Improve signal quality check (#254)

* output SCI as a function of time * Add compatibility if signal processing toolbox is not available * Fix detect bad channels * file cleanup * simplify process: use file instead of custom * Rename process and first POC for computing CV * Add POC for continious CV, SCI and power * Clean code and speed up SCI * Rename Quality Check * Clean code. * dont delete SCI file * Move to deprecated folder * Add warning to SCI * Rename files * Keep signals event * add figure * fix folder
Nirstorm · Feb 4, 2025 · b570d37 · b570d37
1 parent b28ee8a
commit b570d37
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Showing 3 changed files with 388 additions and 19 deletions.
diff --git a/bst_plugin/preprocessing/process_nst_sci.m → bst_plugin/deprecated/process_nst_sci.m b/bst_plugin/preprocessing/process_nst_sci.m → bst_plugin/deprecated/process_nst_sci.m
@@ -31,7 +31,7 @@
 sProcess.Comment     = 'Scalp Coupling Index';
 sProcess.Category    = 'Custom';
 sProcess.SubGroup    = {'NIRS', 'Pre-process'};
-sProcess.Index       = 1201;
+sProcess.Index       = 0;
 sProcess.isSeparator = 0;
 sProcess.Description = 'https://github.com/Nirstorm/nirstorm/wiki/Scalp-coupling-index';
 
@@ -61,6 +61,9 @@
 end
 
 function OutputFiles = Run(sProcess, sInputs)
+
+warning('This process has been deprecated. Use Signal Quality Control instead')
+
 OutputFiles = {};
 for iInput=1:length(sInputs)
     % Load recordings

diff --git a/bst_plugin/preprocessing/process_nst_detect_bad.m b/bst_plugin/preprocessing/process_nst_detect_bad.m
@@ -268,11 +268,11 @@
     channel_flags   = sData.ChannelFlag;
     nirs_flags = strcmpi({channel_def.Channel.Type}, 'NIRS');
 
-    signal=sData.F';
-    nirs_signal=signal(:,nirs_flags);
+    signal      = sData.F';
+    nirs_signal = signal(:,nirs_flags);
 
-    nb_chnnels=size(signal,2);
-    nb_sample= size(signal,1);
+    nb_chnnels  = size(signal,2);
+    nb_sample   = size(signal,1);
 
 
     % Remove negative channel
@@ -282,11 +282,12 @@
 
     % Remove channel with low SCI or power
     if options.option_sci.Value 
-        fs = 1 / diff(sData.Time(1:2));
-        [SCI, power] = process_nst_sci('compute',nirs_signal',channel_def.Channel(nirs_flags), fs);
+
+        window_length = 10;
+        [~, SCI, power] = process_nst_quality_check('compute_SCI', sData.Time, nirs_signal', window_length, channel_def.Channel(nirs_flags));
 
-        SCI = SCI *100;
-        power = power*100;
+        SCI     = median(SCI,2)   * 100;
+        power   = median(power,2) * 100;
 
         SCI_threshold = options.sci_threshold.Value{1};
         SCI_channels = false(1,nb_chnnels);
@@ -325,18 +326,14 @@
     % Remove channel with high CV
     if options.option_coefficient_variation.Value
         CV_threshold = options.coefficient_variation.Value{1};                 
-        low_cutoff  = 1/200;
-        high_cutoff = 0.1;
-        order       = 2;
-        fs = 1 / diff(sData.Time(1:2));
-
-        [nirs_filtered, transient] = process_nst_iir_filter('Compute',nirs_signal(100:end,:), fs, 'bandpass', low_cutoff, ...
-                                  high_cutoff, order, 1);
-
-        CV = std(nirs_filtered,1,'omitnan')./mean(nirs_filtered,1).*100;
 
+        window_length = 1000;
+        [~,  CV ] = process_nst_quality_check('compute_CV', sData.Time, nirs_signal', window_length);
+
+        CV = median(CV,2) * 100;
+
         CV_channels = false(1,nb_chnnels);
-        CV_channels(nirs_flags) = CV>CV_threshold ;
+        CV_channels(nirs_flags) = CV > CV_threshold ;
 
         channel_flags(CV_channels) = -1; 
         criteria(end+1,:)= {'high coeffience variation channels', CV_channels,{}};