers_mm(:,4));
 end
 ea_dispercent(1,'end');
 ea_savefibertracts([M.ui.groupdir,options.prefs.FTR_normalized],normalized_fibers_mm,allidx,'mm');