From e5d9e04cf5afba8d4f128b165e3ee4e199e9d2d7 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Thu, 23 May 2024 10:19:32 +0200
Subject: [PATCH 01/17] add FA

---
 .../magnetic-resonance-imaging-data.md                        | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 6396aa0e8c..cb0fce15b8 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -696,8 +696,8 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
-Scanner-generated TRACE and ADC volumes MAY be included using the
-`TRACE` and `ADC` suffixes.
+Scanner-generated TRACE, ADC and FA volumes MAY be included using the
+`TRACE`, `FA` and `ADC` suffixes.
 If TRACE or ADC volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD be computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),

From 691e73d3c12f974e3e1ba147acc4e2b96740cffc Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Thu, 23 May 2024 10:24:23 +0200
Subject: [PATCH 02/17] FA suffix

---
 src/schema/objects/suffixes.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 5f57b28ba8..970c22e306 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -47,6 +47,11 @@ DF:
   display_name: Dark-field microscopy
   description: |
     Dark-field microscopy imaging data
+FA:
+  value: FA
+  display_name: Fractional Anisotropy image
+  description: |
+    Diffusion images reflecting the directionality of the diffusion tensor
 FLAIR:
   value: FLAIR
   display_name: Fluid attenuated inversion recovery image

From 45c14fddb947c677637479f2e0f603f89e4e47b3 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Thu, 23 May 2024 10:27:22 +0200
Subject: [PATCH 03/17] add FA

---
 src/schema/rules/files/raw/dwi.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index ff18501af9..ad7644bb60 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -43,6 +43,7 @@ sbref:
 isotropic:
   suffixes:
     - ADC
+    - FA
     - TRACE
   extensions:
     - .nii.gz

From 2e4627ee73b7d10ddc0f80ba5201a5f794b82b9f Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Mon, 27 May 2024 13:21:15 +0200
Subject: [PATCH 04/17] Update src/schema/rules/files/raw/dwi.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/files/raw/dwi.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index ad7644bb60..3e7bc37005 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -40,7 +40,7 @@ sbref:
     chunk: optional
 
 # Common scanner-generated derivatives need raw names
-isotropic:
+ScannerDerivatives:
   suffixes:
     - ADC
     - FA

From 4040942d0edcdef8920de2775be29ce154283537 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Mon, 27 May 2024 13:22:05 +0200
Subject: [PATCH 05/17] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../magnetic-resonance-imaging-data.md                      | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index cb0fce15b8..604e15062f 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -696,9 +696,9 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
-Scanner-generated TRACE, ADC and FA volumes MAY be included using the
-`TRACE`, `FA` and `ADC` suffixes.
-If TRACE or ADC volume filenames match a diffusion series with all applicable entities,
+Scanner-generated TRACE, ADC and fractional anisotropy (FA) volumes MAY be included
+using the `TRACE`, `ADC`, and `FA` suffixes, respectively
+If TRACE, ADC or FA volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD be computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.

From 0b3a49838416b671aee296784ec7ac7a198ea911 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Mon, 27 May 2024 13:29:12 +0200
Subject: [PATCH 06/17] add colFA

---
 .../magnetic-resonance-imaging-data.md                    | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 604e15062f..04d12380b8 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -667,7 +667,7 @@ The definitions of these fields can be found in
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_suffix_table(["ADC", "TRACE"]) }}
+{{ MACROS___make_suffix_table(["ADC", "TRACE", "FA", "colFA"]) }}
 
 <!--
 This block generates a filename templates.
@@ -696,9 +696,9 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
-Scanner-generated TRACE, ADC and fractional anisotropy (FA) volumes MAY be included
-using the `TRACE`, `ADC`, and `FA` suffixes, respectively
-If TRACE, ADC or FA volume filenames match a diffusion series with all applicable entities,
+Scanner-generated TRACE, ADC and fractional anisotropy (FA and colFA) volumes MAY be included
+using the `TRACE`, `ADC`, `FA` and `colFA` suffixes, respectively
+If TRACE, ADC, FA, colFA volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD be computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.

From f28e5392db15519d9f68ae0f89054ac9efe7c179 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Mon, 27 May 2024 13:32:24 +0200
Subject: [PATCH 07/17] add colFA

---
 src/schema/rules/files/raw/dwi.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 3e7bc37005..987206718b 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -43,6 +43,7 @@ sbref:
 ScannerDerivatives:
   suffixes:
     - ADC
+    - colFA
     - FA
     - TRACE
   extensions:

From 74220cf82504c1df97226c4dabf3abb686c9312f Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Mon, 27 May 2024 13:38:35 +0200
Subject: [PATCH 08/17] colFA description

---
 src/schema/objects/suffixes.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 970c22e306..8d28426f71 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -42,6 +42,13 @@ DIC:
   display_name: Differential interference contrast microscopy
   description: |
     Differential interference contrast microscopy imaging data
+colFA:
+  value: colFA
+  display_name: coloured Fractional Anisotropy image
+  description: |
+    Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for 
+    left-right oriented fibers, in blue for superior-inferior oriented fibers and green for 
+    anterior-posterior oriented fibers.
 DF:
   value: DF
   display_name: Dark-field microscopy

From 12b780e15ef5c0d2f93ee919c06ffaa20c45dd0f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 May 2024 11:39:22 +0000
Subject: [PATCH 09/17] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/schema/objects/suffixes.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 8d28426f71..efa5dddada 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -46,8 +46,8 @@ colFA:
   value: colFA
   display_name: coloured Fractional Anisotropy image
   description: |
-    Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for 
-    left-right oriented fibers, in blue for superior-inferior oriented fibers and green for 
+    Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for
+    left-right oriented fibers, in blue for superior-inferior oriented fibers and green for
     anterior-posterior oriented fibers.
 DF:
   value: DF

From 081a59fa3e4521a67b2e395411147d1f930e1a4f Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 29 May 2024 10:23:18 -0400
Subject: [PATCH 10/17] fix(schema): Rename raw reference in derivative rules

---
 src/schema/rules/files/deriv/imaging.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/schema/rules/files/deriv/imaging.yaml b/src/schema/rules/files/deriv/imaging.yaml
index c9a0e12877..07f7678115 100644
--- a/src/schema/rules/files/deriv/imaging.yaml
+++ b/src/schema/rules/files/deriv/imaging.yaml
@@ -26,10 +26,10 @@ dwi_volumetric:
     density: optional
     description: optional
 
-dwi_isotropic:
-  $ref: rules.files.raw.dwi.isotropic
+dwi_scannerderivatives:
+  $ref: rules.files.raw.dwi.ScannerDerivatives
   entities:
-    $ref: rules.files.raw.dwi.isotropic.entities
+    $ref: rules.files.raw.dwi.ScannerDerivatives.entities
     space: optional
     resolution: optional
     density: optional

From b78b033a367425097b5f46d1ebe8c30bc9c88a56 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 21 Jun 2024 05:12:10 +0200
Subject: [PATCH 11/17] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/modality-specific-files/magnetic-resonance-imaging-data.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 04d12380b8..19b46157ef 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -697,7 +697,7 @@ The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
 Scanner-generated TRACE, ADC and fractional anisotropy (FA and colFA) volumes MAY be included
-using the `TRACE`, `ADC`, `FA` and `colFA` suffixes, respectively
+using the `TRACE`, `ADC`, `FA` and `colFA` suffixes, respectively.
 If TRACE, ADC, FA, colFA volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD be computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),

From 583acd17e1f03dbe8adabfdc2170e41a27c6d1e5 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 21 Jun 2024 05:12:48 +0200
Subject: [PATCH 12/17] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/modality-specific-files/magnetic-resonance-imaging-data.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 19b46157ef..a173acbfdc 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -698,7 +698,7 @@ The user is free to choose any other label than `singleband` and
 
 Scanner-generated TRACE, ADC and fractional anisotropy (FA and colFA) volumes MAY be included
 using the `TRACE`, `ADC`, `FA` and `colFA` suffixes, respectively.
-If TRACE, ADC, FA, colFA volume filenames match a diffusion series with all applicable entities,
+If TRACE, ADC, FA, or colFA volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD be computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.

From 5cabca0592e65adf2ab115b623e89ef8b255d361 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 21 Jun 2024 05:13:02 +0200
Subject: [PATCH 13/17] Update src/schema/objects/suffixes.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/objects/suffixes.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index efa5dddada..5bc30ce9bb 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -44,7 +44,7 @@ DIC:
     Differential interference contrast microscopy imaging data
 colFA:
   value: colFA
-  display_name: coloured Fractional Anisotropy image
+  display_name: Colored Fractional Anisotropy image
   description: |
     Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for
     left-right oriented fibers, in blue for superior-inferior oriented fibers and green for

From 04a96f5412f61fb1f90b4dfea23cb033242bcf0f Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Thu, 27 Jun 2024 13:13:11 +1000
Subject: [PATCH 14/17] Changes to scanner-generated DWI derivatives

- Rename "TRACE" suffix to "trace".
- Add "exponentiated ADC" measure.
- Fix description of trace-weighted image, resolving #1862.
- Modify descriptions of FA and colFA.
- Fix alphabetic sorting of suffices.
---
 .../magnetic-resonance-imaging-data.md        | 10 +++---
 src/schema/objects/suffixes.yaml              | 35 ++++++++++++-------
 src/schema/rules/files/raw/dwi.yaml           |  5 +--
 3 files changed, 30 insertions(+), 20 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index a173acbfdc..1961785f6c 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -667,7 +667,7 @@ The definitions of these fields can be found in
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_suffix_table(["ADC", "TRACE", "FA", "colFA"]) }}
+{{ MACROS___make_suffix_table(["ADC", "expADC", "trace", "FA", "colFA"]) }}
 
 <!--
 This block generates a filename templates.
@@ -696,10 +696,10 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
-Scanner-generated TRACE, ADC and fractional anisotropy (FA and colFA) volumes MAY be included
-using the `TRACE`, `ADC`, `FA` and `colFA` suffixes, respectively.
-If TRACE, ADC, FA, or colFA volume filenames match a diffusion series with all applicable entities,
-such volumes SHOULD be computed from that series.
+Scanner-generated trace-weighted, ADC, exponentiated ADC, and fractional anisotropy (FA and colFA) volumes
+MAY be included using the `trace`, `ADC`, `expADC`, `FA` and `colFA` suffixes, respectively.
+If trace, ADC, expADC, FA, or colFA volume filenames match a diffusion series with all applicable entities,
+such volumes SHOULD have been computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.
 
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 5bc30ce9bb..afef8b593b 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -42,13 +42,6 @@ DIC:
   display_name: Differential interference contrast microscopy
   description: |
     Differential interference contrast microscopy imaging data
-colFA:
-  value: colFA
-  display_name: Colored Fractional Anisotropy image
-  description: |
-    Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for
-    left-right oriented fibers, in blue for superior-inferior oriented fibers and green for
-    anterior-posterior oriented fibers.
 DF:
   value: DF
   display_name: Dark-field microscopy
@@ -58,7 +51,8 @@ FA:
   value: FA
   display_name: Fractional Anisotropy image
   description: |
-    Diffusion images reflecting the directionality of the diffusion tensor
+    Scanner-generated derivative parametric map
+    reflecting the anisotropy of the diffusion tensor
 FLAIR:
   value: FLAIR
   display_name: Fluid attenuated inversion recovery image
@@ -477,11 +471,6 @@ TEM:
   display_name: Transmission electron microscopy
   description: |
     Transmission electron microscopy imaging data
-TRACE:
-  value: TRACE
-  display_name: Trace diffusion weighted image
-  description: |
-    Diffusion images proportional to the trace of the diffusion tensor
 UNIT1:
   value: UNIT1
   display_name: Homogeneous (flat) T1-weighted MP2RAGE image
@@ -559,6 +548,15 @@ channels:
   display_name: Channels File
   description: |
     Channel information.
+colFA:
+  value: colFA
+  display_name: Colored Fractional Anisotropy image
+  description: |
+    Scanner-derived parametric map encoding both the anisotropy and principal direction of the diffusion tensor.
+    Image intensity is proportional to the Fractional Anisotropy (FA) measure;
+    image colour is determined by the principal eigenvector of the diffusion tensor,
+    where red encodes the magnitude of the left-right component of that orientation,
+    with green and blue similarly encoding the anterior-posterior and inferior-superior components respectively.
 coordsystem:
   value: coordsystem
   display_name: Coordinate System File
@@ -617,6 +615,12 @@ events:
   display_name: Events
   description: |
     Event timing information from a behavioral task.
+expADC:
+  value: expADC
+  display_name: Exponental ADC
+  description: |
+    Exponental ADC / Attenuation Coefficient / Attenuation Factor map,
+    as the ratio of trace-weighted to non-diffusion-weighted image intensity
 fieldmap:
   value: fieldmap
   display_name: Fieldmap
@@ -831,6 +835,11 @@ stim:
   display_name: Continuous recording
   description: |
     Continuous measures, such as parameters of a film or audio stimulus.
+trace:
+  value: trace
+  display_name: Trace-weighted diffusion image
+  description: |
+    Trace-weighted image, as the mean intensity of diffusion-weighted images
 uCT:
   value: uCT
   display_name: Micro-CT
diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 987206718b..3afa08ce1e 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -43,9 +43,10 @@ sbref:
 ScannerDerivatives:
   suffixes:
     - ADC
-    - colFA
     - FA
-    - TRACE
+    - colFA
+    - expADC
+    - trace
   extensions:
     - .nii.gz
     - .nii

From 04377624469601a549cf564e6c9db8a0638e212c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 5 Aug 2024 15:31:48 -0400
Subject: [PATCH 15/17] Update src/schema/objects/suffixes.yaml

---
 src/schema/objects/suffixes.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index afef8b593b..eab03bce91 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -554,7 +554,7 @@ colFA:
   description: |
     Scanner-derived parametric map encoding both the anisotropy and principal direction of the diffusion tensor.
     Image intensity is proportional to the Fractional Anisotropy (FA) measure;
-    image colour is determined by the principal eigenvector of the diffusion tensor,
+    image color is determined by the principal eigenvector of the diffusion tensor,
     where red encodes the magnitude of the left-right component of that orientation,
     with green and blue similarly encoding the anterior-posterior and inferior-superior components respectively.
 coordsystem:

From a4d10f164d7fe7501137b1f073c45e27eeaa7be8 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Mon, 12 Aug 2024 16:27:04 +1000
Subject: [PATCH 16/17] MRI: DWI scanner derivatives: Adopt "S0map" suffix

---
 .../magnetic-resonance-imaging-data.md                 | 10 ++++++----
 src/schema/objects/suffixes.yaml                       |  9 ++++++++-
 src/schema/rules/files/raw/dwi.yaml                    |  1 +
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 8f2c44429b..113d77be73 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -671,7 +671,7 @@ The definitions of these fields can be found in
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_suffix_table(["ADC", "expADC", "trace", "FA", "colFA"]) }}
+{{ MACROS___make_suffix_table(["ADC", "expADC", "trace", "FA", "colFA", "S0map"]) }}
 
 <!--
 This block generates a filename templates.
@@ -700,9 +700,11 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
-Scanner-generated trace-weighted, ADC, exponentiated ADC, and fractional anisotropy (FA and colFA) volumes
-MAY be included using the `trace`, `ADC`, `expADC`, `FA` and `colFA` suffixes, respectively.
-If trace, ADC, expADC, FA, or colFA volume filenames match a diffusion series with all applicable entities,
+Scanner-generated derivative images,
+such as trace-weighted, ADC, exponentiated ADC,
+fractional anisotropy (FA and colFA), and estimated unweighted signal intensity,
+MAY be included using the `trace`, `ADC`, `expADC`, `FA`, `colFA` and `S0map` suffixes, respectively.
+If trace, ADC, expADC, FA, colFA, or S0 volume filenames match a diffusion series with all applicable entities,
 such volumes SHOULD have been computed from that series.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 68bd39baba..f11740b65b 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -292,9 +292,11 @@ RB1map:
   unit: arbitrary
 S0map:
   value: S0map
-  display_name: Observed signal amplitude (S0) image
+  display_name: Projected baseline signal amplitude (S0) image
   description: |
     In arbitrary units (arbitrary).
+    This represents a model-based estimate of signal intensity
+    in the absence of the contrast under investigation.
     For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal
     before exponential (T2-star) signal decay.
     In other words: the exponential of the intercept for a linear decay model
@@ -302,6 +304,11 @@ S0map:
     [the tedana documentation](https://tedana.readthedocs.io/en/latest/\
     approach.html#monoexponential-decay-model-fit).
     S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset.
+    For a diffusion-weighted sequence,
+    S0 maps represent the model-based estimate of the signal intensity
+    in the absence of any diffusion weighting;
+    in other words, the image intensity at *b*=0
+    as estimated by a diffusion model fit.
 SEM:
   value: SEM
   display_name: Scanning electron microscopy
diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 3afa08ce1e..91319046dc 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -44,6 +44,7 @@ ScannerDerivatives:
   suffixes:
     - ADC
     - FA
+    - S0map
     - colFA
     - expADC
     - trace

From 97d6a94656038a273c28200e83b088e118ad348d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 29 Aug 2024 14:35:46 -0400
Subject: [PATCH 17/17] Update src/schema/objects/suffixes.yaml

Co-authored-by: Robert Smith <robert.smith@florey.edu.au>
---
 src/schema/objects/suffixes.yaml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index d49789a7bc..1e2825ced2 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -297,8 +297,10 @@ S0map:
     In arbitrary units (arbitrary).
     This represents a model-based estimate of signal intensity
     in the absence of the contrast under investigation.
-    For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal
-    before exponential (T2-star) signal decay.
+    For a multi-echo sequence
+    (for example, multi-echo spin echo T2 relaxometry or multi-echo fMRI),
+    S0 maps index the baseline signal at a hypothetical echo time of zero
+    (that is, in the absence of any T2 or T2-star decay).
     In other words: the exponential of the intercept for a linear decay model
     across log-transformed echos. For more information, please see, for example,
     [the tedana documentation](https://tedana.readthedocs.io/en/latest/\