20250520 - include general folder structure for processing

Author: jncaskey

eegERP.Rmd

@@ -57,6 +57,16 @@ These may include:
 
 ## Oddball Processing Pipeline 
 
+### Recommended Folder Strucure
+
+1. `1a - Files for HAPPE`
+1. `1b - Manual Processing`
+1. `2 - Processed Files`
+1. `3 - Files for PCA`
+1. `4 - EPT Averages`
+1. `5 - PCA`
+1. `6 - PCA Components`
+
 ### MATLAB Script
 
 The following section describes the MATLAB scripts used to manage HAPPE output files for the Oddball task data. If you are running HAPPE manually (i.e., without integrating these scripts), skip to the [Oddball HAPPE inputs](#inputOddballHAPPE) section. 
@@ -452,6 +462,17 @@ These actions will take place automatically upon completion of the HAPPE pipelin
 
 ## FishShark Processing Pipeline
 
+### Recommended Folder Strucure
+
+1. `0 - Raw`
+1. `1a - Files for HAPPE`
+1. `1b - Manual Processing`
+1. `2 - Processed Files`
+1. `3 - Files for PCA`
+1. `4 - EPT Averages`
+1. `5 - PCA`
+1. `6 - PCA Components`
+
 ### MATLAB Script
 
 The following section describes the MATLAB scripts used to manage HAPPE input and output files for the FishShark task data. If you are running HAPPE manually (i.e., without integrating these scripts), skip to the [FishShark HAPPE inputs](#inputFishSharkHAPPE) section.