Added skip if all channels in a run excluded to prevent error in kilo…

…sort
ayalab1 · Mar 3, 2023 · ee3da40 · ee3da40
1 parent d4e068f
commit ee3da40
Showing 1 changed file with 9 additions and 4 deletions.
diff --git a/preProcessing/preprocessSession.m b/preProcessing/preprocessSession.m
@@ -238,13 +238,18 @@ function  preprocessSession(varargin)
         kilosortGroup = ceil(((1:length(shanks))/nKilosortRuns));
         for i=1:nKilosortRuns
             channels = cat(2,shanks{kilosortGroup==i});
+            excludeChannels = [];
             excludeChannels = find(~ismember((1:session.extracellular.nChannels),channels));
             excludeChannels = cat(2,excludeChannels,session.channelTags.Bad.channels);
             excludeChannels = unique(excludeChannels);
-            kilosortFolder = KiloSortWrapper('SSD_path',SSD_path,'rejectchannels',excludeChannels);
-            if cleanRez
-                load(fullfile(kilosortFolder,'rez.mat'),'rez');
-                CleanRez(rez,'savepath',kilosortFolder);
+            if (length(excludeChannels)==session.extracellular.nChannels)
+                warning(['Run number ' num2str(i) ' excluded, moving on']);
+            else
+                kilosortFolder = KiloSortWrapper('SSD_path',SSD_path,'rejectchannels',excludeChannels);
+                if cleanRez
+                    load(fullfile(kilosortFolder,'rez.mat'),'rez');
+                    CleanRez(rez,'savepath',kilosortFolder);
+                end
             end
         end
     else