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 01/16] 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 02/16] 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 03/16] 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 04/16] 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 05/16] 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 06/16] 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 07/16] 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 08/16] 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 09/16] [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 10/16] 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 11/16] 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 12/16] 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 13/16] 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 ac7584e41f9e1aaa3f6d34a01c83d9880d5c5966 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 28 Jun 2024 16:34:05 +0900
Subject: [PATCH 14/16] all lower case

---
 .../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 4db527fa35..9722b7824b 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", "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 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,
+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.
 Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
 SHOULD be used to indicate that the files are unrelated.

From 3e991a55571f1b48938e44101fb33feb1af74742 Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 28 Jun 2024 16:37:05 +0900
Subject: [PATCH 15/16] all lower case

---
 src/schema/objects/suffixes.yaml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index ba4770b9b2..e642b8367e 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -6,8 +6,8 @@ TwoPE:
   display_name: 2-photon excitation microscopy
   description: |
     2-photon excitation microscopy imaging data
-ADC:
-  value: ADC
+adc:
+  value: adc
   display_name: Apparent diffusion coefficient (ADC)
   description:
     Apparent diffusion coefficient (ADC) map
@@ -42,8 +42,8 @@ DIC:
   display_name: Differential interference contrast microscopy
   description: |
     Differential interference contrast microscopy imaging data
-colFA:
-  value: colFA
+colfa:
+  value: colfa
   display_name: Colored Fractional Anisotropy image
   description: |
     Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for
@@ -54,8 +54,8 @@ DF:
   display_name: Dark-field microscopy
   description: |
     Dark-field microscopy imaging data
-FA:
-  value: FA
+fa:
+  value: fa
   display_name: Fractional Anisotropy image
   description: |
     Diffusion images reflecting the directionality of the diffusion tensor
@@ -477,8 +477,8 @@ TEM:
   display_name: Transmission electron microscopy
   description: |
     Transmission electron microscopy imaging data
-TRACE:
-  value: TRACE
+trace:
+  value: trace
   display_name: Trace diffusion weighted image
   description: |
     Diffusion images proportional to the trace of the diffusion tensor

From 7c492c28efbf8f8ba462ab631618212c2044188b Mon Sep 17 00:00:00 2001
From: Cyril Pernet <wamcyril@gmail.com>
Date: Fri, 28 Jun 2024 16:38:53 +0900
Subject: [PATCH 16/16] scanner deriv as lower case.yaml

---
 src/schema/rules/files/raw/dwi.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 987206718b..b006f7efb3 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -42,10 +42,10 @@ sbref:
 # Common scanner-generated derivatives need raw names
 ScannerDerivatives:
   suffixes:
-    - ADC
-    - colFA
-    - FA
-    - TRACE
+    - adc
+    - colfa
+    - fa
+    - trace
   extensions:
     - .nii.gz
     - .nii