directories.md

@@ -6,11 +6,16 @@ This goal of this page is to provide a working understanding of how the *pipelin
 ## Main Pipeline Directory
 Baseline initialization scripts and remote configuration scripts can be found at the highest level directory.
 
-| **Filename** | **Explanation** |
-| ------------- |-------------|
-| col 3 is      | right-aligned |
-| col 2 is      | centered      |
-| zebra stripes | are neat      |
+|**Filename**|**Explanation**|
+|-------------|-------------|
+|bids|See BIDS section|
+|remote_archive|Mounting point for software to transfer data|
+|remote_work|Secondary mounting point for software to transfer data|
+|bids_init_path.m|h|
+|eeg_init_path.m|h|
+|lossless_path.m|Matlab script to check if necessary dependencies are present and if so, adds them to the Matlab path|
+|setup-remote.m|Configuration script for building dependencies on remote clusters. See [here](configuring-remote)|
+*Note: Excluded files at this level are git repository specific and have no actual effect on the pipeline*
 
 
 ## Log  <a name="log"></a>