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# Directories
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All of the BUCANL 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__________________________________________.
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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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# Data
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**0_raw:** Your raw data files and location files will be placed here, they will have a extension such as .bdf. These files are loaded into the *init* script.
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**1_init:** Your data files will go here after they have been initialled and are have the .set/.fdt extension. These files are loaded into the *scalpart* script.
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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.
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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 and are ready for analysis.
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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 your own *init* script or the StudyBuddy 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 initialled 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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# Log
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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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# Support
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**Config** This folder contains all of the configuration files that are needed for the EEGLAB plugins. Configuration files will have a **.cfg** or **.txt** extension.
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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 the configuration files should mirror the script that they 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, and EEG location models.
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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 history Batch Files as they are executed with the *batch_context* extension.
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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 **B**atch **F**iles 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 design.
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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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