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[[_TOC_]]
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# Overview
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This script is an attempt to create a standardised import function for the BUCANL lossless pipeline. It accepts raw data files and will preform all of the necessary steps to prepare the raw files for the [eeg_pipe_asr_amica pipeline](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/home) (this pipeline). This script was designed to be very versatile for any level of automation and knowledge base of [batch context](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) configuration scripts.
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This script is an attempt to create a standardised import function for the BUCANL lossless pipeline. It accepts raw data files and will preform all of the necessary steps to prepare the raw files for the [eeg_pipe_asr_amica pipeline](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/wikis/home) (this pipeline). This script was designed to be very versatile for any level of automation and knowledge base of [batch context](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) configuration scripts.
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Raw files can vary greatly depending on the modality used to collect the data, while init files going into the pipeline need to be prepared in a particular way for smooth processing during the initial stages and for ICA. This script currently can prepare data from two different styles:
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**1. ESS Capsule**
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To load a capsule make sure it it is at the level 1 stage, and load the study_description.xml file into the [run history batch file GUI](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) under the file upload section. The metadata stored in the capsule will be automatically accessed in the script and be used to find all the files the study contains. Using the [file structure](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/directories) designed for this pipeline is best as the saved files will be directed into the *analysis/data/1_init* folder when they are complete.
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To load a capsule make sure it it is at the level 1 stage, and load the study_description.xml file into the [run history batch file GUI](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) under the file upload section. The metadata stored in the capsule will be automatically accessed in the script and be used to find all the files the study contains. Using the [file structure](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/wikis/directories) designed for this pipeline is best as the saved files will be directed into the *analysis/data/1_init* folder when they are complete.
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:so: We recommend storing the *Main_Study_Folder* inside of *analysis/data/0_raw* making the study_description.xml available in *analysis/data/0_raw/Main_Study_Folder/level_1/study_description.xml*
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:so: To find out more about ESS capsules go to the [Big EEG Consortium](http://www.bigeeg.org/).
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**2. Raw Files**
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You can also load raw files into the [run history batch file GUI]](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) file upload as normal. Using the [file structure](https://git.sharcnet.ca/bucanl_pipelines/eeg_pipe_asr_amica/wikis/directories) for this pipeline is best as the saved files will be directed into the *analysis/data/1_init* folder when they are complete. This means uploading your raw files from the *analysis/data/0_raw* folder.
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You can also load raw files into the [run history batch file GUI]](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) file upload as normal. Using the [file structure](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/wikis/directories) for this pipeline is best as the saved files will be directed into the *analysis/data/1_init* folder when they are complete. This means uploading your raw files from the *analysis/data/0_raw* folder.
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:so: On a side note make sure your EEGLAB work space is set to the *eeglab_asr_amica* folder so that *analysis* is the first folder on your path.
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... | ... | @@ -263,4 +263,4 @@ ESS capsule references on this page are to the *RSVP Target Detection* study fou |
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***
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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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[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_pipelines/bids_lossless_eeg/wikis/home) |
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