... | ... | @@ -3,41 +3,6 @@ The BIDS Lossless EEG pipeline is unsurprisingly, BIDS compliant. As such, data |
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This goal of this page is to provide a working understanding of how the *pipeline* is configured. As such, when folder contain external dependencies please refer to their respective documentation.
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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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### 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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1. Remove all the default folders from the Data directory.
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2. Copy your subject folders into this directory (assumes that each subject's files for all steps will be stored within its own subject folder).
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3. When running a job through the File->Batch->Run History Template Batch menu, replace the values for '[in_path]' and '[out_path]' (if it exists),
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located in the "replace_string" field of each batch config file, with analysis/data.
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*Example:*
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[in_path],analysis/data/1_init ----- change to -----> [in_path],analysis/data
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[out_path],analysis/data/2_preproc ----- change to -----> [out_path],analysis/data
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4. For now, the path to the folder containing the subject folders must be manually typed/pasted into the "path:" field. This will usually be analysis/data if that's
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the folder you'd like to use. Likewise, the _init.set file name(s) must be manually typed/pasted into the "file:" field. In this case they must include the name
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of the subject folder in the name.
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*Example:*
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subj001/subj001_init.set
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subj002/subj002_init.set
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subj003/subj003_init.set
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This should work regardless of how many folders deep the init file is stored.
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5. If you are running your jobs remotely, repeat steps 1 and 2 on the remote end.
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## Log <a name="log"></a>
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Log is automatically populated with scripts when you execute the pipeline. You will see a folder generated for every script identified by the script that was run followed by the date and time of the scripts execution. These folders contain:
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* A specific **.m** file for each subject data file.
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