From 375c04018f7eec77c3021b17012769541546210c Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:07:14 -0500
Subject: [PATCH 01/12] RF: use lowercase optional instead of OPTIONAL

IMHO there is not need to capitalize it in the text.  Moreover it was
inconsistent - some places had it capitalized and some not
---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

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 69ca882ca1..94e714d9fd 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
@@ -142,7 +142,7 @@ run labels). When there is only one scan of a given type the run key MAY be
 omitted. Please note that diffusion imaging data is stored elsewhere (see
 below).
 
-The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label the user
+The optional `acq-<label>` key/value pair corresponds to a custom label the user
 MAY use to distinguish a different set of parameters used for acquiring the same
 modality. For example this should be used when a study includes two T1w images -
 one full brain low resolution and and one restricted field of view but high
@@ -155,12 +155,12 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
-Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
+Similarly the optional `ce-<label>` key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
 JSON file, with the same label.
 
-Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
+Similarly the optional `rec-<label>` key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
 If the structural images included in the dataset were defaced (to protect
@@ -215,7 +215,7 @@ If more than one run of the same task has been acquired a key/value pair:
 defined as the same task, but in some cases it can mean different set of stimuli
 (for example randomized order) and participant responses.
 
-The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label one may
+The optional `acq-<label>` key/value pair corresponds to a custom label one may
 use to distinguish different set of parameters used for acquiring the same task.
 For example this should be used when a study includes two resting state images -
 one single band and one multiband. In such case two files could have the
@@ -224,7 +224,7 @@ following names: `sub-01_task-rest_acq-singleband_bold.nii.gz` and
 other label than `singleband` and `multiband` as long as they are consistent
 across subjects and sessions and consist only of the legal label characters.
 
-Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
+Similarly the optional `ce-<label>` key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key ContrastBolusIngredient MAY be also be added in the JSON
 file, with the same label.
@@ -452,7 +452,7 @@ This is a common output for build in fieldmap sequence on Siemens scanners. In
 this particular case the sidecar JSON file has to define the Echo Times of the
 two phase images used to create the difference image. `EchoTime1` corresponds to
 the shorter echo time and `EchoTime2` to the longer echo time. Similarly
-`_magnitude1` image corresponds to the shorter echo time and the OPTIONAL
+`_magnitude1` image corresponds to the shorter echo time and the optional
 `_magnitude2` image to the longer echo time. For example:
 
 ```JSON

From 1c4b19afc8774b16cf5af2f9a78f7ba60c359412 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:09:25 -0500
Subject: [PATCH 02/12] [DATALAD RUNCMD] No need for session_ prefix in
 ses-<session_label> -- implied

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi 'ses-<session_label>' 'ses-<label>'",
 "exit": 0,
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 src/03-modality-agnostic-files.md             |  4 +-
 .../01-magnetic-resonance-imaging-data.md     | 66 +++++++++----------
 .../03-task-events.md                         |  2 +-
 ...ological-and-other-continous-recordings.md |  2 +-
 .../05-behavioural-experiments.md             | 18 ++---
 src/05-longitudinal-and-multi-site-studies.md |  8 +--
 6 files changed, 50 insertions(+), 50 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 781887d391..ac9112c897 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -152,8 +152,8 @@ questionnaire).
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
-    sub-<participant_label>[_ses-<session_label>]_scans.tsv
+sub-<participant_label>/[ses-<label>/]
+    sub-<participant_label>[_ses-<label>]_scans.tsv
 ```
 
 Optional: Yes
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 94e714d9fd..2ec3e05e83 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
@@ -110,10 +110,10 @@ whenever possible.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     anat/
-        sub-<participant_label>[_ses-<session_label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
-        sub-<participant_label>[_ses-<session_label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
+        sub-<participant_label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
+        sub-<participant_label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 
 Anatomical (structural) data acquired for that participant. Currently supported
@@ -191,10 +191,10 @@ Currently supported image contrasts include:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     func/
-        sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-        sub-<participant_label>[_ses-<session_label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
+        sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+        sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
 ```
 
 Imaging data acquired during functional imaging (i.e. imaging which supports
@@ -327,14 +327,14 @@ participant, task and run takes precedence.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     dwi/
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.bval
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.bvec
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_dwi.json
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_sbref.nii[.gz]
-       sub-<participant_label>[_ses-<session_label>][_acq-<label>][_run-<index>]_sbref.json
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bval
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bvec
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.json
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.nii[.gz]
+       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.json
 ```
 
 Diffusion-weighted imaging data acquired for that participant. The optional
@@ -433,19 +433,19 @@ the user may use to distinguish different set of parameters.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phasediff.nii[.gz]
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phasediff.json
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
 ```
 
 (optional)
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
 ```
 
 This is a common output for build in fieldmap sequence on Siemens scanners. In
@@ -468,14 +468,14 @@ the shorter echo time and `EchoTime2` to the longer echo time. Similarly
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phase1.nii[.gz]
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phase1.json
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phase2.nii[.gz]
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_phase2.json
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
-        sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase2.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
 ```
 
 Similar to the case above, but instead of a precomputed phase difference map two
@@ -494,11 +494,11 @@ corresponding `EchoTime` values. For example:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     fmap/
-       sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_magnitude.nii[.gz]
-       sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_fieldmap.nii[.gz]
-       sub-<label>[_ses-<session_label>][_acq-<label>][_run-<run_index>]_fieldmap.json
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_fieldmap.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_fieldmap.json
 ```
 
 In some cases (for example GE) the scanner software will output a precomputed
@@ -518,10 +518,10 @@ the fieldmap. The possible options are: `Hz`, `rad/s`, or `Tesla`. For example:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<session_label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.nii[.gz]
-        sub-<label>[_ses-<session_label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.json
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.json
 ```
 
 The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo
diff --git a/src/04-modality-specific-files/03-task-events.md b/src/04-modality-specific-files/03-task-events.md
index 0dde7002d0..f9e1aa4958 100644
--- a/src/04-modality-specific-files/03-task-events.md
+++ b/src/04-modality-specific-files/03-task-events.md
@@ -3,7 +3,7 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>]
+sub-<participant_label>/[ses-<label>]
     func/
         <matches>_events.tsv
         <matches>_events.json
diff --git a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md b/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
index 917a610a64..319cf7772b 100644
--- a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
+++ b/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
@@ -3,7 +3,7 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     func/
         <matches>[_recording-<label>]_physio.tsv.gz
         <matches>[_recording-<label>]_physio.json
diff --git a/src/04-modality-specific-files/05-behavioural-experiments.md b/src/04-modality-specific-files/05-behavioural-experiments.md
index de2155bc5c..5549539ddf 100644
--- a/src/04-modality-specific-files/05-behavioural-experiments.md
+++ b/src/04-modality-specific-files/05-behavioural-experiments.md
@@ -3,16 +3,16 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<session_label>/]
+sub-<participant_label>/[ses-<label>/]
     beh/
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.tsv
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_events.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.tsv
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_beh.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.tsv.gz
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_physio.json
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.tsv.gz
-        sub-<participant_label>[_ses-<session_label>]_task-<task_name>_stim.json
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_events.tsv
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_events.json
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_beh.tsv
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_beh.json
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_physio.tsv.gz
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_physio.json
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_stim.tsv.gz
+        sub-<participant_label>[_ses-<label>]_task-<task_name>_stim.json
 ```
 
 In addition to logs from behavioral experiments performed along imaging data
diff --git a/src/05-longitudinal-and-multi-site-studies.md b/src/05-longitudinal-and-multi-site-studies.md
index 234a7c3894..a3c62e08e3 100644
--- a/src/05-longitudinal-and-multi-site-studies.md
+++ b/src/05-longitudinal-and-multi-site-studies.md
@@ -1,18 +1,18 @@
 # Longitudinal studies with multiple sessions (visits)
 
 Multiple sessions (visits) are encoded by adding an extra layer of directories
-and file names in the form of `ses-<session_label>`. Session label can consist
+and file names in the form of `ses-<label>`. Session label can consist
 only of alphanumeric characters `[a-zA-Z0-9]` and should be consistent across
 subjects. If numbers are used in session labels we recommend using zero padding
 (for example `ses-01`, `ses-11` instead of `ses-1`, `ses-11`). This makes
 results of alphabetical sorting more intuitive. Acquisition time of session can
 be defined in the sessions file (see below for details).
 
-The extra session layer (at least one `/ses-<session_label>` subfolder) should
+The extra session layer (at least one `/ses-<label>` subfolder) should
 be added for all subjects if at least one subject in the dataset has more than
 one session. Skipping the session layer for only some subjects in the dataset is
-not allowed. If a `/ses-<session_label>` subfolder is included as part of the
-directory hierarchy, then the same `ses-<session_label>` tag must also be
+not allowed. If a `/ses-<label>` subfolder is included as part of the
+directory hierarchy, then the same `ses-<label>` tag must also be
 included as part of the file names themselves.
 
 ```Text

From 611a1a809f5bc9bdd12a7170ed8fbbd938d7bc27 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:10:17 -0500
Subject: [PATCH 03/12] [DATALAD RUNCMD] No need for participant_ prefix in
 sub-<participant_label> -- implied (and inconsistent)

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi 'sub-<participant_label>' 'sub-<label>'",
 "exit": 0,
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 src/03-modality-agnostic-files.md             |  8 ++--
 .../01-magnetic-resonance-imaging-data.md     | 38 +++++++++----------
 .../02-magnetoencephalography.md              | 22 +++++------
 .../03-task-events.md                         |  2 +-
 ...ological-and-other-continous-recordings.md |  2 +-
 .../05-behavioural-experiments.md             | 18 ++++-----
 src/05-longitudinal-and-multi-site-studies.md |  4 +-
 src/99-appendices/06-meg-file-formats.md      | 18 ++++-----
 8 files changed, 56 insertions(+), 56 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index ac9112c897..6e13ae2606 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -84,7 +84,7 @@ Optional: Yes
 
 The purpose of this file is to describe properties of participants such as age,
 handedness, sex, etc. In case of single session studies this file has one
-compulsory column `participant_id` that consists of `sub-<participant_label>`,
+compulsory column `participant_id` that consists of `sub-<label>`,
 followed by a list of optional columns describing participants. Each participant
 needs to be described by one and only one row.
 
@@ -102,7 +102,7 @@ example responses from multiple questionnaires) they can be split into
 individual files separate from `participants.tsv`. Those measurements should be
 kept in phenotype/ folder and end with the `.tsv` extension. They can include
 arbitrary set of columns, but one of them has to be participant_id with matching
-`sub-<participant_label>`. As with all other tabular data, those additional
+`sub-<label>`. As with all other tabular data, those additional
 phenotypic information files can be accompanied by a JSON file describing the
 columns in detail (see [here](02-common-principles.md#tabular-files)).
 In addition to the column description, a
@@ -152,8 +152,8 @@ questionnaire).
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
-    sub-<participant_label>[_ses-<label>]_scans.tsv
+sub-<label>/[ses-<label>/]
+    sub-<label>[_ses-<label>]_scans.tsv
 ```
 
 Optional: Yes
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 2ec3e05e83..f20b6ca78d 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
@@ -110,10 +110,10 @@ whenever possible.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     anat/
-        sub-<participant_label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
-        sub-<participant_label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 
 Anatomical (structural) data acquired for that participant. Currently supported
@@ -191,10 +191,10 @@ Currently supported image contrasts include:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     func/
-        sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-        sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
 ```
 
 Imaging data acquired during functional imaging (i.e. imaging which supports
@@ -318,7 +318,7 @@ If this information is the same for all participants, sessions and runs it can
 be provided in `task-<task_label>_bold.json` (in the root directory of the
 dataset). However, if the information differs between subjects/runs it can be
 specified in the
-`sub-<participant_label>/func/sub-<participant_label>_task-<task_label>[_acq-<label>][_run-<index>]_bold.json` file.
+`sub-<label>/func/sub-<label>_task-<task_label>[_acq-<label>][_run-<index>]_bold.json` file.
 If both files are specified fields from the file corresponding to a particular
 participant, task and run takes precedence.
 
@@ -327,14 +327,14 @@ participant, task and run takes precedence.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     dwi/
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bval
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bvec
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.json
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.nii[.gz]
-       sub-<participant_label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.json
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bval
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.bvec
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_dwi.json
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_sbref.json
 ```
 
 Diffusion-weighted imaging data acquired for that participant. The optional
@@ -433,7 +433,7 @@ the user may use to distinguish different set of parameters.
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     fmap/
         sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.json
@@ -443,7 +443,7 @@ sub-<participant_label>/[ses-<label>/]
 (optional)
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     fmap/
         sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
 ```
@@ -468,7 +468,7 @@ the shorter echo time and `EchoTime2` to the longer echo time. Similarly
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     fmap/
         sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.json
@@ -494,7 +494,7 @@ corresponding `EchoTime` values. For example:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     fmap/
        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_fieldmap.nii[.gz]
@@ -518,7 +518,7 @@ the fieldmap. The possible options are: `Hz`, `rad/s`, or `Tesla`. For example:
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     fmap/
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.json
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 695b164bcd..89f5e53b3e 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -15,11 +15,11 @@ academic literature:
 Template:
 
 ```Text
-sub-<participant_label>/
+sub-<label>/
     [ses-<label>]/
       meg/
-        sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.<manufacturer_specific_extension>
-        [sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.json]
+        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.<manufacturer_specific_extension>
+        [sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.json]
 ```
 
 Unprocessed MEG data MUST be stored in the native file format of the MEG
@@ -177,10 +177,10 @@ on local REB/IRB ethics board policy.
 Template:
 
 ```Text
-sub-<participant_label>/
+sub-<label>/
     [ses-<label>]/
       meg/
-        [sub-<participant_label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_channels.tsv]
+        [sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_channels.tsv]
 ```
 
 This file is RECOMMENDED as it provides easily searchable information across
@@ -272,10 +272,10 @@ UADC001 AUDIO V envelope of audio signal presented to participant
 Template:
 
 ```Text
-sub-<participant_label>/
+sub-<label>/
     [ses-<label>]/
       meg/
-        [sub-<participant_label>[_ses-<label>][_acq-<label>]_coordsystem.json]
+        [sub-<label>[_ses-<label>][_acq-<label>]_coordsystem.json]
 ```
 
 OPTIONAL. A JSON document specifying the coordinate system(s) used for the MEG,
@@ -362,10 +362,10 @@ Photos of the anatomical landmarks and/or head localization coils
 Template:
 
 ```Text
-sub-<participant_label>/
+sub-<label>/
     [ses-<label>]/
       meg/
-        [sub-<participant_label>[_ses-<label>][_acq-<label>]_photo.jpg]
+        [sub-<label>[_ses-<label>][_acq-<label>]_photo.jpg]
 ```
 
 Photos of the anatomical landmarks and/or head localization coils on the
@@ -385,10 +385,10 @@ actual anatomical nasion: `sub-0001_ses-001_acq-NAS_photo.jpg`
 Template:
 
 ```Text
-sub-<participant_label>/
+sub-<label>/
     [ses-<label>]/
       meg/
-        [sub-<participant_label>[_ses-<label>][_acq-<label>]_headshape.<manufacturer_specific_extension>]
+        [sub-<label>[_ses-<label>][_acq-<label>]_headshape.<manufacturer_specific_extension>]
 ```
 
 This file is RECOMMENDED.
diff --git a/src/04-modality-specific-files/03-task-events.md b/src/04-modality-specific-files/03-task-events.md
index f9e1aa4958..966762e304 100644
--- a/src/04-modality-specific-files/03-task-events.md
+++ b/src/04-modality-specific-files/03-task-events.md
@@ -3,7 +3,7 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>]
+sub-<label>/[ses-<label>]
     func/
         <matches>_events.tsv
         <matches>_events.json
diff --git a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md b/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
index 319cf7772b..b4236af057 100644
--- a/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
+++ b/src/04-modality-specific-files/04-physiological-and-other-continous-recordings.md
@@ -3,7 +3,7 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     func/
         <matches>[_recording-<label>]_physio.tsv.gz
         <matches>[_recording-<label>]_physio.json
diff --git a/src/04-modality-specific-files/05-behavioural-experiments.md b/src/04-modality-specific-files/05-behavioural-experiments.md
index 5549539ddf..83c2018384 100644
--- a/src/04-modality-specific-files/05-behavioural-experiments.md
+++ b/src/04-modality-specific-files/05-behavioural-experiments.md
@@ -3,16 +3,16 @@
 Template:
 
 ```Text
-sub-<participant_label>/[ses-<label>/]
+sub-<label>/[ses-<label>/]
     beh/
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_events.tsv
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_events.json
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_beh.tsv
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_beh.json
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_physio.tsv.gz
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_physio.json
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_stim.tsv.gz
-        sub-<participant_label>[_ses-<label>]_task-<task_name>_stim.json
+        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
diff --git a/src/05-longitudinal-and-multi-site-studies.md b/src/05-longitudinal-and-multi-site-studies.md
index a3c62e08e3..37fe5e27e6 100644
--- a/src/05-longitudinal-and-multi-site-studies.md
+++ b/src/05-longitudinal-and-multi-site-studies.md
@@ -64,8 +64,8 @@ CHANGES
 Template:
 
 ```Text
-sub-<participant_label>/
-    sub-<participant_label>_sessions.tsv
+sub-<label>/
+    sub-<label>_sessions.tsv
 ```
 
 Optional: Yes
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 9b1b43ce74..9592d6739f 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -22,8 +22,8 @@ are usually stored in a separate `.pos` file, not necessarily within the `.ds`
 folder.
 
 ```Text
-[sub-<participant_label>[_ses-<label>]_headshape.pos]
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.ds>
+[sub-<label>[_ses-<label>]_headshape.pos]
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.ds>
 ```
 
 CTF’s data storage is therefore via directories containing multiple files. The
@@ -57,7 +57,7 @@ inside the fif file along with the MEG data, with typically no `_headshape`
 file.
 
 ```Text
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.fif
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.fif
 ```
 
 Note that we do not provide specific specifications for cross-talk and
@@ -119,8 +119,8 @@ Each experimental run on a 4D neuroimaging/BTi system results in a folder
 containing multiple files without extensions.
 
 ```Text
-[sub-<participant_label>[_ses-<label>]_headshape.pos]
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg>
+[sub-<label>[_ses-<label>]_headshape.pos]
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg>
 ```
 
 One SHOULD rename/create a father run specific directory and keep the original
@@ -195,10 +195,10 @@ the head points (\_digitizer.txt), the position of the center of the MEG coils
 (.chn) and the event markers (.trg).
 
 ```Text
-[sub-<participant_label>[_ses-<label>]_headshape.txt]
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.kdf
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.chn
-sub-<participant_label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.trg
+[sub-<label>[_ses-<label>]_headshape.txt]
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.kdf
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.chn
+sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.trg
 ```
 
 Example:

From e5538b9d4cb76f6ba59d6cd0bc3d88b63e19c041 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:11:21 -0500
Subject: [PATCH 04/12] [DATALAD RUNCMD] No need for task_ prefix in
 task-<task_label> -- implied

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi 'task-<task_label>' 'task-<label>'",
 "exit": 0,
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 .../01-magnetic-resonance-imaging-data.md            |  8 ++++----
 .../02-magnetoencephalography.md                     |  6 +++---
 src/99-appendices/06-meg-file-formats.md             | 12 ++++++------
 3 files changed, 13 insertions(+), 13 deletions(-)

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 f20b6ca78d..299f5cbbf7 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
@@ -193,8 +193,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     func/
-        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
 ```
 
 Imaging data acquired during functional imaging (i.e. imaging which supports
@@ -315,10 +315,10 @@ sub-control01/
 ```
 
 If this information is the same for all participants, sessions and runs it can
-be provided in `task-<task_label>_bold.json` (in the root directory of the
+be provided in `task-<label>_bold.json` (in the root directory of the
 dataset). However, if the information differs between subjects/runs it can be
 specified in the
-`sub-<label>/func/sub-<label>_task-<task_label>[_acq-<label>][_run-<index>]_bold.json` file.
+`sub-<label>/func/sub-<label>_task-<label>[_acq-<label>][_run-<index>]_bold.json` file.
 If both files are specified fields from the file corresponding to a particular
 participant, task and run takes precedence.
 
diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md
index 89f5e53b3e..fbd6e8a810 100644
--- a/src/04-modality-specific-files/02-magnetoencephalography.md
+++ b/src/04-modality-specific-files/02-magnetoencephalography.md
@@ -18,8 +18,8 @@ Template:
 sub-<label>/
     [ses-<label>]/
       meg/
-        sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.<manufacturer_specific_extension>
-        [sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.json]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.<manufacturer_specific_extension>
+        [sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.json]
 ```
 
 Unprocessed MEG data MUST be stored in the native file format of the MEG
@@ -180,7 +180,7 @@ Template:
 sub-<label>/
     [ses-<label>]/
       meg/
-        [sub-<label>[_ses-<label>]_task-<task_label>[_acq-<label>][_run-<index>][_proc-<label>]_channels.tsv]
+        [sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_channels.tsv]
 ```
 
 This file is RECOMMENDED as it provides easily searchable information across
diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 9592d6739f..ccb93ebebe 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -23,7 +23,7 @@ folder.
 
 ```Text
 [sub-<label>[_ses-<label>]_headshape.pos]
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.ds>
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.ds>
 ```
 
 CTF’s data storage is therefore via directories containing multiple files. The
@@ -57,7 +57,7 @@ inside the fif file along with the MEG data, with typically no `_headshape`
 file.
 
 ```Text
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.fif
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.fif
 ```
 
 Note that we do not provide specific specifications for cross-talk and
@@ -120,7 +120,7 @@ containing multiple files without extensions.
 
 ```Text
 [sub-<label>[_ses-<label>]_headshape.pos]
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg>
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg>
 ```
 
 One SHOULD rename/create a father run specific directory and keep the original
@@ -196,9 +196,9 @@ the head points (\_digitizer.txt), the position of the center of the MEG coils
 
 ```Text
 [sub-<label>[_ses-<label>]_headshape.txt]
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.kdf
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.chn
-sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_meg.trg
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.kdf
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.chn
+sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_meg.trg
 ```
 
 Example:

From 6b32ef151931c11aa0866ba94d629a4050aa79ee Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:12:16 -0500
Subject: [PATCH 05/12] [DATALAD RUNCMD] No need for run_ prefix in
 run-<run_index> -- implied

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi 'run-<run_index>' 'run-<index>'",
 "exit": 0,
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 .../01-magnetic-resonance-imaging-data.md     | 30 +++++++++----------
 1 file changed, 15 insertions(+), 15 deletions(-)

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 299f5cbbf7..67bfbb9296 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
@@ -435,9 +435,9 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phasediff.json
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
 ```
 
 (optional)
@@ -445,7 +445,7 @@ sub-<label>/[ses-<label>/]
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.nii[.gz]
 ```
 
 This is a common output for build in fieldmap sequence on Siemens scanners. In
@@ -470,12 +470,12 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase1.json
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase2.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_phase2.json
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude1.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase1.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.json
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.nii[.gz]
 ```
 
 Similar to the case above, but instead of a precomputed phase difference map two
@@ -496,9 +496,9 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_magnitude.nii[.gz]
-       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_fieldmap.nii[.gz]
-       sub-<label>[_ses-<label>][_acq-<label>][_run-<run_index>]_fieldmap.json
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.json
 ```
 
 In some cases (for example GE) the scanner software will output a precomputed
@@ -520,8 +520,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<run_index>]_epi.json
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<index>]_epi.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<index>]_epi.json
 ```
 
 The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo

From 568bf6d6978e444e558eddea9332b9805f2baec1 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:13:47 -0500
Subject: [PATCH 06/12] [DATALAD RUNCMD] No need for dir_ prefix in
 dir-<dir_label> -- implied

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi 'dir-<dir_label>' 'dir-<label>'",
 "exit": 0,
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
---
 .../01-magnetic-resonance-imaging-data.md                     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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 67bfbb9296..0e762438f6 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
@@ -520,8 +520,8 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     fmap/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<index>]_epi.nii[.gz]
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<dir_label>[_run-<index>]_epi.json
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.json
 ```
 
 The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo

From 4d4262390e9c2b649cc78e42399f65ef4bc90662 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 20 Nov 2018 15:15:09 -0500
Subject: [PATCH 07/12] ENH: adjusting the text since there is no longer
 dir_label

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 0e762438f6..45e096ac85 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
@@ -544,7 +544,7 @@ example
 }
 ```
 
-`dir_label` value can be set to arbitrary alphanumeric label (`[a-zA-Z0-9]+` for
+`label` value of `_dir-` can be set to arbitrary alphanumeric label (`[a-zA-Z0-9]+` for
 example `LR` or `AP`) that can help users to distinguish between different
 files, but should not be used to infer any scanning parameters (such as phase
 encoding directions) of the corresponding sequence. Please rely only on the JSON

From 50f17356b9bd49ff1e92523f9c6b053c010a77db Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 27 Nov 2018 11:48:13 -0500
Subject: [PATCH 08/12] Revert "RF: use lowercase optional instead of OPTIONAL"

This reverts commit 375c04018f7eec77c3021b17012769541546210c.
---
 .../01-magnetic-resonance-imaging-data.md            | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

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 3b2213f01d..84ca7b6ca8 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
@@ -142,7 +142,7 @@ run labels). When there is only one scan of a given type the run key MAY be
 omitted. Please note that diffusion imaging data is stored elsewhere (see
 below).
 
-The optional `acq-<label>` key/value pair corresponds to a custom label the user
+The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label the user
 MAY use to distinguish a different set of parameters used for acquiring the same
 modality. For example this should be used when a study includes two T1w images -
 one full brain low resolution and and one restricted field of view but high
@@ -155,12 +155,12 @@ can also be used to make that distinction. At what level of detail to make the
 distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
 FLASHsubsampled) remains at the discretion of the researcher.
 
-Similarly the optional `ce-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
 JSON file, with the same label.
 
-Similarly the optional `rec-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
 If the structural images included in the dataset were defaced (to protect
@@ -215,7 +215,7 @@ If more than one run of the same task has been acquired a key/value pair:
 defined as the same task, but in some cases it can mean different set of stimuli
 (for example randomized order) and participant responses.
 
-The optional `acq-<label>` key/value pair corresponds to a custom label one may
+The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label one may
 use to distinguish different set of parameters used for acquiring the same task.
 For example this should be used when a study includes two resting state images -
 one single band and one multiband. In such case two files could have the
@@ -224,7 +224,7 @@ following names: `sub-01_task-rest_acq-singleband_bold.nii.gz` and
 other label than `singleband` and `multiband` as long as they are consistent
 across subjects and sessions and consist only of the legal label characters.
 
-Similarly the optional `ce-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL `ce-<label>` key/value can be used to distinguish
 sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key ContrastBolusIngredient MAY be also be added in the JSON
 file, with the same label.
@@ -458,7 +458,7 @@ This is a common output for build in fieldmap sequence on Siemens scanners. In
 this particular case the sidecar JSON file has to define the Echo Times of the
 two phase images used to create the difference image. `EchoTime1` corresponds to
 the shorter echo time and `EchoTime2` to the longer echo time. Similarly
-`_magnitude1` image corresponds to the shorter echo time and the optional
+`_magnitude1` image corresponds to the shorter echo time and the OPTIONAL
 `_magnitude2` image to the longer echo time. For example:
 
 ```JSON

From d4de435e59a1dca143bed241081e90021423fb6d Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 27 Nov 2018 11:52:20 -0500
Subject: [PATCH 09/12] Consistent use of OPTIONAL (not optional or (optional))
 keyword in MRI portion

---
 .../01-magnetic-resonance-imaging-data.md      | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

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 84ca7b6ca8..fa6d75290c 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
@@ -68,9 +68,9 @@ first "effective" echo and the center of the last "effective" echo.
 | :--------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | EchoTime               | RECOMMENDED. The echo time (TE) for the acquisition, specified in seconds. This parameter is REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence. Corresponds to DICOM Tag 0018, 0081 `Echo Time` (please note that the DICOM term is in milliseconds not seconds).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | InversionTime          | RECOMMENDED. The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 `Inversion Time` (please note that the DICOM term is in milliseconds not seconds).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| SliceTiming            | RECOMMENDED. The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times (in JSON format) containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the (optional) `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis (i.e., the final entry in the `SliceTiming` list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the `DelayTime` field set. In addition without this parameter slice time correction will not be possible. |
+| SliceTiming            | RECOMMENDED. The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times (in JSON format) containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis (i.e., the final entry in the `SliceTiming` list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the `DelayTime` field set. In addition without this parameter slice time correction will not be possible. |
 | SliceEncodingDirection | RECOMMENDED. Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which SliceTiming is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of SliceTiming are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present ,the axis defined by SliceEncodingDirection needs to be consistent with the ‘slice_dim’ field in the NIfTI header. When absent, the entries in SliceTiming must be in the order of increasing slice index as defined by the NIfTI header.                                                                                                                                                                                                   |
-| DwellTime              | RECOMMENDED. Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the (optional) readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn’t captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction).                                                                                                                                                                                                                                                                                                                                               |
+| DwellTime              | RECOMMENDED. Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the OPTIONAL readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn’t captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction).                                                                                                                                                                                                                                                                                                                                               |
 
 #### RF & Contrast
 
@@ -229,10 +229,10 @@ sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key ContrastBolusIngredient MAY be also be added in the JSON
 file, with the same label.
 
-Similarly the optional `rec-<label>` key/value can be used to distinguish
+Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
-Similarly the optional `dir-<label>` and `rec-<label>` key/values
+Similarly the OPTIONAL `dir-<label>` and `rec-<label>` key/values
 can be used to distinguish different phase-encoding directions and
 reconstruction algorithms (for example ones using motion correction).
 See [`fmap` Case 4](01-magnetic-resonance-imaging-data.md#case-4-multiple-phase-encoded-directions-pepolar)
@@ -265,7 +265,7 @@ JSON file.
 | :------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. |
 | VolumeTiming   | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with RepetitionTime and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either SliceTiming or AcquisitionDuration be defined.                                              |
-| TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. An optional but RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                          |
+| TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                          |
 
 For the fields described above and in the following section, the term "Volume"
 refers to a reconstruction of the object being imaged (e.g., brain or part of a
@@ -343,7 +343,7 @@ sub-<label>/[ses-<label>/]
        sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_sbref.json
 ```
 
-Diffusion-weighted imaging data acquired for that participant. The optional
+Diffusion-weighted imaging data acquired for that participant. The OPTIONAL
 `acq-<label>` key/value pair corresponds to a custom label the user may use to
 distinguish different set of parameters. For example this should be used when a
 study includes two diffusion images - one single band and one multiband. In such
@@ -427,11 +427,11 @@ slashes. Here’s an example with multiple target scans:
 }
 ```
 
-The IntendedFor field is optional and in case the fieldmaps do not correspond to
+The IntendedFor field is OPTIONAL and in case the fieldmaps do not correspond to
 any particular scans it does not have to be filled.
 
 Multiple fieldmaps can be stored. In such case the `_run-1`, `_run-2` should be
-used. The optional `acq-<label>` key/value pair corresponds to a custom label
+used. The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label
 the user may use to distinguish different set of parameters.
 
 #### Phase difference image and at least one magnitude image
@@ -446,7 +446,7 @@ sub-<label>/[ses-<label>/]
         sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
 ```
 
-(optional)
+OPTIONAL
 
 ```Text
 sub-<label>/[ses-<label>/]

From c961824f538c202d8fddbb6401aaf9166122346e Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 27 Nov 2018 11:54:30 -0500
Subject: [PATCH 10/12] Consistent use of OPTIONAL and REQUIRED (instead of
 lower etc case) in 04-entity-table

---
 src/99-appendices/04-entity-table.md | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index a42f4c8721..ced370f881 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -3,21 +3,21 @@
 This section compiles the entities (key-value pairs) described throughout this
 specification, and establishes a common order within a filename. For example, if
 a file has an acquisition and reconstruction label, the acquisition entity must
-precede the reconstruction entity. Required and optional entities for a given
+precede the reconstruction entity. REQUIRED and OPTIONAL entities for a given
 file type are denoted. Entity formats indicate whether the value is alphanumeric
 (`<label>`) or numeric (`<index>`).
 
 | Entity                   | Format              | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | anat<br>(defacemask) | func<br>(bold sbref events) | func<br>(physio stim) | dwi<br>(dwi bvec bval) | fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap) | fmap<br>(epi) | beh<br>(events stim physio) | meg<br>(meg channels) | meg<br>(photo coordsystem headshape) |
 | :----------------------- | :------------------ | :--------------------------------------------------------------------------------------------- | :------------------- | :-------------------------- | :-------------------- | :--------------------- | :------------------------------------------------------------------------- | :------------ | :-------------------------- | :-------------------- | :----------------------------------- |
-| Subject                  | `sub-<label>`       | Required                                                                                       | Required             | Required                    | Required              | Required               | Required                                                                   | Required      | Required                    | Required              | Required                             |
-| Session                  | `ses-<label>`       | Optional                                                                                       | Optional             | Optional                    | Optional              | Optional               | Optional                                                                   | Optional      | Optional                    | Optional              | Optional                             |
-| Task                     | `task-<label>`      |                                                                                                |                      | Required                    | Required              |                        |                                                                            |               | Required                    | Required              | Required                             |
-| Acquisition              | `acq-<label>`       | Optional                                                                                       | Optional             | Optional                    | Optional              | Optional               | Optional                                                                   | Optional      |                             | Optional              | Optional                             |
-| Contrast Enhancing Agent | `ce-<label>`        | Optional                                                                                       | Optional             | Optional                    |                       |                        |                                                                            | Optional      |                             |                       |                                      |
-| Reconstruction           | `rec-<label>`       | Optional                                                                                       | Optional             | Optional                    | Optional              |                        |                                                                            |               |                             |                       |                                      |
-| Phase-Encoding Direction | `dir-<label>`       |                                                                                                |                      | Optional                    |                       | Optional               |                                                                            | Required      |                             |                       |                                      |
-| Run                      | `run-<index>`       |                                                                                                |                      | Optional                    | Optional              | Optional               | Optional                                                                   | Optional      |                             | Optional              | Optional                             |
-| Corresponding modality   | `mod-<label>`       |                                                                                                | Optional             |                             |                       |                        |                                                                            |               |                             |                       |                                      |
-| Echo                     | `echo-<index>`      |                                                                                                |                      | Optional                    |                       |                        |                                                                            |               |                             |                       |                                      |
-| Recording                | `recording-<label>` |                                                                                                |                      |                             | Optional              |                        |                                                                            |               |                             |                       |                                      |
-| Processed (on device)    | `proc-<label>`      |                                                                                                |                      |                             | Optional              |                        |                                                                            |               |                             | Optional              | Optional                             |
+| Subject                  | `sub-<label>`       | REQUIRED                                                                                       | REQUIRED             | REQUIRED                    | REQUIRED              | REQUIRED               | REQUIRED                                                                   | REQUIRED      | REQUIRED                    | REQUIRED              | REQUIRED                             |
+| Session                  | `ses-<label>`       | OPTIONAL                                                                                       | OPTIONAL             | OPTIONAL                    | OPTIONAL              | OPTIONAL               | OPTIONAL                                                                   | OPTIONAL      | OPTIONAL                    | OPTIONAL              | OPTIONAL                             |
+| Task                     | `task-<label>`      |                                                                                                |                      | REQUIRED                    | REQUIRED              |                        |                                                                            |               | REQUIRED                    | REQUIRED              | REQUIRED                             |
+| Acquisition              | `acq-<label>`       | OPTIONAL                                                                                       | OPTIONAL             | OPTIONAL                    | OPTIONAL              | OPTIONAL               | OPTIONAL                                                                   | OPTIONAL      |                             | OPTIONAL              | OPTIONAL                             |
+| Contrast Enhancing Agent | `ce-<label>`        | OPTIONAL                                                                                       | OPTIONAL             | OPTIONAL                    |                       |                        |                                                                            | OPTIONAL      |                             |                       |                                      |
+| Reconstruction           | `rec-<label>`       | OPTIONAL                                                                                       | OPTIONAL             | OPTIONAL                    | OPTIONAL              |                        |                                                                            |               |                             |                       |                                      |
+| Phase-Encoding Direction | `dir-<label>`       |                                                                                                |                      | OPTIONAL                    |                       | OPTIONAL               |                                                                            | REQUIRED      |                             |                       |                                      |
+| Run                      | `run-<index>`       |                                                                                                |                      | OPTIONAL                    | OPTIONAL              | OPTIONAL               | OPTIONAL                                                                   | OPTIONAL      |                             | OPTIONAL              | OPTIONAL                             |
+| Corresponding modality   | `mod-<label>`       |                                                                                                | OPTIONAL             |                             |                       |                        |                                                                            |               |                             |                       |                                      |
+| Echo                     | `echo-<index>`      |                                                                                                |                      | OPTIONAL                    |                       |                        |                                                                            |               |                             |                       |                                      |
+| Recording                | `recording-<label>` |                                                                                                |                      |                             | OPTIONAL              |                        |                                                                            |               |                             |                       |                                      |
+| Processed (on device)    | `proc-<label>`      |                                                                                                |                      |                             | OPTIONAL              |                        |                                                                            |               |                             | OPTIONAL              | OPTIONAL                             |

From d5c628d696b269aba04d7edf2d5c29b075d2a759 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 27 Nov 2018 11:56:14 -0500
Subject: [PATCH 11/12] One more OPTIONAL instead of (optional)

---
 src/99-appendices/06-meg-file-formats.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index ccb93ebebe..7c475c47a7 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -17,7 +17,7 @@ Below are specifications for each system brand.
 ## CTF
 
 Each experimental run with a CTF system yields a folder with a `.ds` extension,
-containing several files. The (optional) digitized positions of the head points
+containing several files. The OPTIONAL digitized positions of the head points
 are usually stored in a separate `.pos` file, not necessarily within the `.ds`
 folder.
 

From 92211499e64728f2412ec13015722f8a2baa89c2 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Tue, 27 Nov 2018 12:03:38 -0500
Subject: [PATCH 12/12] BF: fixed table formatting

---
 .../01-magnetic-resonance-imaging-data.md                   | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

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 fa6d75290c..01768d3fcc 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
@@ -68,9 +68,9 @@ first "effective" echo and the center of the last "effective" echo.
 | :--------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | EchoTime               | RECOMMENDED. The echo time (TE) for the acquisition, specified in seconds. This parameter is REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence. Corresponds to DICOM Tag 0018, 0081 `Echo Time` (please note that the DICOM term is in milliseconds not seconds).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | InversionTime          | RECOMMENDED. The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 `Inversion Time` (please note that the DICOM term is in milliseconds not seconds).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
-| SliceTiming            | RECOMMENDED. The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times (in JSON format) containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis (i.e., the final entry in the `SliceTiming` list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the `DelayTime` field set. In addition without this parameter slice time correction will not be possible. |
+| SliceTiming            | RECOMMENDED. The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times (in JSON format) containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis (i.e., the final entry in the `SliceTiming` list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the `DelayTime` field set. In addition without this parameter slice time correction will not be possible.   |
 | SliceEncodingDirection | RECOMMENDED. Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which SliceTiming is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of SliceTiming are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present ,the axis defined by SliceEncodingDirection needs to be consistent with the ‘slice_dim’ field in the NIfTI header. When absent, the entries in SliceTiming must be in the order of increasing slice index as defined by the NIfTI header.                                                                                                                                                                                                   |
-| DwellTime              | RECOMMENDED. Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the OPTIONAL readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn’t captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction).                                                                                                                                                                                                                                                                                                                                               |
+| DwellTime              | RECOMMENDED. Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the OPTIONAL readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn’t captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction).                                                                                                                                                                                                                                                                                                                                                 |
 
 #### RF & Contrast
 
@@ -265,7 +265,7 @@ JSON file.
 | :------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. |
 | VolumeTiming   | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with RepetitionTime and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either SliceTiming or AcquisitionDuration be defined.                                              |
-| TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                          |
+| TaskName       | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                        |
 
 For the fields described above and in the following section, the term "Volume"
 refers to a reconstruction of the object being imaged (e.g., brain or part of a