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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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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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2. Warping Channel locations to MNI head
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3. Creating events and marks to indicate In/Out Task Time
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The picture below shows how each section develops the file.
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![masterinit](/uploads/bb4608e6da4476784e2104121065ec0b/masterinit.png)
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# Configuration and GUI
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This script will only produce GUI's if it is missing a necessary piece of information. This means that if you carefully fill out the configuration file then you can run the complete pipeline autonomously. On the other hand if you are not comfortable with the configuration files this file can be run with no configuration and will use GUI's to prompt you for the information as needed. This process is more time consuming but will help you understand what is needed in the configuration, and you can always run a smaller batch first to sort out these details.
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# Mandatory Variables
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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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**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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| LOADTYPE |ESS | ESS | OTHER | OTHER | OTHER | |
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|----------------|:---:|:------:|:------:|:------:|:------:|---------------------------------------------------------------------------------|
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| Variable | XML | Config | Manual | Config | Manual | Description |
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| loadType | | x | x | x | x | ESS or OTHER type of study you are loading |
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| ref_loc_file | | x | | x | | Warp reference surface, default is the MNI head if no config is given |
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| oneloc | | x | x | x | x | 1 if you are using a single montage location file, 0 for subject specific files |
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| modality | x | | | x | x | System used for recording |
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| locs_file_name | x | | | x | x | Path to montage or naming convention for subject specific files |
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| srate | x | | | x | x | Number of data points collected per second |
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| NotEEG_chans | x | | | x | | Channel numbers that do not contain EEG data |
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| Fid_chans | x | | | x | x | Channel numbers of the Fiducials for warping reference |
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| tMatrix | | x | x | x | x | Matrix used to warp your location files to MNI head |
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| Onevents | | x | x | x | x | Events that represent HED tag 'Custom/Marks/RecStart' |
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| Offevents | | x | x | x | x | Events that represent HED tag 'Custom/Marks/RecStop' |
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| Inevents | | x | x | x | x | Events that represent HED tag 'Custom/Marks/InEvent' |
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# Variable Specifics
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***
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