From ecfbf73e50c449648fd9b5bf1d206cd697117398 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 6 Mar 2019 12:18:21 +0100
Subject: [PATCH 01/18] =?UTF-8?q?dcm2nii=20=E2=86=92=20dcm2niix?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Change dicom converter recommendation from obsolete dcm2nii to modern dcm2niix.
---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index 2138fe03b6..bbe754ea61 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -206,7 +206,7 @@ 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/)
+Extraction of BIDS compatible metadata can be performed using [dcm2niix](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/bids-standard/bids-validator)

From 5ad238bb0566c735188f1c877683130251634a24 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Wed, 6 Mar 2019 08:26:31 -0800
Subject: [PATCH 02/18] updated link to dcm2niix

---
 src/02-common-principles.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index bbe754ea61..ecaf302dc4 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -206,7 +206,7 @@ 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 [dcm2niix](https://www.nitrc.org/projects/dcm2nii/)
+Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
 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/bids-standard/bids-validator)

From 4f36c755cf9c2c08d1ad8d00dee5febbe0e4eafd Mon Sep 17 00:00:00 2001
From: Elizabeth DuPre <emd222@cornell.edu>
Date: Thu, 7 Mar 2019 20:24:17 -0500
Subject: [PATCH 03/18] fix: fixes spelling of continuous

---
 CONTRIBUTING.md                                                 | 2 +-
 mkdocs.yml                                                      | 2 +-
 ...s.md => 06-physiological-and-other-continuous-recordings.md} | 0
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename src/04-modality-specific-files/{06-physiological-and-other-continous-recordings.md => 06-physiological-and-other-continuous-recordings.md} (100%)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 1869a5e8d6..b3ccb3db16 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -46,7 +46,7 @@ can validate your changes against the guide using [remark](https://github.com/re
 [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). Remark preserves consistent markdown styling across the contributions. Please ensure before submitting a contribution that you do not have any linter errors in your text editor.
 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.
 
-We have deployed a continous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continously. The CI is testing that the changes are inline with our standard styling.
+We have deployed a continuous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continuously. The CI is testing that the changes are inline with our standard styling.
 
 GitHub has a helpful page on [getting started with writing and formatting on GitHub](https://help.github.com/articles/getting-started-with-writing-and-formatting-on-github).
 
diff --git a/mkdocs.yml b/mkdocs.yml
index 39322ae87c..cc1194b1a6 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -15,7 +15,7 @@ nav:
         - Electroencephalography: 04-modality-specific-files/03-electroencephalography.md
         - intracranial Electroencephalography: 04-modality-specific-files/04-intracranial-electroencephalography.md
         - Task events: 04-modality-specific-files/05-task-events.md
-        - Physiological and other continous recordings: 04-modality-specific-files/06-physiological-and-other-continous-recordings.md
+        - Physiological and other continuous recordings: 04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
         - Behavioral experiments (with no MRI): 04-modality-specific-files/07-behavioral-experiments.md
       - Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md
       - Extending the BIDS specification: 06-extensions.md
diff --git a/src/04-modality-specific-files/06-physiological-and-other-continous-recordings.md b/src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
similarity index 100%
rename from src/04-modality-specific-files/06-physiological-and-other-continous-recordings.md
rename to src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md

From fabcf9375b97dc075a5b0fa08b2e089c75271c93 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Wed, 20 Feb 2019 09:40:17 +0100
Subject: [PATCH 04/18] New contributor

---
 CODEOWNERS                           | 2 +-
 src/99-appendices/01-contributors.md | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/CODEOWNERS b/CODEOWNERS
index 39a7964049..0ef42927de 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -9,6 +9,6 @@
 /src/CHANGES.md @chrisfilo @sappelhoff @CPernet
 
 # Individual sections
-/src/01-common-principles.md @chrisfilo
+/src/01-common-principles.md @chrisfilo @DimitriPapadopoulos
 /src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisfilo
 /src/04-modality-specific-files/03-electroencephalography.md @sappelhoff
diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index a530f8325a..491e97ac69 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -89,6 +89,7 @@ your name is not listed, please add it.
 -   Dylan Nielson 📖💻🔧
 -   Guiomar Niso 📖💡📢
 -   Robert Oostenveld 📖🔧📢💡✅⚠️🤔
+-   Dimitri Papadopoulos Orfanos 📖💡🤔💬
 -   Patrick Park 📖💡💬
 -   Dianne Patterson 📖
 -   John Pellman 📖

From f5972b4c21ce44aadb3f09ecfda8585af5b0512e Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Mon, 4 Mar 2019 09:54:38 -0800
Subject: [PATCH 05/18] Removing leftover file

---
 .../05-behavioral-experiments.md              | 26 -------------------
 1 file changed, 26 deletions(-)
 delete mode 100644 src/04-modality-specific-files/05-behavioral-experiments.md

diff --git a/src/04-modality-specific-files/05-behavioral-experiments.md b/src/04-modality-specific-files/05-behavioral-experiments.md
deleted file mode 100644
index 83c2018384..0000000000
--- a/src/04-modality-specific-files/05-behavioral-experiments.md
+++ /dev/null
@@ -1,26 +0,0 @@
-# Behavioral experiments (with no MRI)
-
-Template:
-
-```Text
-sub-<label>/[ses-<label>/]
-    beh/
-        sub-<label>[_ses-<label>]_task-<task_name>_events.tsv
-        sub-<label>[_ses-<label>]_task-<task_name>_events.json
-        sub-<label>[_ses-<label>]_task-<task_name>_beh.tsv
-        sub-<label>[_ses-<label>]_task-<task_name>_beh.json
-        sub-<label>[_ses-<label>]_task-<task_name>_physio.tsv.gz
-        sub-<label>[_ses-<label>]_task-<task_name>_physio.json
-        sub-<label>[_ses-<label>]_task-<task_name>_stim.tsv.gz
-        sub-<label>[_ses-<label>]_task-<task_name>_stim.json
-```
-
-In addition to logs from behavioral experiments performed along imaging data
-acquisitions one can also include data from experiments performed outside of the
-scanner. The results of those experiments can be stored in the beh folder using
-the same formats for event timing (`_events.tsv`), metadata (`_events.json`),
-physiological (`_physio.tsv.gz`, `_physio.json`) and other continuous recordings
-(`_stim.tsv.gz`, `_stim.json`) as for tasks performed during MRI acquisitions.
-Additionally, events files that do not include the mandatory `onset` and
-`duration` columns can still be included, but should be labelled `_beh.tsv`
-rather than `_events.tsv`.

From 4674d496491fb3ec1ccb641ad064824f7222dabe Mon Sep 17 00:00:00 2001
From: Changelog-bot <franklin.feingold@gmail.com>
Date: Mon, 11 Mar 2019 15:49:30 +0000
Subject: [PATCH 06/18] [DOC] Auto-generate changelog entry for PR #166

---
 src/CHANGES.md | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 4b0e7a81a6..7f583724b5 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -1,8 +1,18 @@
 Changelog
 
-## [v1.2.0](https://bids-specification.readthedocs.io/en/v1.2.0/)
+## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisfilo](https://github.com/chrisfilo))
+
+## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
+
+-   REL: v1.2.0 [#161](https://github.com/bids-standard/bids-specification/pull/161) ([chrisfilo](https://github.com/chrisfilo))
+-   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   RF: use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
+-   Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   Update Pipfile.lock [#144](https://github.com/bids-standard/bids-specification/pull/144) ([franklin-feingold](https://github.com/franklin-feingold))
+-   \[MRG] clarify decimal sep and numerical notation convention [#143](https://github.com/bids-standard/bids-specification/pull/143) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MRG] clarify encoding of README, CHANGES, TSV, and JSON files [#140](https://github.com/bids-standard/bids-specification/pull/140) ([sappelhoff](https://github.com/sappelhoff))
 -   Update site_name and release protocol [#137](https://github.com/bids-standard/bids-specification/pull/137) ([franklin-feingold](https://github.com/franklin-feingold))
 -   BF: Example for IntendedFor was missing session indicator in the filename [#129](https://github.com/bids-standard/bids-specification/pull/129) ([yarikoptic](https://github.com/yarikoptic))
@@ -13,10 +23,10 @@ Changelog
 -   Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisfilo](https://github.com/chrisfilo))
 -   \[MRG] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
-## [v.1.1.2](https://github.com/bids-standard/bids-specification/tree/v.1.1.2) (2019-01-10)
-
 ## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
 
+## [v.1.1.2](https://github.com/bids-standard/bids-specification/tree/v.1.1.2) (2019-01-10)
+
 -   REL: v.1.1.2 [#121](https://github.com/bids-standard/bids-specification/pull/121) ([chrisfilo](https://github.com/chrisfilo))
 -   Update 01-contributors.md [#120](https://github.com/bids-standard/bids-specification/pull/120) ([oesteban](https://github.com/oesteban))
 -   Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisfilo](https://github.com/chrisfilo))

From 9373171b6e2efbec4b08dcd3b9506bdfe4e0998a Mon Sep 17 00:00:00 2001
From: Changelog-bot <franklin.feingold@gmail.com>
Date: Wed, 13 Mar 2019 13:25:19 +0000
Subject: [PATCH 07/18] [DOC] Auto-generate changelog entry for PR #171

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 7f583724b5..28e291f1a4 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@ Changelog
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[FIX] Fixes spelling of continuous [#171](https://github.com/bids-standard/bids-specification/pull/171) ([emdupre](https://github.com/emdupre))
 -   \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisfilo](https://github.com/chrisfilo))
 

From e28a9738dbd0923272992ac305fb202edbbeca3c Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Wed, 13 Mar 2019 08:33:11 -0700
Subject: [PATCH 08/18] Adding rules about maintainers

---
 DECISION-MAKING.md | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index 51aebda63c..9cc1684a85 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -25,6 +25,15 @@ community decides on the content of this file using the same process as any
 other change to the Repository (see below) allowing the meaning of "Contributor"
 to evolve independently of the Decision-making rules.
 
+**Maintainer** - a Contributor responsible for the long term health of the 
+project and the community. Maintainers have additional rights (see Rules) 
+helping them to resolve conflicts and increase the pace of the development 
+when necessary. Current Maintainers:
+
+| Name | Time commitment |
+|------|-----------------|
+| Stefan Appelhoff (@sappelhoff) | 5h/week |
+
 ## Rules
 
 1. Every modification of the specification (including a correction of a typo, 
@@ -45,6 +54,10 @@ to evolve independently of the Decision-making rules.
    1. Does not feature any [Reviews that Request changes](https://help.github.com/articles/about-required-reviews-for-pull-requests/).
    1. Does not feature "WIP" in the title (Work in Progress).
    1. Passes all automated tests.
+   1. Is not proposing a new release or has been approved by at least one 
+      Maintainer.
+1. A Maintainer can merge any PR - even if it's not eligible to merge according
+   to Rule 4.
 1. Any Contributor can Review a PR and Request changes. If a Contributor 
    Request changes they need to provide an explanation what changes 
    should be added and justification of their importance. Reviews requesting 
@@ -54,7 +67,7 @@ to evolve independently of the Decision-making rules.
 1. If the author of a PR and Contributor who provided Review that Requests 
    changes cannot find a solution that would lead to the Contributor dismissing 
    their review or accepting the changes the Review can be Dismissed with a 
-   vote. Rules governing voting:
+   vote or by a Maintainer. Rules governing voting:
    1. A Vote can be triggered by any Contributor, but only after 5 working days 
       from the time a Review Requesting Changes has been raised and in case a 
       Vote has been triggered previously no sooner than 15 working days since 
@@ -70,6 +83,9 @@ to evolve independently of the Decision-making rules.
 
 ## Comments
 
+1. Researchers preparing academic manuscripts describing work that has been 
+   merged into this repository are strongly encouraged to invite all 
+   Maintainers as co-authors as a form of appreciation for their work.
 1. There are no restrictions on how the content of the PR is prepared. For 
    example it is perfectly fine for a PR to consist of content developed by a 
    group of experts over an extended period of time via in person meetings and 

From fd449379a38fb7eb16907e8a41b690d6a17576aa Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Wed, 13 Mar 2019 08:35:48 -0700
Subject: [PATCH 09/18] fix a table

---
 DECISION-MAKING.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index 9cc1684a85..491f80826b 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -30,9 +30,9 @@ project and the community. Maintainers have additional rights (see Rules)
 helping them to resolve conflicts and increase the pace of the development 
 when necessary. Current Maintainers:
 
-| Name | Time commitment |
-|------|-----------------|
-| Stefan Appelhoff (@sappelhoff) | 5h/week |
+| Name                           | Time commitment |
+|--------------------------------|-----------------|
+| Stefan Appelhoff (@sappelhoff) | 5h/week         |
 
 ## Rules
 

From 9d84e38b34f4ca2ea33a7adbc29dd7f86922d634 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Wed, 13 Mar 2019 09:36:32 -0700
Subject: [PATCH 10/18] added a link and a clarification

---
 DECISION-MAKING.md | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index 491f80826b..a83dc08e1d 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -30,9 +30,9 @@ project and the community. Maintainers have additional rights (see Rules)
 helping them to resolve conflicts and increase the pace of the development 
 when necessary. Current Maintainers:
 
-| Name                           | Time commitment |
-|--------------------------------|-----------------|
-| Stefan Appelhoff (@sappelhoff) | 5h/week         |
+| Name                                                            | Time commitment |
+|-----------------------------------------------------------------|-----------------|
+| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff)) | 5h/week         |
 
 ## Rules
 
@@ -55,7 +55,8 @@ when necessary. Current Maintainers:
    1. Does not feature "WIP" in the title (Work in Progress).
    1. Passes all automated tests.
    1. Is not proposing a new release or has been approved by at least one 
-      Maintainer.
+      Maintainer (i.e., PRs proposing new releases need to be approved by at 
+      least one Maintainer).
 1. A Maintainer can merge any PR - even if it's not eligible to merge according
    to Rule 4.
 1. Any Contributor can Review a PR and Request changes. If a Contributor 

From bb67fd7286b99ae63f5af47e930569c44b9e5619 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 15 Mar 2019 11:01:26 -0700
Subject: [PATCH 11/18] [INFRA] Adding instructions for naming PRs

---
 CONTRIBUTING.md          | 16 ++++++++++++++++
 pull_request_template.md | 17 +++++++++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 pull_request_template.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b3ccb3db16..6732f9f22b 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -95,6 +95,22 @@ Try to keep the changes focused. If you submit a large amount of work in all in
 
 #### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
 
+Please keep the title of your pull request short but informative - it will 
+appear in the changelog.
+
+Use one of the following prefixes in the title of your pull request:
+  - `[ENH]` - enhancement of the specification that adds a new feature or 
+    support for a new data type
+  - `[FIX]` - fix of a typo or language clarification
+  - `[INFRA]` - changes to the infrastructure automating the specification 
+    release (for example building HTML docs etc.)
+  - `[MISC]` - everything else including changes to the file listing 
+    contributors
+
+If you are opening a pull request to obtain early feedback, but the changes 
+are not ready to be merged (a.k.a. Work in Progress pull request) please 
+use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+
 A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
 
 A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your github notifications and be prepared to join in that conversation.
diff --git a/pull_request_template.md b/pull_request_template.md
new file mode 100644
index 0000000000..82f0ea4863
--- /dev/null
+++ b/pull_request_template.md
@@ -0,0 +1,17 @@
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE PULL REQUEST ---
+
+- Please keep the title of your pull request short but informative - it will 
+  appear in the changelog
+- Use one of the following prefixes in the title of your pull request:
+  - `[ENH]` - enhancement of the specification that adds a new feature or 
+    support for a new data type
+  - `[FIX]` - fix of a typo or language clarification
+  - `[INFRA]` - changes to the infrastructure automating the specification 
+    release (for example building HTML docs etc.)
+  - `[MISC]` - everything else including changes to the file listing 
+    contributors
+- If you are opening a pull request to obtain early feedback, but the changes 
+  are not ready to be merged (a.k.a. Work in Progress pull request) please 
+  use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
\ No newline at end of file

From 9c2f74f73f797375645182e6c20231686d286ca8 Mon Sep 17 00:00:00 2001
From: Changelog-bot <franklin.feingold@gmail.com>
Date: Tue, 19 Mar 2019 19:37:29 +0000
Subject: [PATCH 12/18] [DOC] Auto-generate changelog entry for PR #176

---
 src/CHANGES.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 28e291f1a4..71f33b35b3 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,6 +2,7 @@ Changelog
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[MISC] Introducing Stefan Appelhoff as the first Maintainer [#176](https://github.com/bids-standard/bids-specification/pull/176) ([chrisfilo](https://github.com/chrisfilo))
 -   \[FIX] Fixes spelling of continuous [#171](https://github.com/bids-standard/bids-specification/pull/171) ([emdupre](https://github.com/emdupre))
 -   \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisfilo](https://github.com/chrisfilo))

From b467a05f750691289f5d240a1b06e8f12d6831ce Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Fri, 15 Mar 2019 21:09:52 +0100
Subject: [PATCH 13/18] Spelling

---
 CODEOWNERS                                                    | 2 +-
 CONTRIBUTING.md                                               | 4 ++--
 DECISION-MAKING.md                                            | 4 ++--
 Release_Protocol.md                                           | 2 +-
 src/01-introduction.md                                        | 2 +-
 .../01-magnetic-resonance-imaging-data.md                     | 2 +-
 6 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/CODEOWNERS b/CODEOWNERS
index 0ef42927de..a2a1aa2467 100644
--- a/CODEOWNERS
+++ b/CODEOWNERS
@@ -5,7 +5,7 @@
 # Request for Review) please add your GitHub username next to the file you want to
 # monitor below.
 
-# Add your github name below to get notified about proposed releases
+# Add your GitHub name below to get notified about proposed releases
 /src/CHANGES.md @chrisfilo @sappelhoff @CPernet
 
 # Individual sections
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b3ccb3db16..b1f67a1d85 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -44,7 +44,7 @@ The specification documents follow the [Markdown Style Guide](http://www.cirosan
 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). Remark preserves consistent markdown styling across the contributions. Please ensure before submitting a contribution that you do not have any linter errors in your text editor.
-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.
+You can also use [prettier](https://github.com/prettier/prettier) to automatically correct some of the style issues that might be found in the proposed changes.
 
 We have deployed a continuous integrator ([circle CI](https://circleci.com/)) to further allow for integrating changes continuously. The CI is testing that the changes are inline with our standard styling.
 
@@ -97,7 +97,7 @@ Try to keep the changes focused. If you submit a large amount of work in all in
 
 A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
 
-A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your github notifications and be prepared to join in that conversation.
+A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your GitHub notifications and be prepared to join in that conversation.
 
 You can update your [fork](https://help.github.com/articles/about-forks/) of the BIDS Specification and the pull request will automatically update with those commits. You don't need to submit a new pull request when you make a change in response to a review.
 
diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index a83dc08e1d..32c9d064a7 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -91,9 +91,9 @@ when necessary. Current Maintainers:
    example it is perfectly fine for a PR to consist of content developed by a 
    group of experts over an extended period of time via in person meetings and 
    online collaborations using a Google Document.
-1. To facilitate triaging of incoming PR you can subscribe to 
+1. To facilitate triage of incoming PR you can subscribe to 
    notifications for new PRs proposing changes to specific files. To do this
-   add your Github name next to the file you want to subscribe to in the 
+   add your GitHub name next to the file you want to subscribe to in the 
    [CODEOWNERS](CODEOWNERS). This way you will be ask to review each relevant
    PR. Please mind that lack of your review will not prevent the PR from being
    merged so if you think the PR needs your attention, please review it 
diff --git a/Release_Protocol.md b/Release_Protocol.md
index 519be65c63..3ff0608a0e 100644
--- a/Release_Protocol.md
+++ b/Release_Protocol.md
@@ -19,7 +19,7 @@ Important note: The pull request title **needs** to follow this protocol. REL: v
 
 ### This will open a period of discussion for 5 business days regarding if we are ready to release. This will also freeze all pull request merging.
 
-If we determine we are ready to release, please have the PR submitter add an additional commit with the date in year-month-date format in parentheses after the version of the date of merging (not opening) (i.e. it should read v1.1.2 (2018-12-28)) and merge this PR. This will mark a new release. On the same day, please also do a github release. To do this please see below.
+If we determine we are ready to release, please have the PR submitter add an additional commit with the date in year-month-date format in parentheses after the version of the date of merging (not opening) (i.e. it should read v1.1.2 (2018-12-28)) and merge this PR. This will mark a new release. On the same day, please also do a GitHub release. To do this please see below.
 
 ![GH-release-1](release_images/GH-release_1.png "GH-release-1")
 
diff --git a/src/01-introduction.md b/src/01-introduction.md
index e077e6cbb9..fe0f66b676 100644
--- a/src/01-introduction.md
+++ b/src/01-introduction.md
@@ -45,7 +45,7 @@ different backgrounds.
 ## Extensions
 
 The BIDS specification can be extended in a backwards compatible way and will
-evolve over time. This is accomplished through community-driven BIDS Extention
+evolve over time. This is accomplished through community-driven BIDS Extension
 Proposals (BEPs). For more information about the BEP process, and list of
 current BEP proposals, see
 [Extending the BIDS specification](06-extensions.md).
diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
index 905586e8b8..341602fd4b 100644
--- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
+++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
@@ -20,7 +20,7 @@ by Ben Inglis:
 | HardcopyDeviceSoftwareVersion | (Deprecated) Manufacturer’s designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A `Hardcopy Device Software Version`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
 | MagneticFieldStrength         | RECOMMENDED. Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 `Magnetic Field Strength`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
 | ReceiveCoilName               | RECOMMENDED. Information describing the receiver coil. Corresponds to DICOM Tag 0018, 1250 `Receive Coil Name`, although not all vendors populate that DICOM Tag, in which case this field can be derived from an appropriate private DICOM field                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
-| ReceiveCoilActiveElements     | RECOMMENDED. Information describing the active/selected elements of the receiver coil. This doesn’t correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. As an example, for Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemen’s private DICOM fields (e.g., `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected |
+| ReceiveCoilActiveElements     | RECOMMENDED. Information describing the active/selected elements of the receiver coil. This doesn’t correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. As an example, for Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemens’ private DICOM fields (e.g., `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected |
 | GradientSetType               | RECOMMENDED. It should be possible to infer the gradient coil from the scanner model. If not, e.g. because of a custom upgrade or use of a gradient insert set, then the specifications of the actual gradient coil should be reported independently                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 | MRTransmitCoilSequence        | RECOMMENDED. This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 `MR Transmit Coil Sequence`                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
 | MatrixCoilMode                | RECOMMENDED. (If used) A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (e.g. GRAPPA, SENSE) imaging                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |

From ebe69efd30a83f17970a3638fc23387d28402e5a Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 15 Mar 2019 12:16:13 -0700
Subject: [PATCH 14/18] [ENH] Alternative folder organization for raw, derived,
 and source data

---
 src/02-common-principles.md | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/src/02-common-principles.md b/src/02-common-principles.md
index ecaf302dc4..3dfc31a501 100644
--- a/src/02-common-principles.md
+++ b/src/02-common-principles.md
@@ -109,6 +109,29 @@ these data are to be included:
 1.  We RECOMMEND including the PDF print-out with the actual sequence parameters
     generated by the scanner in the `sourcedata` folder.
 
+Alternatively one can organize their data in the following way
+
+```Text
+my_dataset/
+  sourcedata/
+    ...
+  rawdata/
+    dataset_description.json
+    participants.tsv
+    sub-01/
+    sub-02/
+    ...
+  derivatives/
+    ...
+```
+
+In this example **only the `rawdata` subfolder needs to be BIDS compliant** 
+dataset. This specification does not prescribe anything about the contents of 
+`sourcedata` and `derivatives` folders in the above example - nor does it 
+prescribe the `sourcedata`, `derivatives`, or `rawdata` folder names. The above 
+example is just a convention that can be useful for organizing raw, source, and 
+derived data while maintaining BIDS compliancy of the raw data folder.
+
 ## The Inheritance Principle
 
 Any metadata file (`.json`, `.bvec`, `.tsv`, etc.) may be defined at any

From b2c7706e845a167a6c07722cd16bef46aa13823f Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 15 Mar 2019 11:01:26 -0700
Subject: [PATCH 15/18] [INFRA] Adding instructions for naming PRs

---
 CONTRIBUTING.md          | 16 ++++++++++++++++
 pull_request_template.md | 17 +++++++++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 pull_request_template.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b1f67a1d85..05fbc493d3 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -95,6 +95,22 @@ Try to keep the changes focused. If you submit a large amount of work in all in
 
 #### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
 
+Please keep the title of your pull request short but informative - it will 
+appear in the changelog.
+
+Use one of the following prefixes in the title of your pull request:
+  - `[ENH]` - enhancement of the specification that adds a new feature or 
+    support for a new data type
+  - `[FIX]` - fix of a typo or language clarification
+  - `[INFRA]` - changes to the infrastructure automating the specification 
+    release (for example building HTML docs etc.)
+  - `[MISC]` - everything else including changes to the file listing 
+    contributors
+
+If you are opening a pull request to obtain early feedback, but the changes 
+are not ready to be merged (a.k.a. Work in Progress pull request) please 
+use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+
 A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
 
 A [review](https://help.github.com/articles/about-pull-request-reviews/) will probably consist of a few questions to help clarify the work you've done. Keep an eye on your GitHub notifications and be prepared to join in that conversation.
diff --git a/pull_request_template.md b/pull_request_template.md
new file mode 100644
index 0000000000..82f0ea4863
--- /dev/null
+++ b/pull_request_template.md
@@ -0,0 +1,17 @@
+--- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE PULL REQUEST ---
+
+- Please keep the title of your pull request short but informative - it will 
+  appear in the changelog
+- Use one of the following prefixes in the title of your pull request:
+  - `[ENH]` - enhancement of the specification that adds a new feature or 
+    support for a new data type
+  - `[FIX]` - fix of a typo or language clarification
+  - `[INFRA]` - changes to the infrastructure automating the specification 
+    release (for example building HTML docs etc.)
+  - `[MISC]` - everything else including changes to the file listing 
+    contributors
+- If you are opening a pull request to obtain early feedback, but the changes 
+  are not ready to be merged (a.k.a. Work in Progress pull request) please 
+  use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
+
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
\ No newline at end of file

From 63bcdbc0a259ecc400c753dac7d6285c806705d0 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 15 Mar 2019 11:22:51 -0700
Subject: [PATCH 16/18] Update CONTRIBUTING.md

Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 05fbc493d3..3b115dac9b 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -109,7 +109,7 @@ Use one of the following prefixes in the title of your pull request:
 
 If you are opening a pull request to obtain early feedback, but the changes 
 are not ready to be merged (a.k.a. Work in Progress pull request) please 
-use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
 
 A member of the BIDS Specification team will review your changes to confirm that they can be merged into the main codebase.
 

From 5186060c0a4271c92c974997b283fa72018c69de Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Fri, 15 Mar 2019 11:30:36 -0700
Subject: [PATCH 17/18] add link to the changelog

---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3b115dac9b..07ebbc74dd 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -96,7 +96,7 @@ Try to keep the changes focused. If you submit a large amount of work in all in
 #### 4. Submit a [pull request](https://help.github.com/articles/about-pull-requests/)
 
 Please keep the title of your pull request short but informative - it will 
-appear in the changelog.
+appear in the [changelog](src/CHANGES.md).
 
 Use one of the following prefixes in the title of your pull request:
   - `[ENH]` - enhancement of the specification that adds a new feature or 

From c0e95605a7d13bb7c248a0b2ee2ea335faf09755 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 15 Mar 2019 12:25:26 -0700
Subject: [PATCH 18/18] Update pull_request_template.md

Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
---
 pull_request_template.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pull_request_template.md b/pull_request_template.md
index 82f0ea4863..7f01ddbc69 100644
--- a/pull_request_template.md
+++ b/pull_request_template.md
@@ -12,6 +12,6 @@
     contributors
 - If you are opening a pull request to obtain early feedback, but the changes 
   are not ready to be merged (a.k.a. Work in Progress pull request) please 
-  use [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
+  use a [draft pull request](https://github.blog/2019-02-14-introducing-draft-pull-requests/)
 
---- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---
\ No newline at end of file
+--- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---