pipeline-scripts.md

@@ -7,23 +7,20 @@ This section is designed to outline the key procedures of each of the pipeline s
 [link](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/essinit)
 
 # Scalpart     
-Load  
-Standard Deviation comically bad on epochs, % goes to bad channel  
-Re-reference to interpolated average site of MNI surface: without SD flagged channels    
-High filter  
-Low Filter  
-Nearest Neighbour R on epochs, % goes to bad channel
+1. Load  an _init.set file
+2. Standard Deviation or quantiles used to reject comically bad epochs (% goes to bad channel)  
+3. Re-reference to interpolated average site of MNI surface: without flagged channels   
+4. High pass filter
+5. Low pass filter
+6. Nearest Neighbour R on epochs, % goes to bad channel
     * low correlation
     *  too high
-
-Rank channel - highest correlation removed    
-ALL BAD CHANNELS GONE    
-Re-reference to interpolated average site of MNI surface: without all flagged channels
-  
-Nearest Neighbour R on epochs  for time removal
+7. Rank channel - highest correlation removed    
+8. ALL BAD CHANNELS GONE    
+9. Re-reference to interpolated average site of MNI surface: without all flagged channels
+10. Nearest Neighbour R on epochs  for time removal
     * low correlation only by time segment
-
-Save
+11. Save an _sa.set file
 
 | Variable            | Default in Config File                           | Description |
 |--------------------|--------------------------------------------------|-------------|
@@ -138,10 +135,7 @@ Versions
 | [epoch_trim] | 20                      |  Percentage trim for confidence intervals during channel neighbour r criteria (20 = 10% top and bottom)           |
 | [min_gap_ms] | 4000                    |    Minimum time (ms) to allow between periods marked for rejection         |
 
-# Dipfit (Local)
-
-
-
+# Dipfit
 
 
 ***