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example:bids_eeg [2018/10/21 15:00]
42.49.180.224 [Preparing an EEG dataset for sharing]
example:bids_eeg [2018/09/14 13:13] (current)
robert [Step 3b: convert the data and create the sidecar files for each subject]
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 This example describes how to prepare an EEG dataset for sharing in the BIDS format. The example starts from a single publicly available EEG recording of a single subject, which is copied multiple times to simulate a dataset comprising data from ten subjects. ​ This example describes how to prepare an EEG dataset for sharing in the BIDS format. The example starts from a single publicly available EEG recording of a single subject, which is copied multiple times to simulate a dataset comprising data from ten subjects. ​
  
-&lt;note important&​gt; ​If you want to share data, there are multiple things to consider. For example the file format of the data, the access mechanism for the data (ftp/​http/​sftp),​ the data use agreement, whether all data or some part of the data is shared, using pseudonyms in the description of the data, scrubbing the date and time of recording, removing identifying features from the data, etc.+<note importantIf you want to share data, there are multiple things to consider. For example the file format of the data, the access mechanism for the data (ftp/​http/​sftp),​ the data use agreement, whether all data or some part of the data is shared, using pseudonyms in the description of the data, scrubbing the date and time of recording, removing identifying features from the data, etc.
  
 In this example we will only be dealing with the format in which the data is organized (over directories) and stored (in files), for which we use the [[http://​bids.neuroimaging.io|Brain Imaging Data Structure]]. In this example we will only be dealing with the format in which the data is organized (over directories) and stored (in files), for which we use the [[http://​bids.neuroimaging.io|Brain Imaging Data Structure]].
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 Prior to conversion the data comprises 10 files (one file per subject). After conversion there are 52 or 72 files (for the two options described below), which includes the sidecar files with metadata. Prior to conversion the data comprises 10 files (one file per subject). After conversion there are 52 or 72 files (for the two options described below), which includes the sidecar files with metadata.
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 We will describe two alternative approaches: in the first one the files are kept in their original file format, in the second one the files are explicitly converted to the recommended format for BIDS. We will describe two alternative approaches: in the first one the files are kept in their original file format, in the second one the files are explicitly converted to the recommended format for BIDS.
  
-After each of the automated steps the results should be checked. For that I have been using the command line applications like &quot;find DIR -name PATTERN | wc -l&​quot; ​to count the number of files, but also a graphical databrowser to check the directory structure and a text editor to check the content of the JSON and TSV sidecar files. ​+After each of the automated steps the results should be checked. For that I have been using the command line applications like "find DIR -name PATTERN | wc -l" ​to count the number of files, but also a graphical databrowser to check the directory structure and a text editor to check the content of the JSON and TSV sidecar files. ​
  
 It is important that you use appropriate tools. Command line utilities are very handy, but also a good graphical (code) editor that allows you to navigate through the full directory structure and check the file content. I have been using the Atom editor with the network directory mounted on my desktop computer. There are good [[https://​alternativeto.net/​software/​atom/​|alternatives]]. It is important that you use appropriate tools. Command line utilities are very handy, but also a good graphical (code) editor that allows you to navigate through the full directory structure and check the file content. I have been using the Atom editor with the network directory mounted on my desktop computer. There are good [[https://​alternativeto.net/​software/​atom/​|alternatives]].
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 In reusing the data, either by yourself, your (future) colleagues in your lab, or people outside your lab, this type of information is very relevant. Although it is frustrating to encounter these inconsistencies when converting to BIDS, it actually reveals that these aspects need to be represented and documented properly in the (meta)data. In reusing the data, either by yourself, your (future) colleagues in your lab, or people outside your lab, this type of information is very relevant. Although it is frustrating to encounter these inconsistencies when converting to BIDS, it actually reveals that these aspects need to be represented and documented properly in the (meta)data.
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