Merge pull request bids-standard#3 from bids-standard/master

update 10-12

.prettierrc

@@ -0,0 +1,13 @@
+{
+  "parser": "markdown",
+  "proseWrap": "always",
+  "tabWidth": 2,
+  "overrides": [
+    {
+      "files": "*.md",
+      "options": {
+        "tabWidth": 4
+      }
+    }
+  ]
+}

.remarkrc

@@ -0,0 +1,6 @@
+{
+  "plugins": [
+    "preset-lint-markdown-style-guide",
+    ["lint-no-duplicate-headings", false]
+  ]
+}

.travis.yml

@@ -0,0 +1,10 @@
+language: node_js
+node_js:
+  - "10"
+cache:
+  directories:
+  - node_modules # NPM packages
+before_script:
+  - npm install remark-cli@5.0.0 remark-lint@6.0.2 remark-preset-lint-recommended@3.0.2 remark-preset-lint-markdown-style-guide@2.1.2
+script:
+  - remark src/*.md src/*/*.md --frail

CONTRIBUTING.md

@@ -0,0 +1,14 @@
+# Contributors guide
+
+## Markdown style
+
+The specification documents follow the
+[Markdown Style Guide](http://www.cirosantilli.com/markdown-style-guide/). You
+can validate your changes against the guide using
+[remark](https://github.com/remarkjs/remark-lint) which works as a
+[standalone command line tool](https://github.com/remarkjs/remark/tree/master/packages/remark-cli)
+as well as
+[a plugin for various text editors](https://github.com/remarkjs/remark-lint#editor-integrations).
+You can also use [prettier](https://github.com/prettier/prettier) to
+automatically correct some of the style issuse that might be found in the
+proposed changes.

README.md

@@ -1 +1,3 @@
-# bids-specification
+# bids-specification
+
+[![Build Status](https://travis-ci.com/bids-standard/bids-specification.svg?branch=master)](https://travis-ci.com/bids-standard/bids-specification)

src/01-introduction.md

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+# Introduction
+
+## Motivation
+
+Neuroimaging experiments result in complicated data that can be arranged in many
+different ways. So far there is no consensus how to organize and share data
+obtained in neuroimaging experiments. Even two researchers working in the same
+lab can opt to arrange their data in a different way. Lack of consensus (or a
+standard) leads to misunderstandings and time wasted on rearranging data or
+rewriting scripts expecting certain structure. Here we describe a simple and
+easy-to-adopt way of organising neuroimaging and behavioural data. By using this
+standard you will benefit in the following ways:
+
+-   It will be easy for another researcher to work on your data. To understand
+    the organisation of the files and their format you will only need to refer
+    them to this document. This is especially important if you are running your
+    own lab and anticipate more than one person working on the same data over
+    time. By using BIDS you will save time trying to understand and reuse data
+    acquired by a graduate student or postdoc that has already left the lab.
+
+-   There are a growing number of data analysis software packages that can
+    understand data organised according to BIDS (see
+    [http://bids.neuroimaging.io](http://bids.neuroimaging.io) for the most up
+    to date list).
+
+-   Databases such as OpenNeuro.org accept datasets organised according to BIDS.
+    If you ever plan to share your data publicly (nowadays some journals require
+    this) you can minimize the additional time and energy spent on publication,
+    and speed up the curation process by using BIDS to structure and describe
+    your data right after acquisition.
+
+-   There are [validation tools](https://github.com/Squishymedia/BIDS-Validator)
+    that can check your dataset integrity and let you easily spot missing
+    values.
+
+BIDS is heavily inspired by the format used internally by OpenfMRI.org and has
+been supported by the International Neuroinformatics Coordinating Facility and
+the Neuroimaging Data Sharing Task Force. While working on BIDS we consulted
+many neuroscientists to make sure it covers most common experiments, but at the
+same time is intuitive and easy to adopt. The specification is intentionally
+based on simple file formats and folder structures to reflect current lab
+practices and make it accessible to a wide range of scientists coming from
+different backgrounds.
+
+## Extensions
+
+The BIDS specification can be extended in a backwards compatible way and will
+evolve over time. A number of extensions are currently being worked on:
+
+| Extension label                                                                           | Title                                                                                                                                                                                         | Moderators/leads                                               |
+| :---------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------- |
+| [BEP001](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | [Structural acquisitions that include multiple contrasts (multi echo, flip angle, inversion time) sequences](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | Gilles de Hollander                                            |
+| [BEP002](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M) | [The BIDS Models Specification](https://docs.google.com/document/d/1bq5eNDHTb6Nkx3WUiOBgKvLNnaa5OMcGtD0AZ9yms2M)                                                                              | Tal Yarkoni                                                    |
+| [BEP003](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4) | [Common Derivatives](https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4)                                                                                         | Chris Gorgolewski                                              |
+| [BEP004](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc) | [Susceptibility Weighted Imaging (SWI)](https://docs.google.com/document/d/1kyw9mGgacNqeMbp4xZet3RnDhcMmf4_BmRgKaOkO2Sc)                                                                      | Fidel Alfaro Almagro                                           |
+| [BEP005](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c) | [Arterial Spin Labeling (ASL)](https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c)                                                                               | Henk-Jan Mutsaerts and Michael Chappell                        |
+| [BEP006](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE) | [Electroencephalography (EEG)](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE)                                                                               | Cyril R Pernet, Robert Oostenveld, Stefan Appelhoff            |
+| [BEP009](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0) | [Positron Emission Tomography (PET)](https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0)                                                                         | Melanie Ganz                                                   |
+| [BEP010](https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY) | [intracranial Electroencephalography (iEEG)](https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY)                                                                 | Dora Hermes and Chris Holdgraf                                 |
+| [BEP011](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y) | [The structural preprocessing derivatives](https://docs.google.com/document/d/1YG2g4UkEio4t_STIBOqYOwneLEs1emHIXbGKynx7V0Y)                                                                   | Andrew Hoopes                                                  |
+| [BEP012](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU) | [The functional preprocessing derivatives](https://docs.google.com/document/d/16CvBwVMAs0IMhdoKmlmcm3W8254dQmNARo-7HhE-lJU)                                                                   | Camille Maumet and Chris Markiewicz                            |
+| [BEP013](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw) | [The resting state fMRI derivatives](https://docs.google.com/document/d/1qBNQimDx6CuvHjbDvuFyBIrf2WRFUOJ-u50canWjjaw)                                                                         | Steven Giavasis                                                |
+| [BEP014](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE) | [The affine transformations and nonlinear field warps](https://docs.google.com/document/d/11gCzXOPUbYyuQx8fErtMO9tnOKC3kTWiL9axWkkILNE)                                                       | Oscar Esteban                                                  |
+| [BEP015](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE) | [Mapping file](https://docs.google.com/document/d/1WYOTXDB7GzlHoWqLjd45I3uGBgPxXddST-NTqBnroJE)                                                                                               | Eric Earl, Camille Maumet, and Vasudev Raguram                 |
+| [BEP016](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60) | [The diffusion weighted imaging derivatives](https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60)                                                                 | Franco Pestilli and Oscar Esteban                              |
+| [BEP017](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA) | [Generic BIDS connectivity data schema](https://docs.google.com/document/d/1ugBdUF6dhElXdj3u9vw0iWjE6f_Bibsro3ah7sRV0GA)                                                                      | Eugene Duff and Paul McCarthy                                  |
+| [BEP018](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs) | [Genetic information](https://docs.google.com/document/d/1uRkgyzESLKuGjXi98Z97Wh6vt-iLN5nOAb9TG16CjUs)                                                                                        | Cyril R Pernet, Clara Moreau, and Thomas Nichols               |
+| [BEP019](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU) | [DICOM Metadata](https://docs.google.com/document/d/1FqJI791ycXr0bfRg2qyLqAf0RpVttJ2cInOgMWrKsNU)                                                                                             | Satrajit Ghosh                                                 |
+| [BEP020](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw) | [Eye Tracking including Gaze Position and Pupil Size(ET)](https://docs.google.com/document/d/1eggzTCzSHG3AEKhtnEDbcdk-2avXN6I94X8aUPEBVsw)                                                    | Benjamin Gagl and Dejan Draschkow                              |
+| [BEP021](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw) | [Common Electrophysiological Derivatives](https://docs.google.com/document/d/1PmcVs7vg7Th-cGC-UrX8rAhKUHIzOI-uIOh69_mvdlw)                                                                    | Stefan Appelhoff, Cyril Pernet, Robert Oostenveld, Teon Brooks |
+
+When an extension reaches maturity it is merged into the main body of the
+specification. If you would like to contribute to BIDS please consult the
+[BIDS Contributor Guide](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/edit?usp%3Dsharing&sa=D&ust=1537468908724000)
+All of the ideas that are not backwards compatible and thus will have to wait
+for BIDS 2.0 are listed
+[here](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw)
+
+## Citing BIDS
+
+When referring to BIDS in context of academic literature please cite:
+
+> 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., Handwerker,
+> D.A., Hanke, M., Keator, D., Li, X., Michael, Z., Maumet, C., Nichols, B.N.,
+> Nichols, T.E., Pellman, J., Poline, J.-B., Rokem, A., Schaefer, G., Sochat,
+> V., Triplett, W., Turner, J.A., Varoquaux, G., Poldrack, R.A., 2016.
+> [The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments](https://www.nature.com/articles/sdata201644).
+> Sci Data 3, 160044.
+
+as well as other papers describing specific BIDS extensions (see below).
+
+BIDS has also a
+[Research Resource Identifier (RRID)](https://www.force11.org/group/resource-identification-initiative)
+- `RRID:SCR_016124` - which you can also include in your manuscript in addition
+to citing the paper.