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# **Table of contents**
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* [Directories](#directories)
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* [Data](#data)
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* [Stage-wise](#stage-wise)
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* [Subject-wise](#subject-wise)
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* [Log](#log)
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* [Support](#support)
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## Directories <a name="directories"></a>
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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.
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:so: After downloading the pipeline please rename the outermost folder *project_name* to the name of your project.
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The next directories below the project name are analysis, remote_archive and remote work. Analysis contains the majority of the project information and remote_archive and remote_work contain are placeholder folders if you choose to [mount your remote work](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/remote-start-up#mounting-the-project).
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![folders](/uploads/0ff4703fe808462d68c7d4f5749b004e/folders.png)
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## Data <a name="data"></a>
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This is where you can store all the data files for all stages of the pipeline.
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### Stage-wise <a name="stage-wise"></a>
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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:
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* **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.
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* **1_init:** Your data files will go here after they have been initialized and are have the .set/.fdt extension. If the files only have a .set part make sure your eeglab options are correct, and that you loaded the matlab.minit file in your configs.These files are loaded into the rest of the pipeline.
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* **2_preproc:** All of the processed files created by the pipeline will be saved into this folder. The final file from the main pipeline is the *_comp* file. This file then goes into *dipfit* for the final local part. These files are essentially backups so you can go look at the data during any stage of the processing you want.
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* **3_check:** The pipeline does not automatically save any files into this folder, but it is useful to store files after they have been visually inspected or segmented and are ready for analysis.
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* **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.
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### Subject-wise <a name="subject-wise"></a>
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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.
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1. Remove all the default folders from the Data directory.
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2. Copy your subject folders into this directory (assumes that each subject's files for all steps will be stored within its own subject folder).
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3. When running a job through the File->Batch->Run History Template Batch menu, replace the values for '[in_path]' and '[out_path]' (if it exists),
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located in the "replace_string" field of each batch config file, with analysis/data.
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*Example:*
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[in_path],analysis/data/1_init ----- change to -----> [in_path],analysis/data
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[out_path],analysis/data/2_preproc ----- change to -----> [out_path],analysis/data
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4. For now, the path to the folder containing the subject folders must be manually typed/pasted into the "path:" field. This will usually be analysis/data if that's
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the folder you'd like to use. Likewise, the _init.set file name(s) must be manually typed/pasted into the "file:" field. In this case they must include the name
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of the subject folder in the name.
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*Example:*
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subj001/subj001_init.set
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subj002/subj002_init.set
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subj003/subj003_init.set
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This should work regardless of how many folders deep the init file is stored.
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5. If you are running your jobs remotely, repeat steps 1 and 2 on the remote end.
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## Log <a name="log"></a>
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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:
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* A specific **.m** file for each subject data file.
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* A specific **.err** file for each subject if an error occurred.
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* A specific **.log** file for each subject that records the remote system command window.
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* A single **.sh** submit script that contains the job commands that were sent to the remote servers. (Remote Jobs Only)
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When debugging errors this is the most important folder as you can see what is happening by using these four files.
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# Support <a name="support"></a>
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**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.
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**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).
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**Misc:** This folder contains a bunch of miscellaneous support pieces such amica parameter files, EEG location models, and event renaming files.
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**Scripts:** This folder contains all of the [Script Files](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/pipeline-scripts) that make up process behind the pipeline. These have the extension **.htb** and are called **H**istory **T**emplate **B**atch as they are executed in the *batch_context* extension.
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***
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It is important to note that the folder design is built into pipeline, and in order for it to run smoothly the directory structure should not be changed without carefully consulting each part of the pipeline.
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[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/home) |
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