From 0f383a23de88d88e59a2a722994ad0ef6bfcb851 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 17 Oct 2022 16:29:03 +0200
Subject: [PATCH 1/7] add consistency definition

---
 src/schema/objects/common_principles.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index a418b74004..970663c844 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -93,6 +93,9 @@ label:
     for example, it is `rest` in `task-rest` following `task-<label>` specification.
     Note that labels MUST not collide when casing is ignored
     (see [Case collision intolerance](SPEC_ROOT/02-common-principles.md#case-collision-intolerance)).
+    For a given data type, labels MUST be consistent across subjects and sessions.
+    For example label `acq-hires` for the `anat` data of a given subject
+    must mean the same thing as the label `acq-hires` used for the `anat` of any other subject.
 modality:
   name: Modality
   display_name: Modality

From f500e59a3765f6863e207fc3359deeb55da648c0 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 17 Oct 2022 16:33:56 +0200
Subject: [PATCH 2/7] rm mention of consistency for other labels

---
 .../01-magnetic-resonance-imaging-data.md                      | 2 +-
 src/04-modality-specific-files/07-behavioral-experiments.md    | 1 -
 .../09-positron-emission-tomography.md                         | 3 ---
 src/04-modality-specific-files/10-microscopy.md                | 3 +--
 4 files changed, 2 insertions(+), 7 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 e09bb59eb6..fb3b2f51fa 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
@@ -590,7 +590,7 @@ MUST be used to distinguish both images.
 In such a case, two files could have the following names:
 `sub-01_acq-singleband_dwi.nii.gz` and `sub-01_acq-multiband_dwi.nii.gz`.
 The user is free to choose any other label than `singleband` and
-`multiband`, as long as they are consistent across subjects and sessions.
+`multiband`.
 
 ### REQUIRED gradient orientation information
 
diff --git a/src/04-modality-specific-files/07-behavioral-experiments.md b/src/04-modality-specific-files/07-behavioral-experiments.md
index 4c27add5a4..e4c05ad9e3 100644
--- a/src/04-modality-specific-files/07-behavioral-experiments.md
+++ b/src/04-modality-specific-files/07-behavioral-experiments.md
@@ -24,7 +24,6 @@ rather than `_events.tsv`.
 Each task has a unique label that MUST only consist of letters and/or numbers
 (other characters, including spaces and underscores, are not allowed) with the
 [`task-<label>`](../appendices/entities.md#task) entity.
-Those labels MUST be consistent across subjects and sessions.
 
 The OPTIONAL [`acq-<label>`](../appendices/entities.md#acq) entity corresponds to a custom label to
 distinguish different conditions present during multiple runs of the same task.
diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md
index 0c04f86612..60d7f47f6b 100644
--- a/src/04-modality-specific-files/09-positron-emission-tomography.md
+++ b/src/04-modality-specific-files/09-positron-emission-tomography.md
@@ -80,7 +80,6 @@ Volumes MUST be stored in chronological order (the order they were acquired in).
 
 The OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used to
 indicate a task subjects were asked to perform in the scanner.
-Those labels MUST be consistent across subjects and sessions.
 For task based PET, a corresponding [`task events`](./05-task-events.md) file MUST be provided
 (please note that this file is not necessary for resting scans).
 
@@ -91,8 +90,6 @@ but REQUIRED to distinguish between tracers if multiple are used.
 The label used is arbitrary and each file requires a separate JSON sidecar
 with details of the tracer used (see below).
 Examples are `trc-18FFDG` for fludeoxyglucose or `trc-11CPIB` for Pittsburgh compound B.
-Other labels are permitted, as long as they are consistent across subjects and sessions
-and consist only of the legal label characters.
 
 If more than one run of the same task and acquisition (tracer) are acquired during
 the same session, the [`run-<index>`](../appendices/entities.md#run) entity MUST be used:
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index f8e1ec771f..12feb257f0 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -133,8 +133,7 @@ MAY be used to distinguish a different set of parameters used for acquiring the
 For example, two images of the same sample acquired by bright-field microscopy (BF) in PNG format at
 different magnification of 40x and 60x.
 In such case two files could have the following names: `sub-01_sample-01_acq-40x_BF.png` and
-`sub-01_sample-01_acq-60x_BF.png`, however the user is free to choose any other label as long as
-they are consistent across subjects and sessions.
+`sub-01_sample-01_acq-60x_BF.png`.
 
 The [`stain-<label>`](../appendices/entities.md#stain) entity MAY be used to distinguish
 image files from the same sample using different stains or antibodies for contrast enhancement.

From 0b26a61afcfefed53363fb73754ab7687dba6aa7 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 17 Oct 2022 16:37:15 +0200
Subject: [PATCH 3/7] rm consistent from schema

---
 src/schema/objects/entities.yaml | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 2f97f01c8b..90577152c1 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -13,9 +13,7 @@ acquisition:
     For example, this should be used when a study includes two T1w images -
     one full brain low resolution and one restricted field of view but high resolution.
     In such case two files could have the following names:
-    `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`;
-    however, the user is free to choose any other label than `highres` and `lowres` as long
-    as they are consistent across subjects and sessions.
+    `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`.
 
     In case different sequences are used to record the same modality
     (for example, `RARE` and `FLASH` for T1w)
@@ -381,8 +379,6 @@ task:
     a given task may have different sets of stimuli (for example, randomized order) and participant responses
     across subjects, sessions, and runs.
 
-    The `task-<label>` MUST be consistent across subjects and sessions.
-
     Files with the `task-<label>` entity SHOULD have an associated
     [events file](SPEC_ROOT/04-modality-specific-files/05-task-events.md#task-events),
     as well as certain metadata fields in the associated JSON file.

From 8bea7df1c7bec1ee287ecc3c09419b3af3ebd4ab Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 17 Oct 2022 16:41:54 +0200
Subject: [PATCH 4/7] update microscopy sample label paragraph

---
 src/04-modality-specific-files/10-microscopy.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
index 12feb257f0..19d111476d 100644
--- a/src/04-modality-specific-files/10-microscopy.md
+++ b/src/04-modality-specific-files/10-microscopy.md
@@ -102,7 +102,8 @@ Consistent with other data types in BIDS, the session entity is optional.
 
 The [`sample-<label>`](../appendices/entities.md#sample) entity is REQUIRED for
 Microscopy data and is used to distinguish between different samples from the same subject.
-The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
+Contrary to other labels, the `sample-<label>` MUST be unique per subject
+and is RECOMMENDED to be unique throughout the dataset.
 
 For example: Three brain slices (`sample-01` to `sample-03`) extracted from subject `sub-01`,
 imaged by scanning electron microscopy (SEM) in PNG format

From 9d30948497f2ede3e40a0347f16f58fb112aded6 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 18 Oct 2022 20:24:45 +0200
Subject: [PATCH 5/7] Update src/schema/objects/common_principles.yaml

Co-authored-by: Taylor Salo <tsalo90@gmail.com>
---
 src/schema/objects/common_principles.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index 970663c844..e7ec44c375 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -95,7 +95,7 @@ label:
     (see [Case collision intolerance](SPEC_ROOT/02-common-principles.md#case-collision-intolerance)).
     For a given data type, labels MUST be consistent across subjects and sessions.
     For example label `acq-hires` for the `anat` data of a given subject
-    must mean the same thing as the label `acq-hires` used for the `anat` of any other subject.
+    MUST mean the same thing as `acq-hires` in `anat` files of any other subject.
 modality:
   name: Modality
   display_name: Modality

From e4b43651877d337bd1f4368a716b69f9d79735ca Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 18 Oct 2022 20:24:52 +0200
Subject: [PATCH 6/7] Update src/schema/objects/common_principles.yaml

Co-authored-by: Taylor Salo <tsalo90@gmail.com>
---
 src/schema/objects/common_principles.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index e7ec44c375..55516e31d6 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -94,7 +94,7 @@ label:
     Note that labels MUST not collide when casing is ignored
     (see [Case collision intolerance](SPEC_ROOT/02-common-principles.md#case-collision-intolerance)).
     For a given data type, labels MUST be consistent across subjects and sessions.
-    For example label `acq-hires` for the `anat` data of a given subject
+    For example, an `acq` entity label `hires` used on the `anat` data of a given subject
     MUST mean the same thing as `acq-hires` in `anat` files of any other subject.
 modality:
   name: Modality

From c8a4844a2c3263a8b2f5e4625c59d2646a90e301 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 19 Apr 2024 09:09:37 +0200
Subject: [PATCH 7/7] Update src/schema/objects/common_principles.yaml

---
 src/schema/objects/common_principles.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index 99b1fc819b..349b0df59b 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -87,9 +87,9 @@ label:
     for example, it is `rest` in `task-rest` following `task-<label>` specification.
     Note that labels MUST not collide when casing is ignored
     (see [Case collision intolerance](SPEC_ROOT/common-principles.md#case-collision-intolerance)).
-    For a given data type, labels MUST be consistent across subjects and sessions.
+    Labels MUST be consistent across subjects and sessions and data types.
     For example, an `acq` entity label `hires` used on the `anat` data of a given subject
-    MUST mean the same thing as `acq-hires` in `anat` files of any other subject.
+    MUST mean the same thing as `acq-hires` in `func` files of any other subject.
 modality:
   display_name: Modality
   description: |