From c66376db82d21ac27259a6463111b4e6a93553cd Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sun, 6 Sep 2020 14:51:10 +0200
Subject: [PATCH 1/4] [FIX] tighter rules for sharing cross-talk and
 fine-calibration .fif files

Based on discussion in https://github.com/bids-standard/bids-validator/pull/1053

Specifically see https://github.com/bids-standard/bids-validator/pull/1053#issuecomment-687735083
---
 src/99-appendices/06-meg-file-formats.md | 57 ++++++++++++++++++------
 1 file changed, 43 insertions(+), 14 deletions(-)

diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 1a48b25fbe..785cf6ba76 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -76,29 +76,58 @@ process of regular system maintenance.
 In BIDS, the cross-talk and fine-calibration files are shared unmodified,
 but with BIDS file naming convention and by using the `acq` entity.
 
--   cross-talk file template: `[sub-<label>][_ses-<label>][_]acq-crosstalk_meg.dat`
--   fine-calibration file template: `[sub-<label>][_ses-<label>][_]acq-calibration_meg.fif`
+-   cross-talk file template: `sub-<label>[_ses-<label>]_acq-crosstalk_meg.dat`
+-   fine-calibration file template: `sub-<label>[_ses-<label>]_acq-calibration_meg.fif`
 
 Note that cross-talk files MUST be denoted using `acq-crosstalk` and
 fine-calibration files MUST be denoted using `acq-calibration`.
 
-By making use of the [Inheritance Principle](../02-common-principles.md#the-inheritance-principle),
-the cross-talk and fine-calibration data can be stored at any level of nesting within the BIDS dataset.
-For example for each session, or only once for a whole dataset.
+The cross-talk and fine-calibration data MUST be stored in the subject level `meg` folder,
+optionally nested in a subject specific `ses-<label>` folder, as shown in the following examples.
 
-Example FIFF dataset with cross-talk and fine-calibration files stored once at the dataset root:
+#### Example 1:
 
 ```Text
-acq-crosstalk_meg.dat
-acq-calibration_meg.fif
 sub-control01/
-    ses-001/
-        sub-control01_ses-001_scans.tsv
+    ses-01/
+        sub-control01_ses-01_scans.tsv
         meg/
-            sub-control01_ses-001_coordsystem.json
-            sub-control01_ses-001_task-rest_run-01_meg.fif
-            sub-control01_ses-001_task-rest_run-01_meg.json
-            sub-control01_ses-001_task-rest_run-01_channels.tsv
+            sub-control01_ses-01_coordsystem.json
+            sub-control01_ses-01_task-rest_run-01_meg.fif
+            sub-control01_ses-01_task-rest_run-01_meg.json
+            sub-control01_ses-01_task-rest_run-01_channels.tsv
+            sub-control01_ses-01_acq-crosstalk_meg.dat
+            sub-control01_ses-01_acq-calibration_meg.fif
+    ses-02/
+        sub-control01_ses-02_scans.tsv
+        meg/
+            sub-control01_ses-02_coordsystem.json
+            sub-control01_ses-02_task-rest_run-01_meg.fif
+            sub-control01_ses-02_task-rest_run-01_meg.json
+            sub-control01_ses-02_task-rest_run-01_channels.tsv
+            sub-control01_ses-02_acq-crosstalk_meg.dat
+            sub-control01_ses-02_acq-calibration_meg.fif
+```
+
+#### Example 2:
+
+```Text
+sub-01/
+    meg/
+        sub-01_coordsystem.json
+        sub-01_task-rest_meg.fif
+        sub-01_task-rest_meg.json
+        sub-01_task-rest_channels.tsv
+        sub-01_acq-crosstalk_meg.dat
+        sub-01_acq-calibration_meg.fif
+sub-02/
+    meg/
+        sub-02_coordsystem.json
+        sub-02_task-rest_meg.fif
+        sub-02_task-rest_meg.json
+        sub-02_task-rest_channels.tsv
+        sub-02_acq-crosstalk_meg.dat
+        sub-02_acq-calibration_meg.fif
 ```
 
 ### Sharing FIFF data after signal-space separation (SSS)

From 37d16b878ff98e62f66e2f3369afaaae54c81bb5 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sun, 6 Sep 2020 14:58:11 +0200
Subject: [PATCH 2/4] remove trailing punctuation from headings

---
 src/99-appendices/06-meg-file-formats.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 785cf6ba76..0d7225c948 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -85,7 +85,7 @@ fine-calibration files MUST be denoted using `acq-calibration`.
 The cross-talk and fine-calibration data MUST be stored in the subject level `meg` folder,
 optionally nested in a subject specific `ses-<label>` folder, as shown in the following examples.
 
-#### Example 1:
+#### Example 1
 
 ```Text
 sub-control01/
@@ -109,7 +109,7 @@ sub-control01/
             sub-control01_ses-02_acq-calibration_meg.fif
 ```
 
-#### Example 2:
+#### Example 2
 
 ```Text
 sub-01/

From c840c4821407f661fdd14a95db45d5bdf9a6bf9a Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sun, 6 Sep 2020 20:41:55 +0200
Subject: [PATCH 3/4] fix wording, go from easy to hard in examples
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
---
 src/99-appendices/06-meg-file-formats.md | 54 ++++++++++++------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/src/99-appendices/06-meg-file-formats.md b/src/99-appendices/06-meg-file-formats.md
index 0d7225c948..d4b036377c 100644
--- a/src/99-appendices/06-meg-file-formats.md
+++ b/src/99-appendices/06-meg-file-formats.md
@@ -82,34 +82,10 @@ but with BIDS file naming convention and by using the `acq` entity.
 Note that cross-talk files MUST be denoted using `acq-crosstalk` and
 fine-calibration files MUST be denoted using `acq-calibration`.
 
-The cross-talk and fine-calibration data MUST be stored in the subject level `meg` folder,
-optionally nested in a subject specific `ses-<label>` folder, as shown in the following examples.
+The cross-talk and fine-calibration data MUST be stored in the subject-level `meg` folder,
+which may be nested inside a `ses-<label>` folder, as shown in the following examples.
 
-#### Example 1
-
-```Text
-sub-control01/
-    ses-01/
-        sub-control01_ses-01_scans.tsv
-        meg/
-            sub-control01_ses-01_coordsystem.json
-            sub-control01_ses-01_task-rest_run-01_meg.fif
-            sub-control01_ses-01_task-rest_run-01_meg.json
-            sub-control01_ses-01_task-rest_run-01_channels.tsv
-            sub-control01_ses-01_acq-crosstalk_meg.dat
-            sub-control01_ses-01_acq-calibration_meg.fif
-    ses-02/
-        sub-control01_ses-02_scans.tsv
-        meg/
-            sub-control01_ses-02_coordsystem.json
-            sub-control01_ses-02_task-rest_run-01_meg.fif
-            sub-control01_ses-02_task-rest_run-01_meg.json
-            sub-control01_ses-02_task-rest_run-01_channels.tsv
-            sub-control01_ses-02_acq-crosstalk_meg.dat
-            sub-control01_ses-02_acq-calibration_meg.fif
-```
-
-#### Example 2
+#### Example with single session (omitted session folder)
 
 ```Text
 sub-01/
@@ -130,6 +106,30 @@ sub-02/
         sub-02_acq-calibration_meg.fif
 ```
 
+#### Example with multiple sessions
+
+```Text
+sub-01/
+    ses-01/
+        sub-01_ses-01_scans.tsv
+        meg/
+            sub-01_ses-01_coordsystem.json
+            sub-01_ses-01_task-rest_run-01_meg.fif
+            sub-01_ses-01_task-rest_run-01_meg.json
+            sub-01_ses-01_task-rest_run-01_channels.tsv
+            sub-01_ses-01_acq-crosstalk_meg.dat
+            sub-01_ses-01_acq-calibration_meg.fif
+    ses-02/
+        sub-01_ses-02_scans.tsv
+        meg/
+            sub-01_ses-02_coordsystem.json
+            sub-01_ses-02_task-rest_run-01_meg.fif
+            sub-01_ses-02_task-rest_run-01_meg.json
+            sub-01_ses-02_task-rest_run-01_channels.tsv
+            sub-01_ses-02_acq-crosstalk_meg.dat
+            sub-01_ses-02_acq-calibration_meg.fif
+```
+
 ### Sharing FIFF data after signal-space separation (SSS)
 
 After applying SSS (e.g., by using the MaxFilter software),

From b01be710024b6c4aa2a9064938be0c9930c31655 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Mon, 7 Sep 2020 09:31:14 +0200
Subject: [PATCH 4/4] fix BIDS 2.0 link from deprecated google doc to GH

---
 src/06-longitudinal-and-multi-site-studies.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/06-longitudinal-and-multi-site-studies.md b/src/06-longitudinal-and-multi-site-studies.md
index 063e3083e7..40d4ef4d37 100644
--- a/src/06-longitudinal-and-multi-site-studies.md
+++ b/src/06-longitudinal-and-multi-site-studies.md
@@ -90,7 +90,7 @@ ses-followup  2009-06-17T13:45:30 110
 
 This version of the BIDS specification does not explicitly cover studies with
 data coming from multiple sites or multiple centers (such extension is planned
-in [BIDS `2.0`](https://docs.google.com/document/d/1LEgsMiisGDe1Gv-hBp1EcLmoz7AlKj6VYULUgDD3Zdw/)).
+in [BIDS `2.0`](https://github.com/bids-standard/bids-2-devel).
 There are however ways to model your data without any loss in terms of metadata.
 
 ### Treat each site/center as a separate dataset