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[FIX] number of small corrections to the specification #98

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9e410cd
include beh as 6th data type in the common description
robertoostenveld Nov 28, 2018
d05efb4
renamed case 2 to example 3
robertoostenveld Nov 28, 2018
cb71013
clarify in the example description that it explains an error. The oth…
robertoostenveld Nov 28, 2018
07d7e73
updated link to bids-validator, cleaned up formatting of links
robertoostenveld Nov 28, 2018
aff27ac
move utf8 requirement more to the start of the paragraph, rather than…
robertoostenveld Nov 28, 2018
885042c
fixed links to other pages, included a table with BEPs that have been…
robertoostenveld Nov 28, 2018
e7d4375
updated contributions
robertoostenveld Nov 28, 2018
5f76c2a
Merge branch 'master' into patch
robertoostenveld Nov 29, 2018
9381b9e
use behaviour consistently instead of behaviour
robertoostenveld Nov 29, 2018
9f987b0
made the erroneous example more clear by it having only one error, no…
robertoostenveld Nov 29, 2018
9136f67
BF: also rename 05-behavioural-experiments.md to match behavioral spe…
yarikoptic Dec 12, 2018
c08c4cc
BF: resolve line width and table column indentation errors/warnings
yarikoptic Dec 12, 2018
ea06fef
updated patch to reflect recent changes in master, merged conflicts i…
robertoostenveld Jan 10, 2019
7d1bb72
I seemed to have missed one conflict in the previous merge. This is a…
robertoostenveld Jan 10, 2019
b1d94d4
prevent "Incorrect list-item indent: add 2 spaces"
robertoostenveld Jan 10, 2019
d3d2949
attempt to fix "Misaligned table fence"
robertoostenveld Jan 10, 2019
cfb3770
Update 01-contributors.md
robertoostenveld Feb 11, 2019
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21 changes: 9 additions & 12 deletions src/02-common-principles.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,10 @@ clarify them here.
scanning sequence/protocol.

1. Data type - a functional group of different types of data. In BIDS we define
five data types: func (task based and resting state functional MRI), dwi
six data types: func (task based and resting state functional MRI), dwi
(diffusion weighted imaging), fmap (field inhomogeneity mapping data such as
field maps), anat (structural imaging such as T1, T2, etc.), meg
(magnetoencephalography).
(magnetoencephalography), beh (behavioural).
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1. Task - a set of structured activities performed by the participant. Tasks
are usually accompanied by stimuli and responses, and can greatly vary in
Expand Down Expand Up @@ -128,7 +128,7 @@ participant can exist only at participant level directory, i.e
specific to a participant is to be declared only at top level of dataset for eg:
`task-sist_bold.json` must be placed under `/dataset/task-sist_bold.json`

Example 1: Two JSON files at same level that are applicable for NIfTI file.
Example 1: Two JSON files that are erroneously at the same level.
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```Text
sub-01/
Expand Down Expand Up @@ -168,7 +168,7 @@ apply to different runs and rec files. Also if the JSON file
(`task-xyz_acq-test1_bold.json`) is defined at dataset top level directory, it
will be applicable to all task runs with `test1` acquisition parameter.

Case 2: Multiple json files at different levels for same task and acquisition
Example 3: Multiple json files at different levels for same task and acquisition
parameters

```Text
Expand Down Expand Up @@ -198,12 +198,10 @@ possible. Since the NIfTI standard offers limited support for the various image
acquisition parameters available in DICOM files, we RECOMMEND that users provide
additional meta information extracted from DICOM files in a sidecar JSON file
(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
Extraction of BIDS compatible metadata can be performed using dcm2nii
[https://www.nitrc.org/projects/dcm2nii/](https://www.nitrc.org/projects/dcm2nii/)
and dicm2nii
[http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
Extraction of BIDS compatible metadata can be performed using [dcm2nii](https://www.nitrc.org/projects/dcm2nii/)
and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
DICOM to NIfTI converters. A provided
validator[https://github.com/INCF/bids-validator](https://github.com/INCF/bids-validator)
[validator](https://github.com/bids-standard/bids-validator)
will check for conflicts between the JSON file and the data recorded in the
NIfTI header.

Expand Down Expand Up @@ -262,12 +260,11 @@ Example:
## Key/value files (dictionaries)

JavaScript Object Notation (JSON) files MUST be used for storing key/value
pairs. Extensive documentation of the format can be found here:
pairs. JSON files MUST be in UTF-8 encoding. Extensive documentation of the format can be found here:
[http://json.org/](http://json.org/). Several editors have built-in support for
JSON syntax highlighting that aids manual creation of such files. An online
editor for JSON with built-in validation is available at:
[http://jsoneditoronline.org](http://jsoneditoronline.org). JSON files MUST be
in UTF-8 encoding.
[http://jsoneditoronline.org](http://jsoneditoronline.org). 

Example:

Expand Down
16 changes: 10 additions & 6 deletions src/06-extensions.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,14 @@ There are many ways to get involved with the BIDS community!
### The BIDS Starter Kit
If you're new
to the BIDS community and you'd like to learn a bit more, we recommend checking
out the [BIDS Starter Kit]
(https://github.com/bids-standard/bids-starter-kit/blob/master/README.md).
out the [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit/blob/master/README.md).
This has introductory information about the BIDS specification, tools in
the BIDS ecosystem, and how you can get involved.

### The BIDS Contributor guide

If you'd like to get involved more heavily in helping extend the BIDS
specification or develop tools for it, see the [BIDS Contributor Guide]
(https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/edit?usp%3Dsharing&sa=D&ust=1537468908724000). It contains more in-depth information for getting
specification or develop tools for it, see the [BIDS Contributor Guide](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/edit?usp%3Dsharing&sa=D&ust=1537468908724000). It contains more in-depth information for getting
involved with the BIDS community.

## BIDS Extension Proposals
Expand Down Expand Up @@ -54,8 +52,14 @@ Below is a table of currently-active BEPs.
| [BEP023](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | [PET Preprocessing derivatives](https://docs.google.com/document/d/1yzsd1J9GT-aA0DWhdlgNr5LCu6_gvbjLyfvYq2FuxlY) | Martin Noergaard, Graham Searle, Melanie Ganz |
| [BEP024](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | [Computed Tomography scan (CT)](https://docs.google.com/document/d/1fqnJZ18x5LJC8jiJ8yvPHUGFzNBZ6gW2kywYrUKWtuo) | Hugo Boniface |

When an extension reaches maturity it is merged into the main body of the
specification.
When an extension reaches maturity it is merged into the main body of the specification.
Below is a table of BEPs that have been merged in the main body of the specification.


| Extension label | Title | Moderators/leads |
| :---------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------ |
| [BEP008](https://docs.google.com/document/d/1FWex_kSPWVh_f4rKgd5rxJmxlboAPtQlmBc1gyZlRZM) | [Magnetoencephalography (MEG)](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg) | Guiomar Niso |


All of the extension ideas that are not backwards compatible and thus
will have to wait for BIDS 2.0 are listed
Expand Down
4 changes: 2 additions & 2 deletions src/99-appendices/01-contributors.md
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ Legend (source:
| 🔧 | Tools |
| 🌍 | Translation |
| ⚠️ | Tests |
| ✅ | Tutorials |
| ✅ | Tutorials |
| 📢 | Talks |
| 📹 | Videos |

Expand Down Expand Up @@ -85,7 +85,7 @@ your name is not listed, please add it.
- Thomas E. Nichols 📖📢🔧
- Dylan Nielson 📖💻🔧
- Guiomar Niso 📖💡📢
- Robert Oostenveld 📖🔧📢💡
- Robert Oostenveld 📖🔧📢💡✅⚠️🤔
- Patrick Park 📖💡💬
- Dianne Patterson 📖
- John Pellman 📖
Expand Down