From 02916cae0297512374b1ef1e4070ee57c189d42c Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 16 Nov 2020 10:24:54 -0500
Subject: [PATCH 01/10] [ENH] Improve TR definitions

- Include RepetitionTimePreparation
- Include RepetitionTimeExcitation
- Add explanation on the former RepetitionTime field.
---
 .../01-magnetic-resonance-imaging-data.md                     | 4 +++-
 1 file changed, 3 insertions(+), 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 f52e2b38ea..f328e23915 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
@@ -194,6 +194,8 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type** | **Description**                                                                                                                          |
 | ----------------------- | --------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]    | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
+| RepetitionTimeExcitation | OPTIONAL. The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the (task imaging data)[#task-including-resting-state-imaging-data] section.|
+| RepetitionTimePreparation | OPTIONAL. The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish
@@ -290,7 +292,7 @@ JSON file.
 
 | **Key name**   | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
 | -------------- | --------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| RepetitionTime | REQUIRED              | [number][]               | 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. |
+| RepetitionTime | REQUIRED              | [number][]               | The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST 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`. |
 | VolumeTiming   | REQUIRED              | [array][] of [numbers][] | The time at which each volume was acquired during the acquisition. It is described using a list of times 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              | [string][]               | Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                       |
 

From 3ed775543a6958f8bab40e16d37b8b9e5862f7a3 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Mon, 16 Nov 2020 10:50:01 -0500
Subject: [PATCH 02/10] Typo

---
 .../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 f328e23915..b305b05a35 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
@@ -194,7 +194,7 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type** | **Description**                                                                                                                          |
 | ----------------------- | --------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]    | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
-| RepetitionTimeExcitation | OPTIONAL. The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the (task imaging data)[#task-including-resting-state-imaging-data] section.|
+| RepetitionTimeExcitation | OPTIONAL. The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section.|
 | RepetitionTimePreparation | OPTIONAL. The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)

From f684efdcf316e27bfac0a5d5344bf2e011d765ca Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Mon, 16 Nov 2020 15:45:11 -0500
Subject: [PATCH 03/10] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../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 b305b05a35..679795f2e8 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
@@ -194,8 +194,8 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type** | **Description**                                                                                                                          |
 | ----------------------- | --------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]    | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
-| RepetitionTimeExcitation | OPTIONAL. The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section.|
-| RepetitionTimePreparation | OPTIONAL. The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. |
+| RepetitionTimeExcitation | OPTIONAL              | [number][]    | The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section.|
+| RepetitionTimePreparation | OPTIONAL              | [number][]    | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish

From 1b459a0a205506d1487c90d26526dc5eac7cabe8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Sat, 21 Nov 2020 20:23:37 -0500
Subject: [PATCH 04/10] ENH: Allow for variable RTE/P

---
 .../01-magnetic-resonance-imaging-data.md              | 10 +++++-----
 1 file changed, 5 insertions(+), 5 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 679795f2e8..1ebcfbd2a9 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
@@ -191,11 +191,11 @@ JSON file. See [Common metadata fields](#common-metadata-fields) for a
 list of terms and their definitions. There are also some OPTIONAL JSON
 fields specific to anatomical scans:
 
-| **Key name**            | **Requirement level** | **Data type** | **Description**                                                                                                                          |
-| ----------------------- | --------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------- |
-| ContrastBolusIngredient | OPTIONAL              | [string][]    | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
-| RepetitionTimeExcitation | OPTIONAL              | [number][]    | The time in seconds between successive excitation pulses that excite a spin system. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section.|
-| RepetitionTimePreparation | OPTIONAL              | [number][]    | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. |
+| **Key name**            | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
+| ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
+| RepetitionTimeExcitation | OPTIONAL             | [number][] or [array][] of [numbers][] | The time in seconds between successive excitation pulses that excite a spin system. A single value applies to all volumes, or an array provides a value for each volume. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. 4D files with variable `RepetitionTimeExcitation` should only be used in volume timing is critical for interpretation of the data, as in ASL. |
+| RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. A single value applies to all volumes, or an array provides a value for each volume. 4D files with variable `RepetitionTimePreparation` should only be used in volume timing is critical for interpretation of the data, as in ASL.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish

From 9bc528bf12f7a3ec0910da18f95c4f90eb1af6bc Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Sat, 21 Nov 2020 20:25:23 -0500
Subject: [PATCH 05/10] STY: Update table widths

---
 .../01-magnetic-resonance-imaging-data.md                 | 8 ++++----
 1 file changed, 4 insertions(+), 4 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 1ebcfbd2a9..aa3862d519 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
@@ -290,11 +290,11 @@ JSON file.
 
 ### Required fields
 
-| **Key name**   | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| -------------- | --------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Key name**   | **Requirement level** | **Data type**            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| -------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | RepetitionTime | REQUIRED              | [number][]               | The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST 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`. |
-| VolumeTiming   | REQUIRED              | [array][] of [numbers][] | The time at which each volume was acquired during the acquisition. It is described using a list of times 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              | [string][]               | Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`.                                                                                                                                                                       |
+| VolumeTiming   | REQUIRED              | [array][] of [numbers][] | The time at which each volume was acquired during the acquisition. It is described using a list of times 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              | [string][]               | Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond 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 (for example, brain or part of a

From 81ac117f6227e9b3119af6630c3712de81f1fe1b Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Tue, 24 Nov 2020 10:29:17 -0500
Subject: [PATCH 06/10] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

---
 .../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 aa3862d519..8faade7868 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
@@ -194,7 +194,7 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
 | ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-| RepetitionTimeExcitation | OPTIONAL             | [number][] or [array][] of [numbers][] | The time in seconds between successive excitation pulses that excite a spin system. A single value applies to all volumes, or an array provides a value for each volume. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. 4D files with variable `RepetitionTimeExcitation` should only be used in volume timing is critical for interpretation of the data, as in ASL. |
+| RepetitionTimeExcitation | OPTIONAL             | [number][] | The time elapses (in seconds) between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
 | RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. A single value applies to all volumes, or an array provides a value for each volume. 4D files with variable `RepetitionTimePreparation` should only be used in volume timing is critical for interpretation of the data, as in ASL.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)

From d314835b509426a16ab059db3062bf452abad2ee Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Tue, 24 Nov 2020 10:29:25 -0500
Subject: [PATCH 07/10] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

---
 .../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 8faade7868..f432d39bc8 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
@@ -195,7 +195,7 @@ fields specific to anatomical scans:
 | ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | RepetitionTimeExcitation | OPTIONAL             | [number][] | The time elapses (in seconds) between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
-| RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. A single value applies to all volumes, or an array provides a value for each volume. 4D files with variable `RepetitionTimePreparation` should only be used in volume timing is critical for interpretation of the data, as in ASL.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
+| RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish

From 1a9412c32bdb6aa14314b1e0df2cb63c70a81e59 Mon Sep 17 00:00:00 2001
From: Agah Karakuzu <agahkarakuzu@gmail.com>
Date: Tue, 24 Nov 2020 10:33:47 -0500
Subject: [PATCH 08/10] Change ref to DOI @Remi-Gau

---
 .../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 f432d39bc8..9d87032b5d 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
@@ -194,7 +194,7 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
 | ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-| RepetitionTimeExcitation | OPTIONAL             | [number][] | The time elapses (in seconds) between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://infoscience.epfl.ch/record/172927/files/mp2rage.pdf). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
+| RepetitionTimeExcitation | OPTIONAL             | [number][] | The time elapses (in seconds) between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
 | RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)

From 356966b1e12d50f629b8019daecce71d3a2544c0 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Tue, 1 Dec 2020 14:57:25 -0500
Subject: [PATCH 09/10] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../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 9d87032b5d..9a0a949e8d 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
@@ -194,7 +194,7 @@ fields specific to anatomical scans:
 | **Key name**            | **Requirement level** | **Data type**                          | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
 | ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
-| RepetitionTimeExcitation | OPTIONAL             | [number][] | The time elapses (in seconds) between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
+| RepetitionTimeExcitation | OPTIONAL             | [number][] | The interval, in seconds, between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
 | RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)

From 1bf9b2724cea11079da6587e086dd1f4c9711406 Mon Sep 17 00:00:00 2001
From: Agah <agahkarakuzu@gmail.com>
Date: Tue, 1 Dec 2020 14:57:38 -0500
Subject: [PATCH 10/10] Update
 src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../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 9a0a949e8d..fff48a64be 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
@@ -195,7 +195,7 @@ fields specific to anatomical scans:
 | ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | ContrastBolusIngredient | OPTIONAL              | [string][]                             | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 | RepetitionTimeExcitation | OPTIONAL             | [number][] | The interval, in seconds, between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
-| RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The period of time in seconds that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
+| RepetitionTimePreparation | OPTIONAL            | [number][] or [array][] of [numbers][] | The interval, in seconds, that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data).                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
 
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish