= Export raw files in BIDS format =
''Author: Martin Cousineau''

It is now possible to export your raw files in the [[http://bids.neuroimaging.io/|Brain Imaging Data Structure (BIDS)]] format.

'''Note:''' For the time being, only MEG data files in CTF format can be exported in the BIDS format.

<<TableOfContents(2,2)>>

== How to use ==
 * First, select the raw files you would like to export and drag them in the process box.
 * Click on [Run] to open the pipeline editor window.
 * Select the process "'''File -> Export MEG-BIDS dataset'''".
 {{attachment:meg_bids_process.png}}



== Process options ==
 * '''Output folder''': En empty folder where a BIDS folder organization will be created by the process, or an existing BIDS-formatted folder where new recordings will be appended.
 * '''Subject names''': The naming convention to use for subjects (sub-XXXX)
  * __Custom names__: The Brainstorm subject names will be kept, with non-alphanumeric characters removed. For example, if your subject name in brainstorm is Subject01, the BIDS-formatted name for this subject will be sub-Subject01.
  * __Number index__: An auto-incremented 4 digit index number will be automatically assigned to each subject based on their alphabetical order. For example, Subject01 will be sub-0001. If the output folder specificed above is an existing BIDS-formatted folder, numbering will start from the last subject ID.
 * '''Session names''': The naming convention to use for sessions (ses-XXXX)
  * __Acquisition date__: The acquisition date extracted from the raw file metadata, or the date the data was imported in Brainstorm if that fails, will be used for session names (e.g. ses-20181023). This is the default behavior for the emptyroom subject regardless of the value of this option.
  * Number index: An auto-incremented 4 digit index number will be automatically assigned to each session of a subject, ordered by their acquisition date. For example, if Subject01 has two sessions recorded at 10AM and 2PM the same day, the 10AM session will be ses-0001 and the 2PM session will be ses-0002. If the output folder specified aboveis an existing BIDS-formatted folder with previous sessions of the same subject already present, the numbering will start from the last session ID.
 * '''Keywords to detect empty room recordings''': In order to properly assign empty room recordings to the special emptyroom subject, the process will look for these comma-separated keywords in the condition name (raw folder). If you would like not to have an emptyroom subject, leave this blank.
 * '''Overwrite existing files''': If the output folder provided above is an existing BIDS-formatted folder, this option specifies whether to overwrite existing raw files or not. If not checked, the process will skip existing files.



== Additional documentation ==
'''Website '''

 * http://bids.neuroimaging.io/

'''Articles '''

 * Gorgolewski, K.J., Auer, T., Calhoun, V.D., Craddock, R.C., Das, S., Duff, E.P., Flandin, G., Ghosh, S.S., Glatard, T., Halchenko, Y.O. and Handwerker, D.A. (2016)<<BR>>[[https://www.nature.com/articles/sdata201644|The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments]], Scientific Data, 3, p.160044.
 * Galan, J.G.N., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G., Gramfort, A., Henson, R.N., Jas, M., Litvak, V., Moreau, J. and Oostenveld, R. (2017)<<BR>> [[https://www.biorxiv.org/content/early/2017/08/08/172684|MEG-BIDS: an extension to the Brain Imaging Data Structure for magnetoencephalography]], bioRxiv, p.172684.