automaticanalysis · tiborauer · Nov 19, 2021 · Oct 20, 2021 · Oct 24, 2021 · Oct 24, 2021
diff --git a/.github/workflows/aa_test.yml b/.github/workflows/aa_test.yml
diff --git a/aa.json b/aa.json
@@ -1,6 +1,6 @@
 {
 	"Name": "automaticanalysis",
-	"Version": "5.7.0",
+	"Version": "5.7.1",
 	"Date": "Jun 2021",
 	"ManuscriptRef": "Cusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, Peelle JE (2015). Automatic analysis (aa): Efficient neuroimaging workflows and parallel processing using Matlab and XML. Frontiers in Neuroinformatics 8:90.",
 	"ManuscriptURL": "http:\/\/dx.doi.org\/10.3389\/fninf.2014.00090",

diff --git a/aa_engine/aaq/aaq.m b/aa_engine/aaq/aaq.m
@@ -217,7 +217,9 @@ function save(obj,fn)
                     end
 
                 case 'parallel.cluster.Slurm'
-                    if ~isempty(obj.initialSubmitArguments), obj.initialSubmitArguments = " " + obj.initialSubmitArguments; end
+                    if strlength(obj.initialSubmitArguments) > 0 && ~startsWith(obj.initialSubmitArguments,' ')
+                        obj.initialSubmitArguments = " " + obj.initialSubmitArguments; 
+                    end
                     obj.pool.SubmitArguments = compose("--mem=%dG --time=%d", mem, walltime*60);
                     if isMaxFiltInTasklist && isNeuromagSpec
                         obj.initialSubmitArguments = obj.initialSubmitArguments + " --constraint=maxfilter";
@@ -229,7 +231,9 @@ function save(obj,fn)
                     end
 
                 case 'parallel.cluster.Torque'
-                    if ~isempty(obj.initialSubmitArguments), obj.initialSubmitArguments = " " + obj.initialSubmitArguments; end
+                    if strlength(obj.initialSubmitArguments) > 0 && ~startsWith(obj.initialSubmitArguments,' ')
+                        obj.initialSubmitArguments = " " + obj.initialSubmitArguments; 
+                    end
                     obj.pool.SubmitArguments = compose("-l mem=%dGB, walltime=%d:00:00", mem, walltime);
                     if isMaxFiltInTasklist && isNeuromagSpec
                         % TODO: clarify whether/how NODESET should be eliminated

diff --git a/aa_engine/aaq/aaq_batch.m b/aa_engine/aaq/aaq_batch.m
@@ -320,7 +320,11 @@ function runall(obj, dontcloseexistingworkers, waitforalljobs) %#ok<INUSL>
                                 startTime = char(Task.StartDateTime);
                                 finishTime = char(Task.FinishDateTime);
                                 if ~isempty(finishTime)
-                                    usedTime = char(Task.RunningDuration);
+                                    if isprop(Task,'RunningDuration')
+                                        usedTime = char(Task.RunningDuration);
+                                    else
+                                        usedTime = aas_getTaskDuration(Task);
+                                    end
                                 end
                             elseif isprop(Task,'StartTime')
                                 startTime = Task.StartTime;

diff --git a/aa_engine/aas_getfiles_bystream.m b/aa_engine/aas_getfiles_bystream.m
@@ -137,7 +137,6 @@
     inpstreamdesc = '';
     allfiles = '';
     md5 = '';
-unix('touch /Users/peellelab/000_AAS_GETFILE_FAIL3.txt');
 end
 
 end
diff --git a/aa_modules/aamod_CONN.m b/aa_modules/aamod_CONN.m
@@ -1,4 +1,4 @@
-function [aap,resp]=aamod_CONN_validate(aap,task,subj)
+function [aap,resp]=aamod_CONN(aap,task,subj)
 resp='';
 
 switch task

diff --git a/aa_modules/aamod_firstlevel_threshold.m b/aa_modules/aamod_firstlevel_threshold.m
@@ -130,7 +130,6 @@
         try doTFCE = aap.tasklist.currenttask.settings.threshold.doTFCE; catch, doTFCE = 0; end % TFCE?
         corr = aap.tasklist.currenttask.settings.threshold.correction;		% correction
         u0   = aap.tasklist.currenttask.settings.threshold.p;			% height threshold
-        k   = aap.tasklist.currenttask.settings.threshold.extent;		% extent threshold {voxels}
         nSl = aap.tasklist.currenttask.settings.overlay.nth_slice;
         tra = aap.tasklist.currenttask.settings.overlay.transparency;
         Outputs.thr = '';
@@ -202,6 +201,7 @@
             n = 1; % No conjunction
 
             if doTFCE
+                k = aas_getsetting(aap,'threshold.extent');
                 job.spmmat = {fSPM};
                 job.mask = {fullfile(fileparts(fSPM),'mask.nii,1')};
                 job.conspec = struct( ...
@@ -249,8 +249,8 @@
                 end
 
                 % Extent threshold filtering
-                if ischar(k) % probability-based
-                    k = strsplit(k,':'); k{2} = str2double(k{2});
+                if ischar(aas_getsetting(aap,'threshold.extent')) % probability-based
+                    k = strsplit(aas_getsetting(aap,'threshold.extent'),':'); k{2} = str2double(k{2});
                     iSPM = SPM;
                     iSPM.Ic = c;
                     iSPM.thresDesc = corr;
@@ -268,6 +268,9 @@
                     pInd = strcmp(T.hdr(1,:),'cluster') & strcmp(T.hdr(2,:),k{1});
                     kInd = strcmp(T.hdr(2,:),'equivk');
                     k = min(cell2mat(T.dat(cellfun(@(p) ~isempty(p) && p<k{2}, T.dat(:,pInd)),kInd)));
+                    if isempty(k), k = Inf; end
+                else
+                    k = aas_getsetting(aap,'threshold.extent');
                 end
 
                 A     = spm_clusters(XYZ);

diff --git a/aa_modules/aamod_meeg_preparesourcemodel.m b/aa_modules/aamod_meeg_preparesourcemodel.m
@@ -122,6 +122,11 @@
                 sourceatlas.aparclabel = vertcat(spm_file(atlaslh.aparclabel,'prefix','lh_'),spm_file(atlaslh.aparclabel,'prefix','rh_'));
                 sourceatlas.aparc = vertcat(atlaslh.aparc, atlasrh.aparc+numel(atlaslh.aparclabel));
 
+                % register to sourcemodel
+                FT.addExternal('freesurfer');
+                fsmri = MRIread(mrifn);
+                sourceatlas = ft_transform_geometry(fsmri.vox2ras/fsmri.tkrvox2ras, sourceatlas);
+
                 % diag
                 fname = fullfile(aas_getsubjpath(aap,subj),['diagnostic_' aap.tasklist.main.module(aap.tasklist.currenttask.modulenumber).name '_atlas.jpg']);
                 if ~exist(fname,'file')

diff --git a/aa_modules/aamod_secondlevel_threshold.m b/aa_modules/aamod_secondlevel_threshold.m
@@ -94,7 +94,6 @@
 
         % Init
         u0   = aap.tasklist.currenttask.settings.threshold.p;				% height threshold
-        k   = aap.tasklist.currenttask.settings.threshold.extent;			% extent threshold {voxels}
         nSl = aap.tasklist.currenttask.settings.overlay.nth_slice;
         tra = aap.tasklist.currenttask.settings.overlay.transparency;
 
@@ -190,6 +189,7 @@
                 if strcmp(corr,'TFCE') && strcmp(STAT,'F'), corr = 'FWE'; end % TFCE does not support F-test -> FWE
 
                 if strcmp(corr,'TFCE')
+                    k = aas_getsetting(aap,'threshold.extent');
                     job.spmmat = {fnSPM};
                     job.mask = {fullfile(fileparts(fnSPM),'mask.nii,1')};
                     job.conspec = struct( ...
@@ -236,8 +236,8 @@
                     end
 
                     % Extent threshold filtering
-                    if ischar(k) % probability-based
-                        k = strsplit(k,':'); k{2} = str2double(k{2});
+                    if ischar(aas_getsetting(aap,'threshold.extent')) % probability-based
+                        k = strsplit(aas_getsetting(aap,'threshold.extent'),':'); k{2} = str2double(k{2});
                         iSPM = SPM;
                         iSPM.Ic = c;
                         iSPM.thresDesc = corr;
@@ -255,6 +255,9 @@
                         pInd = strcmp(T.hdr(1,:),'cluster') & strcmp(T.hdr(2,:),k{1});
                         kInd = strcmp(T.hdr(2,:),'equivk');
                         k = min(cell2mat(T.dat(cellfun(@(p) ~isempty(p) && p<k{2}, T.dat(:,pInd)),kInd)));
+                        if isempty(k), k = Inf; end
+                    else
+                        k = aas_getsetting(aap,'threshold.extent');
                     end
 
                     A     = spm_clusters(XYZ);

diff --git a/aa_engine/aas_delete_deststage.m → aa_tools/aa_delete_deststage.m b/aa_engine/aas_delete_deststage.m → aa_tools/aa_delete_deststage.m
@@ -1,5 +1,26 @@
-function dirs2delete = aas_delete_deststage(aap,indices,varargin)
+function dirs2delete = aa_delete_deststage(aap,indices,varargin)
 % recursively delete/backup destination stages
+%
+% It removes or backs up existing (intermediate) steps of a workflow before
+% the re-execution of these steps (with different settings).
+%
+% Compulosory positional arguments:
+%   aap:        aap structure actualised for the stage whose destinations 
+%               are to be removed/backed-up
+%   indices:    array of indices corresponding to the domain of the stage,
+%               e.g.
+%                   study   - []
+%                   subject - [subj]
+%                   session - [subj sess]
+% 
+% Optional parameters (key-value pairs):
+%   includeCurrent: whether to remove/back up the current stage, as well
+%                   (default: false)
+%   dryrun:         whether to only compile the list of stage folders to be
+%                   removed/backed-up (default: false)
+%   backupFolder:   path to the folder in which the stages are backed-up,
+%                   The folder will be created if does not exist. If empty,
+%                   the operation is delete rather than back-up. (default: '')
 
 argParse = inputParser;
 argParse.addParameter('includeCurrent',false,@(x) islogical(x) || isnumeric(x));