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[[_TOC_]]
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# Overview
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This script will take in a ESS capsule study_description.xml file or the names of your raw data file collection from batch config and do all of the necessary steps to prepare the raw files for the eeg_pipe_asr_amica pipeline. This script focuses on being very versatile for any level of automation and knowledge base of configuration scripts.
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This script takes in raw data files and preforms 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 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 to prepared just right for smooth processing. This script current 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 [batch config](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) file upload. The metadata stored in the capsule will be automatically accessed in the script. 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.
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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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**2. Raw Files**
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You can also load raw files into the [batch config](https://git.sharcnet.ca/bucanl_eeglab_extensions/batch_context/wikis/home) file upload. 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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Raw files can vary greatly depending on the modality used to collect the data, while init files going into the pipeline need to to prepared just right for smooth processing.
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This script takes the raw data file through 3 process:
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1. Loading the File
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... | ... | @@ -22,11 +31,10 @@ This script will only produce GUI's if it is missing a necessary piece of inform |
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If you want to run this script fully automatic or on a remote cluster you need to ensure that each of the mandatory variables described below are denoted in either the batch config or the ESS capsule metadata.
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**ESS LoadType**
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Mandatory variables are split between the ESS capsule metadata and the config parameters. Do not worry about the XML variables in this case as they are automatically found by reading the ESS study_description.xml file. that you loaded when batching. The other remaining variables need to be in the config, if they are not, a GUI will pop up for most of them to prompt you for the inputs. This GUI will not work on remote clusters and will ruin the jobs.
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* Mandatory variables are split between the ESS capsule metadata and the config file. Do not worry about the XML variables in this case as they are automatically found by reading the ESS study_description.xml file that you loaded when batching.
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**OTHER LoadType**
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All of the mandatory variables need to be in the config, if they are not, a GUI will pop up for most of them to prompt you for the inputs. This GUI will not work on remote clusters and will ruin the jobs.
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* All of the mandatory variables need to be in the config file.
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| LOADTYPE |ESS | ESS | OTHER | OTHER | OTHER | |
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|----------------|:---:|:------:|:------:|:------:|:------:|---------------------------------------------------------------------------------|
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... | ... | @@ -46,10 +54,13 @@ All of the mandatory variables need to be in the config, if they are not, a GUI |
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# Variable Specifics
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**loadType**
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**loadType**
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The load type refers to whether you are starting from an ESS capsule or from a list of raw files. Use
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```[loadType],ESS``` or ``` [loadType],OTHER ``` in the config replace_string. If you leave config empty the following GUI will be displayed. Simply checkbox your answer.
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![loadtype](/uploads/8c7f6e20088d9e686c54d127cb5bd86d/loadtype.png)
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**modality**
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The modality refers to which system you did you data recording on. The script needs to know this in order to select the right plugin and function to load your data. If you are using ESS then this information is not needed in the config. Use ```[modality],BIOSEMI``` or ``` [modality],BRAINVISION ``` in the config replace_string. If you leave config empty the following GUI will be displayed. Simply checkbox your answer. If you check other it will attempt a multitude of loading functions based on the file extension but there is no guarantee that any of these will work for you unique file type.
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![modality](/uploads/04767b125a3a8f18fe655ce5d8488489/modality.png)
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**oneloc**
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