directories.md

-**Table of contents**
-
-[[_TOC_]]
-# Directories
+# **Table of contents**
+* [Directories](#directories)
+* [Data](#data)
+  * [Stage-wise folder structure](#stage-wise)
+  * [Subject-wise folder structure](#subject-wise)
+* [Log](#log)
+* [Support](#support)
+
+## Directories <a name="directories"></a>
 All of the Brock University Cognitive and Affective Neuroscience Lab pipelines follow the same directory system so that all of the scripts and configuration files can accurately load and save files. 
 :so: After downloading the pipeline please rename the outermost folder *project_name* to the name of your project.  
 
@@ -9,8 +14,11 @@ The next directories below the project name are analysis, remote_archive and rem
 
 ![folders](/uploads/0ff4703fe808462d68c7d4f5749b004e/folders.png)
 
-# Data  
-This is where you can store all the data files for all stages of the pipeline. The current default for this is a step-wise folder structure, which stores all subject files together in each step's folder. This is described below:
+## Data <a name="data"></a>
+This is where you can store all the data files for all stages of the pipeline. 
+
+### Stage-wise <a name="stage-wise"></a>
+The current default for this is a stage-wise folder structure, which stores all subject files together in each step's folder. This is described below:
 
  * **0_raw:** Your raw data files and individual location files will be placed here, they will have a extension such as .bdf. These files are loaded into the *init* script. If you are loading a level 0 ESS capsule then place the main project folder in this folder.  
 
@@ -22,7 +30,8 @@ This is where you can store all the data files for all stages of the pipeline. T
 
  * **4_study:** The pipeline does not automatically save any files into this folder, but it is useful to store files that are included in your study.
 
-**NOTE:** If desired, a subject-wise folder structure is also possible to set up with a few minor changes:
+### Subject-wise <a name="subject-wise"></a>
+If desired, a subject-wise folder structure is also possible to set up with a few minor changes. You may want to to this if you prefer to adhere to a [BIDS](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE/edit#heading=h.4k1noo90gelw) or an [ESS capsule](http://www.eegstudy.org/) standard.
 
 1. Remove all the default folders from the Data directory.
 
@@ -53,7 +62,7 @@ This is where you can store all the data files for all stages of the pipeline. T
 
 5. If you are running your jobs remotely, repeat steps 1 and 2 on the remote end.
 
-# Log
+## Log  <a name="log"></a>
 Log is automatically populated with scripts when you execute the pipeline. You will see a folder generated for every script identified by the script that was run followed by the date and time of the scripts execution. These folders contain:
 * A specific **.m** file for each subject data file.  
 * A specific **.err** file for each subject if an error occurred.
@@ -61,7 +70,7 @@ Log is automatically populated with scripts when you execute the pipeline. You w
 * A single **.sh** submit script that contains the job commands that were sent to the remote servers. (Remote Jobs Only)  
 When debugging errors this is the most important folder as you can see what is happening by using these four files.  
 
-# Support
+# Support <a name="support"></a>
 **Config** This folder contains all of the configuration files and init files that are needed for the EEGLAB plugins. Configuration files will have a **.cfg** or **.txt** extension. The naming of each configuration file should mirror the script that it goes with.  
 
 **Dependencies/eeglab:** This folder will contain the correct [BUCANL EEGLAB](https://git.sharcnet.ca/bucanl_eeglab/eeglab_asr_amica) version to support this pipeline. You can check to see the exact version by following the instructions in [Version Control](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/updates-and-git-version-control).