bids-standard · chrisgorgo · Feb 25, 2019 · Dec 16, 2018 · Dec 16, 2018 · Dec 16, 2018
diff --git a/CODEOWNERS b/CODEOWNERS
@@ -1,13 +1,14 @@
-# This files DOES NOT list people responsible for maintanance of different parts of 
+# This files DOES NOT list people responsible for maintenance of different parts of
 # the specification. It merely serves the purpose of notifying interested
 # contributors when a new Pull Request that proposes changes to a particular file
 # is submitted. If you would like to subscribe to such notifications (in a form of a
-# Request for Review) please add your github username next to the file you want to 
+# 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
-/src/CHANGES.md @chrisfilo
+/src/CHANGES.md @chrisfilo @sappelhoff @CPernet
 
 # Individual sections
 /src/01-common-principles.md @chrisfilo
 /src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @chrisfilo
+/src/04-modality-specific-files/03-electroencephalography.md @sappelhoff
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -12,9 +12,11 @@ nav:
       - Modality specific files:
         - Magnetic Resonance Imaging: 04-modality-specific-files/01-magnetic-resonance-imaging-data.md
         - Magnetoencephalography: 04-modality-specific-files/02-magnetoencephalography.md
-        - Task events: 04-modality-specific-files/03-task-events.md
-        - Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md
-        - Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioral-experiments.md
+        - 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
+        - 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
       - Appendix:

diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md
diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md
diff --git a/...modality-specific-files/03-task-events.md → ...modality-specific-files/05-task-events.md b/...modality-specific-files/03-task-events.md → ...modality-specific-files/05-task-events.md
@@ -31,9 +31,11 @@ REQUIRED and OPTIONAL columns:
 | :------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | onset         | REQUIRED. Onset (in seconds) of the event measured from the beginning of the acquisition of the first volume in the corresponding task imaging data file. If any acquired scans have been discarded before forming the imaging data file, ensure that a time of 0 corresponds to the first image stored. In other words negative numbers in "onset" are allowed<sup>5</sup>.                                                                                                     |
 | duration      | REQUIRED. Duration of the event (measured from onset) in seconds. Must always be either zero or positive. A "duration" value of zero implies that the delta function or event is so short as to be effectively modeled as an impulse.                                                                                                                                                                                                                                            |
+| sample        | OPTIONAL. Onset of the event according to the sampling scheme of the recorded modality (i.e., referring to the raw data file that the `events.tsv` file accompanies).                                                                                                                                                                                                                                                                                                            |
 | trial_type    | OPTIONAL. Primary categorisation of each trial to identify them as instances of the experimental conditions. For example: for a response inhibition task, it could take on values "go" and "no-go" to refer to response initiation and response inhibition experimental conditions.                                                                                                                                                                                              |
 | response_time | OPTIONAL. Response time measured in seconds. A negative response time can be used to represent preemptive responses and "n/a" denotes a missed response.                                                                                                                                                                                                                                                                                                                         |
 | stim_file     | OPTIONAL. Represents the location of the stimulus file (image, video, sound etc.) presented at the given onset time. There are no restrictions on the file formats of the stimuli files, but they should be stored in the /stimuli folder (under the root folder of the dataset; with optional subfolders). The values under the stim_file column correspond to a path relative to "/stimuli". For example "images/cat03.jpg" will be translated to "/stimuli/images/cat03.jpg". |
+| value         | OPTIONAL. Marker value associated with the event (e.g., the value of a TTL trigger that was recorded at the onset of the event).                                                                                                                                                                                                                                                                                                                                                 |
 | HED           | OPTIONAL. Hierarchical Event Descriptor (HED) Tag. See [Appendix III](../99-appendices/03-hed.md) for details.                                                                                                                                                                                                                                                                                                                                                                   |
 
 <sup>5</sup> For example in case there is an in scanner training phase that

diff --git a/...logical-and-other-continous-recordings.md → ...logical-and-other-continous-recordings.md b/...logical-and-other-continous-recordings.md → ...logical-and-other-continous-recordings.md
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -0,0 +1,26 @@
+# 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`.
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes1.png b/src/04-modality-specific-files/images/ieeg_electrodes1.png
diff --git a/src/04-modality-specific-files/images/ieeg_electrodes2.png b/src/04-modality-specific-files/images/ieeg_electrodes2.png
diff --git a/src/06-extensions.md b/src/06-extensions.md
@@ -35,9 +35,7 @@ Below is a table of currently-active BEPs.
 | [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                                                |

diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
@@ -30,7 +30,7 @@ The following individuals have contributed to the Brain Imaging Data Structure
 ecosystem (in alphabetical order). If you contributed to the BIDS ecosystem and
 your name is not listed, please add it.
 
--   Stefan Appelhoff 📖💬🤔🐛💡💻
+-   Stefan Appelhoff 📖💬🤔🐛💡💻👀⚠️📢
 -   Tibor Auer 💬📖💡🔧📢
 -   Sylvain Baillet 📖🔍
 -   Elizabeth Bock 📖💡
@@ -42,6 +42,7 @@ your name is not listed, please add it.
 -   R. Cameron Craddock 📖📢
 -   Samir Das 📖
 -   Alejandro de la Vega 🐛💻⚠️
+-   Arnaud Delorme 📖💡
 -   Eugene P. Duff 📖
 -   Elizabeth DuPre 📖💡🔍🤔
 -   Eric A. Earl 🤔
@@ -94,6 +95,7 @@ your name is not listed, please add it.
 -   Cyril Pernet 💬📖💡📋
 -   Franco Pestilli 📖
 -   Dmitry Petrov 📖💻
+-   Christophe Philips 📖
 -   Russell A. Poldrack 📖🔍📢
 -   Jean-Baptiste Poline 📖📢🤔🎨
 -   Vasudev Raguram 💻🎨📖🔧

diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md
@@ -1,4 +1,4 @@
-# Appendix VIII: preferred names of Coordinate systems
+# Appendix VIII: Preferred Names of Coordinate Systems
 
 To interpret a coordinate (x, y, z), it is required that you know relative to
 which origin the coordinates are expressed, you have to know the interpretation
@@ -7,7 +7,9 @@ expressed. This information is sometimes called the coordinate system.
 
 These letters help describe the coordinate system definition:
 
-A/P means anterior/posterior L/R means left/right S/I means superior/inferior
+-   A/P means anterior/posterior
+-   L/R means left/right
+-   S/I means superior/inferior
 
 For example: `RAS` means that the first dimension (X) points towards the right
 hand side of the head, the second dimension (Y) points towards the Anterior
@@ -16,7 +18,7 @@ head.
 
 Besides coordinate systems, defined by their origin and direction of the axes,
 BIDS defines "spaces" as an artificial frame of reference, created to describe
-different anatomies in a unifying manner (see e.g.
+different anatomies in a unifying manner (see e.g.,
 [https://doi.org/10.1016/j.neuroimage.2012.01.024](https://www.sciencedirect.com/science/article/pii/S1053811912000419?via%3Dihub)).
 The "space" and all coordinates expressed in this space are by design a
 transformation of the real world geometry, and nearly always different from the
@@ -30,41 +32,41 @@ The coordinate systems below all relate to neuroscience and therefore to the
 head or brain coordinates. Please be aware that all data acquisition starts with
 "device coordinates" (scanner), which does not have to be identical to the
 initial "file format coordinates" (DICOM), which are again different from the
-"head" coordinates (e.g. NIFTI). Not only do device coordinate vary between
+"head" coordinates (e.g., NIFTI). Not only do device coordinate vary between
 hardware manufacturers, but also the head coordinates differ, mostly due to
 different conventions used in specific software packages developed by different
 (commercial or academic) groups.
 
-## MEG specific Coordinate Systems
+## Coordinate Systems applicable to MEG, EEG, and iEEG
 
-The first two pieces of information (origin, orientation) are specified in
-`XXXCoordinateSystem`, the units are specified in `XXXCoordinateSystemUnits`.
+Generally, across the MEG, EEG, and iEEG modalities, the first two pieces of
+information (origin, orientation) are specified in `XXXCoordinateSystem`, and
+the units are specified in `XXXCoordinateSystemUnits`.
 
-Restricted keywords for the XXXCoordinateSystem field in the
-`coordinatesystem.json` file for MEG datasets:
-
--   CTF: ALS orientation and the origin between the ears
-
--   ElektaNeuromag: RAS orientation and the origin between the ears
+Allowed values for the `XXXCoordinateSystem` field come from a list of
+restricted keywords, as listed in the sections below. If no value from the
+list of restricted keywords fits, there is always the option to specify the
+value as follows:
 
--   4DBti: ALS orientation and the origin between the ears
+-   `Other`: Use this for other coordinate systems and specify further details
+    in the `XXXCoordinateSystemDescription` field
 
--   KitYokogawa: ALS orientation and the origin between the ears
+## MEG Specific Coordinate Systems
 
--   ChietiItab: RAS orientation and the origin between the ears
-
--   Other: Use this for other coordinate systems and specify further details in
-  the `XXXCoordinateSystemDescription` field
+Restricted keywords for the `XXXCoordinateSystem` field in the
+`coordinatesystem.json` file for MEG datasets:
 
-Note that the short descriptions above do not capture all details, there are
-detailed descriptions of these coordinate systems on the FieldTrip toolbox web
-page:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+-   `CTF`: ALS orientation and the origin between the ears
+-   `ElektaNeuromag`: RAS orientation and the origin between the ears
+-   `4DBti`: ALS orientation and the origin between the ears
+-   `KitYokogawa`: ALS orientation and the origin between the ears
+-   `ChietiItab`: RAS orientation and the origin between the ears
 
-## EEG specific Coordinate Systems
+Note that the short descriptions above do not capture all details, There are
+detailed extensive descriptions of these EEG coordinate systems on the
+[FieldTrip toolbox web page](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
 
-The first two pieces of information (origin, orientation) are specified in
-`XXXCoordinateSystem`, the units are specified in `XXXCoordinateSystemUnits`.
+## EEG Specific Coordinate Systems
 
 Restricted keywords for the `XXXCoordinateSystem` field in the
 `coordsystem.json` file for EEG datasets:
@@ -78,12 +80,31 @@ Restricted keywords for the `XXXCoordinateSystem` field in the
 -   `Captrak`: RAS orientation and the origin between the ears
 
 Note that the short descriptions above do not capture all details, There are
-detailed extensive descriptions of these EEG coordinate systems on the FieldTrip
-toolbox web page and on the BESA wiki:
-[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
-[http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations\#Coordinate_systems](http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations#Coordinate_systems)
+detailed extensive descriptions of these EEG coordinate systems on the
+[FieldTrip toolbox web page](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
+and on the [BESA wiki](http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations#Coordinate_systems).
 
-## Template based Coordinate Systems
+## iEEG Specific Coordinate Systems
+
+Restricted keywords for the `XXXCoordinateSystem` field in the
+`coordsystem.json` file for iEEG datasets:
+
+-   `Pixels`: If electrodes are localized in 2D space (only x and y are
+    specified and z is n/a), then the positions in this file must correspond to
+    the locations expressed in pixels on the photo/drawing/rendering of the
+    electrodes on the brain. In this case, coordinates must be (row,column)
+    pairs, with (0,0) corresponding to the upper left pixel and (N,0)
+    corresponding to the lower left pixel.
+
+-   `ACPC`: The origin of the coordinate system is at the Anterior Commissure
+    and the negative y-axis is passing through the Posterior Commissure. The
+    positive z-axis is passing through a mid-hemispheric point in the superior
+    direction. The anatomical landmarks are determined in the individual's
+    anatomical scan and no scaling or deformations have been applied to the
+    individual's anatomical scan. For more information, see the [ACPC site](http://www.fieldtriptoolbox.org/faq/acpc/)
+    on the FieldTrip toolbox wiki.
+
+## Template Based Coordinate Systems
 
 The transformation of the real world geometry to an artificial frame of
 reference is described in `XXXCoordinateSystem`. Unless otherwise specified

diff --git a/src/CHANGES.md b/src/CHANGES.md
@@ -86,7 +86,7 @@ Changelog
 
 -   Added support for MEG data (merged BEP008)
 -   Added SequenceName field.
--   Added support for describing events with Hierarchical Event Descriptors \[[4.3 Task events](04-modality-specific-files/03-task-events.md)].
+-   Added support for describing events with Hierarchical Event Descriptors \[[4.3 Task events](04-modality-specific-files/05-task-events.md)].
 -   Added VolumeTiming and AcquisitionDuration fields \[[4.1 Task (including resting state) imaging data](04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)].
 -   Added DwellTime field.