... | ... | @@ -3,24 +3,9 @@ The BIDS Lossless EEG pipeline is unsurprisingly, BIDS compliant. As such, data |
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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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