Merge pull request automaticanalysis#400 from jones-michael-s/fall_20…

…24_bugfixes Fall 2024 bugfixes
tiborauer · Nov 8, 2024 · 0c902d9 · 0c902d9
2 parents 882d9ac + fb5ac43
commit 0c902d9
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Showing 8 changed files with 363 additions and 21 deletions.
diff --git a/aa_engine/aas_processBIDS.m b/aa_engine/aas_processBIDS.m
@@ -662,14 +662,21 @@
 
 function LIST = tsvread(fname)
 filestr = fileread(fname);
+% this is counting lines based on the number of newlines (char(10))
+% this is error-prone because some files may have a terminal newline
+% and some may not. We can improve this by stripping any trailing
+% whitespace then adding one...
 nLines = sum(double(filestr)==10);
+filestr = strtrim(filestr);
+nLines = sum(double(filestr)==10)+1;
 LIST = textscan(filestr,'%s','Delimiter','\t');
 LIST = LIST{1};
 % protect against extraneous whitespace in the tsv:
 LIST = LIST(~cellfun(@isempty,LIST));
 LIST = reshape(LIST,[],nLines)';
 end
 
+
 function str = strrep_multi(str, old, new)
 for i = 1:numel(old)
     str = strrep(str, old{i}, new{i});

diff --git a/aa_modules/aamod_firstlevel_model.m b/aa_modules/aamod_firstlevel_model.m
@@ -178,7 +178,7 @@
             SPMdes.xX.W  = sparse(eye(size(SPMdes.xY.P,1)));
             SPMdes.xVi.V = sparse(eye(size(SPMdes.xY.P,1)));            
         end
-
+        
         %%%%%%%%%%%%%%%%%%%
         %% ESTIMATE MODEL%%
         %%%%%%%%%%%%%%%%%%%
@@ -190,7 +190,17 @@
                 spm_unlink(fullfile(SPMdes.swd, prevmask(ind,:)));
             end
         end
-
+
+        % add explicit mask if one is specified
+        % (SPM will intersect this with any implicit masking...)
+
+        if aas_stream_has_contents(aap, subj,'explicitmask')
+            % this will look for mask at subject level, then
+            % try study level is a subject level mask not found
+           explicitmaskfname = aas_getfiles_bystream_multilevel(aap, 'subject', subj, 'explicitmask');
+           SPMdes.xM.VM = spm_vol(explicitmaskfname);
+        end
+
         if (strcmp(aap.tasklist.currenttask.settings.autocorrelation,'wls'))
             SPMest = spm_rwls_spm(SPMdes);
         else
@@ -398,4 +408,4 @@
     otherwise
         aas_log(aap,1,sprintf('Unknown task %s',task));
 
-end
+end
diff --git a/aa_modules/aamod_firstlevel_model.xml b/aa_modules/aamod_firstlevel_model.xml
@@ -35,8 +35,15 @@
 			1 - implicit
 			otherwise (0-1) - fraction threshold
 			-->
+
             <firstlevelmasking>1</firstlevelmasking>
-
+
+            <!-- note you can also provide an explicit mask using the explicitmask -->
+            <!-- input stream (SPM will take the intersection w/ firstlevelmasking) -->
+            <!-- the explicit mask can be subject-level (one for each subject) -->
+            <!-- or study level (one mask applied to all subjects); specify -->
+            <!-- the explicit mask using aas_addinitialstream -->
+
             <!-- 'None' or 'AR(1)' or 'wls' (must have rWLS toolbox installed) -->
             <autocorrelation>AR(1)</autocorrelation>
 
@@ -91,13 +98,15 @@
 
             <inputstreams>
                 <stream isrenameable='1' ismodified='0'>epi</stream>
-				<stream isessential='0'>ppi</stream>
+                <stream isessential='0'>ppi</stream>
                 <stream isessential='0'>listspikes</stream>
                 <stream isessential='0'>epi_dicom_header</stream>
                 <stream isessential='0'>sliceorder</stream>
                 <stream isessential='0'>realignment_parameter</stream>                
-				<stream isessential='0'>compSignal</stream>
-				<stream isessential='0'>gd_results</stream>
+                <stream isessential='0'>compSignal</stream>
+                <stream isessential='0'>gd_results</stream>
+                <stream isessential='0'>physreg</stream>
+                <stream isessential='0'>explicitmask</stream>
             </inputstreams>
 
             <outputstreams>

diff --git a/aa_modules/aamod_firstlevel_model_dot.xml b/aa_modules/aamod_firstlevel_model_dot.xml
@@ -39,7 +39,7 @@
 			otherwise (0-1) - fraction threshold
 			-->
             <firstlevelmasking>1</firstlevelmasking>
-            
+
             <!-- 'None' or 'AR(1)' or 'wls' (must have rWLS toolbox installed) -->
             <autocorrelation>AR(1)</autocorrelation>
 
@@ -54,7 +54,7 @@
             -->
             <writeresiduals></writeresiduals>
 
-			<allowemptymodel>0</allowemptymodel>
+            <allowemptymodel>0</allowemptymodel>
 
             <!-- TR, if we wish to define it within the first level model 
             If empty, we try to find from DICOM headers... -->
@@ -97,12 +97,14 @@
 
             <inputstreams>
                 <stream >dot</stream>
-		<stream isessential='0'>ppi</stream>
+                <stream isessential='0'>ppi</stream>
                 <stream isessential='0'>listspikes</stream>
                 <stream isessential='0'>dot_header</stream>
                 <stream isessential='0'>realignment_parameter</stream>                
 		<stream isessential='0'>compSignal</stream>
 		<stream isessential='0'>gd_results</stream>
+                <stream isessential='0'>physreg</stream>
+                <stream isessential='0'>explicitmask</stream>
             </inputstreams>
 
             <!-- dot outstream used for residuals and will be removed -->