diff --git a/preProcessing/preprocessSession.m b/preProcessing/preprocessSession.m index 17cafa8..be4e0c2 100644 --- a/preProcessing/preprocessSession.m +++ b/preProcessing/preprocessSession.m @@ -89,6 +89,15 @@ function preprocessSession(varargin) addParameter(p, 'path_to_dlc_bat_file', '', @isfile) addParameter(p, 'nKilosortRuns', 1, @isnumeric); addParameter(p, 'sortFiles', true, @islogical); +addParameter(p, 'clean_rez_params', { ... + 'mahalThreshold', 12, ... + 'minNumberOfSpikes', 20, ... + 'multiTrough', true, ... + 'isi', true, ... + 'singleBin', true, ... + 'global', true, ... + }, @iscell); + % addParameter(p,'pullData',[],@isdir); To do... parse(p, varargin{:}); @@ -112,6 +121,7 @@ function preprocessSession(varargin) path_to_dlc_bat_file = p.Results.path_to_dlc_bat_file; nKilosortRuns = p.Results.nKilosortRuns; sortFiles = p.Results.sortFiles; +clean_rez_params = p.Results.clean_rez_params; if ~exist(basepath, 'dir') @@ -213,7 +223,7 @@ function preprocessSession(varargin) fprintf(1, 'There was an error! The message was:\n%s', e.message); try warning('LFPfromDat failed, trying ResampleBinary') - ResampleBinary([basepath, '\', basename, '.dat'],... + ResampleBinary([basepath, '\', basename, '.dat'], ... [basepath, '\', basename, '.lfp'], session.extracellular.nChannels, 1, 16); catch e warning('LFP file could not be generated, moving on'); @@ -281,7 +291,7 @@ function preprocessSession(varargin) kilosortFolder = KiloSortWrapper('SSD_path', SSD_path, 'rejectchannels', excludeChannels); if cleanRez load(fullfile(kilosortFolder, 'rez.mat'), 'rez'); - CleanRez(rez, 'savepath', kilosortFolder); + CleanRez(rez, 'savepath', kilosortFolder, clean_rez_params{:}); end end end @@ -292,7 +302,7 @@ function preprocessSession(varargin) 'rejectchannels', session.channelTags.Bad.channels); % 'NT',20*1024 for long sessions when RAM is overloaded if cleanRez load(fullfile(kilosortFolder, 'rez.mat'), 'rez'); - CleanRez(rez, 'savepath', kilosortFolder); + CleanRez(rez, 'savepath', kilosortFolder, clean_rez_params{:}); end % PhyAutoClustering(kilosortFolder); end