From d9d2324ece477d918044fcb3a28f396a54392dc3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Feb 2020 18:59:51 -0500
Subject: [PATCH 01/33] Add part entity.

---
 .../01-magnetic-resonance-imaging-data.md     | 37 +++++++++++++++--
 src/99-appendices/04-entity-table.md          | 41 ++++++++++---------
 2 files changed, 55 insertions(+), 23 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 66dc0de8b0..18675cb5f0 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
@@ -112,7 +112,7 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<modality_label>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_part-<mag|phase>][_run-<index>]_<modality_label>.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 
@@ -171,6 +171,16 @@ JSON file, with the same label.
 Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).
 
+#### The `part` entity
+
+Complex-valued data MUST be split into one file for each data type.
+Each file shares the same name with the exception of the `part-<mag|phase>`
+key/value.
+
+In cases where both magnitude and phase data are not reconstructed, the
+`part-<mag|phase>` key/value is OPTIONAL.
+If the key/value is not provided, data are assumed to be magnitude.
+
 If the structural images included in the dataset were defaced (to protect
 identity of participants) one CAN provide the binary mask that was used to
 remove facial features in the form of `_defacemask` files. In such cases the
@@ -202,8 +212,10 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     func/
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_phase.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<mag|phase>]_cbv.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<mag|phase>]_sbref.nii[.gz]
 ```
 
 Imaging data acquired during functional imaging (i.e. imaging which supports
@@ -265,6 +277,25 @@ Please note that the `<index>` denotes the number/index (in a form of an
 integer) of the echo not the echo time value which needs to be stored in the
 field EchoTime of the separate JSON file.
 
+Complex-valued data MUST be split into one file for each data type.
+For BOLD data, there are separate suffices for magnitude (`_bold`) and phase
+(`_phase`) data.
+For other contrasts (e.g., `_sbref` or `_cbv`), each file shares the same
+name with the exception of the `part-<mag|phase>` key/value. For example:
+
+```Text
+sub-01/
+   func/
+      sub-01_task-cuedSGT_bold.nii.gz
+      sub-01_task-cuedSGT_bold.json
+      sub-01_task-cuedSGT_phase.nii.gz
+      sub-01_task-cuedSGT_phase.json
+      sub-01_task-cuedSGT_part-mag_sbref.nii.gz
+      sub-01_task-cuedSGT_part-mag_sbref.nii.gz
+      sub-01_task-cuedSGT_part-phase_sbref.nii.gz
+      sub-01_task-cuedSGT_part-phase_sbref.nii.gz
+```
+
 Some meta information about the acquisition MUST be provided in an additional
 JSON file.
 
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 11e485f9dd..f5f93e3807 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -10,23 +10,24 @@ file type are denoted. Entity formats indicate whether the value is alphanumeric
 A general introduction to entities is given in the section on
 [file name structure](../02-common-principles.md#file-name-structure)
 
-| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Processed (on device) | Space           |
-| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :-------------------- | :---------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `proc-<label>`        | `space-<label>` |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     |                       |                 |
-| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                       |                 |
-| func<br>(bold cbv phase sbref events)                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                       |                 |
-| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            | OPTIONAL              |                 |
-| dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     |                       |                 |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |
-| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 |                | REQUIRED                 | OPTIONAL      |                        |                |                     |                       |                 |
-| beh<br>(events stim physio)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          |               |                        |                |                     |                       |                 |
-| meg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     | OPTIONAL              |                 |
-| eeg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |
-| ieeg<br>                                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |
-| channels<br>(meg/eeg/ieeg)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |
-| headshape<br>(meg)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       | OPTIONAL        |
-| markers<br>(meg)                                                                               | REQUIRED      | OPTIONAL      | OPTIONAL       | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       | OPTIONAL        |
-| photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       |                 |        
-| electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                       | OPTIONAL        |
-| events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                       |                 |        
+| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Part               | Processed (on device) | Space           |
+| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :----------------- | :-------------------- | :---------------|
+| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<mag|phase>` | `proc-<label>`        | `space-<label>` |
+| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL           |                       |                 |
+| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                    |                       |                 |
+| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                    |                       |                 |
+| func<br>(cbv sbref events)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL           |                       |                 |
+| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            |                    | OPTIONAL              |                 |
+| dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     | OPTIONAL           |                       |                 |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
+| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 |                | REQUIRED                 | OPTIONAL      |                        |                |                     |                    |                       |                 |
+| beh<br>(events stim physio)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          |               |                        |                |                     |                    |                       |                 |
+| meg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    | OPTIONAL              |                 |
+| eeg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
+| ieeg<br>                                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
+| channels<br>(meg/eeg/ieeg)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
+| headshape<br>(meg)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
+| markers<br>(meg)                                                                               | REQUIRED      | OPTIONAL      | OPTIONAL       | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
+| photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       |                 |        
+| electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
+| events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |        

From 35c02539b0182617e6f165173d84b4fa1a9e985a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Feb 2020 19:03:24 -0500
Subject: [PATCH 02/33] Add self to contributors file.

---
 src/99-appendices/01-contributors.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/99-appendices/01-contributors.md b/src/99-appendices/01-contributors.md
index 487c4dfff7..471d1f4df9 100644
--- a/src/99-appendices/01-contributors.md
+++ b/src/99-appendices/01-contributors.md
@@ -136,6 +136,7 @@ your name is not listed, please add it.
 -   Nick F. Ramsey 📖
 -   Alex Rockhill 📖🔧
 -   Ariel Rokem 📖
+-   Taylor Salo 📖💬
 -   Matt Sanderson 📖💻
 -   Gunnar Schaefer 📖
 -   Jan-Mathijs Schoffelen 📖

From 239c338a8eb39cf43018d7b0e78b063233b88729 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 4 May 2020 16:23:35 -0400
Subject: [PATCH 03/33] Address @yarikoptic's review.

---
 src/99-appendices/04-entity-table.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index f5f93e3807..cbe593fe66 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -12,7 +12,7 @@ A general introduction to entities is given in the section on
 
 | Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Part               | Processed (on device) | Space           |
 | :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :----------------- | :-------------------- | :---------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<mag|phase>` | `proc-<label>`        | `space-<label>` |
+| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>` | `proc-<label>`        | `space-<label>` |
 | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL           |                       |                 |
 | anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                    |                       |                 |
 | func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                    |                       |                 |

From 82f60fd13b817b40028651d0d972c6f900291b99 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 May 2020 12:12:12 -0400
Subject: [PATCH 04/33] Fix entity table spacing.

---
 src/99-appendices/04-entity-table.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index cbe593fe66..8cf0622bd0 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -12,7 +12,7 @@ A general introduction to entities is given in the section on
 
 | Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Part               | Processed (on device) | Space           |
 | :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :----------------- | :-------------------- | :---------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>` | `proc-<label>`        | `space-<label>` |
+| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>`     | `proc-<label>`        | `space-<label>` |
 | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL           |                       |                 |
 | anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                    |                       |                 |
 | func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                    |                       |                 |

From 6bcc2a5f40d726ef9e7788a3f10cd953beb090e7 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 May 2020 12:23:09 -0400
Subject: [PATCH 05/33] Add missing OPTIONAL for part under func (bold phase).

---
 src/99-appendices/04-entity-table.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 8cf0622bd0..3ed0b596ea 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -15,7 +15,7 @@ A general introduction to entities is given in the section on
 | Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>`     | `proc-<label>`        | `space-<label>` |
 | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL           |                       |                 |
 | anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                    |                       |                 |
-| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                    |                       |                 |
+| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL           |                       |                 |
 | func<br>(cbv sbref events)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL           |                       |                 |
 | func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            |                    | OPTIONAL              |                 |
 | dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     | OPTIONAL           |                       |                 |

From 69ea608bce82b12a101f8f4e367617d911cc528f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 5 May 2020 12:25:31 -0400
Subject: [PATCH 06/33] Fix spacing again.

---
 src/99-appendices/04-entity-table.md | 42 ++++++++++++++--------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 3ed0b596ea..1263a847f7 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -10,24 +10,24 @@ file type are denoted. Entity formats indicate whether the value is alphanumeric
 A general introduction to entities is given in the section on
 [file name structure](../02-common-principles.md#file-name-structure)
 
-| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Part               | Processed (on device) | Space           |
-| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :----------------- | :-------------------- | :---------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>`     | `proc-<label>`        | `space-<label>` |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL           |                       |                 |
-| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                    |                       |                 |
-| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL           |                       |                 |
-| func<br>(cbv sbref events)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL           |                       |                 |
-| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            |                    | OPTIONAL              |                 |
-| dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     | OPTIONAL           |                       |                 |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
-| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 |                | REQUIRED                 | OPTIONAL      |                        |                |                     |                    |                       |                 |
-| beh<br>(events stim physio)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          |               |                        |                |                     |                    |                       |                 |
-| meg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    | OPTIONAL              |                 |
-| eeg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
-| ieeg<br>                                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
-| channels<br>(meg/eeg/ieeg)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |
-| headshape<br>(meg)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
-| markers<br>(meg)                                                                               | REQUIRED      | OPTIONAL      | OPTIONAL       | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
-| photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       |                 |        
-| electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                    |                       | OPTIONAL        |
-| events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                    |                       |                 |        
+| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent | Reconstruction | Phase-Encoding Direction | Run           | Corresponding modality | Echo           | Recording           | Part           | Processed (on device) | Space           |
+| :--------------------------------------------------------------------------------------------- | :------------ | :------------ | :------------- | :------------ | :----------------------- | :------------- | :----------------------- | :------------ | :--------------------- | :------------- | :------------------ | :------------- | :-------------------- | :---------------|
+| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>` | `proc-<label>`        | `space-<label>` |
+| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL       |                       |                 |
+| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                |                       |                 |
+| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL       |                       |                 |
+| func<br>(cbv sbref events)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL       |                       |                 |
+| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            |                | OPTIONAL              |                 |
+| dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     | OPTIONAL       |                       |                 |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                |                       |                 |
+| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 |                | REQUIRED                 | OPTIONAL      |                        |                |                     |                |                       |                 |
+| beh<br>(events stim physio)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          |               |                        |                |                     |                |                       |                 |
+| meg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                | OPTIONAL              |                 |
+| eeg<br>                                                                                        | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                |                       |                 |
+| ieeg<br>                                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          |                |                          | OPTIONAL      |                        |                |                     |                |                       |                 |
+| channels<br>(meg/eeg/ieeg)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                |                       |                 |
+| headshape<br>(meg)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                |                       | OPTIONAL        |
+| markers<br>(meg)                                                                               | REQUIRED      | OPTIONAL      | OPTIONAL       | OPTIONAL      |                          |                |                          |               |                        |                |                     |                |                       | OPTIONAL        |
+| photo<br>(meg/eeg/ieeg)                                                                        | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                |                       |                 |        
+| electrodes<br>(eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                |                          |               |                        |                |                     |                |                       | OPTIONAL        |
+| events<br>(meg/eeg/ieeg)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       |               |                          |                |                          | OPTIONAL      |                        |                |                     |                |                       |                 |        

From 2f6701053d19f56351b448de3c2e869f6796cd95 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Wed, 6 May 2020 10:02:10 -0400
Subject: [PATCH 07/33] Remove OPTIONAL under func (bold phase). Wasn't
 missing.

---
 src/99-appendices/04-entity-table.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 1263a847f7..4a8214bd5b 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -15,7 +15,7 @@ A general introduction to entities is given in the section on
 | Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`             | `rec-<label>`  | `dir-<label>`            | `run-<index>` | `mod-<label>`          | `echo-<index>` | `recording-<label>` | `part-<label>` | `proc-<label>`        | `space-<label>` |
 | anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               |                        |                |                     | OPTIONAL       |                       |                 |
 | anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                 | OPTIONAL       |                          |               | OPTIONAL               |                |                     |                |                       |                 |
-| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL       |                       |                 |
+| func<br>(bold phase)                                                                           | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     |                |                       |                 |
 | func<br>(cbv sbref events)                                                                     | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                 | OPTIONAL       | OPTIONAL                 | OPTIONAL      |                        | OPTIONAL       |                     | OPTIONAL       |                       |                 |
 | func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                          | OPTIONAL       |                          | OPTIONAL      |                        |                | OPTIONAL            |                | OPTIONAL              |                 |
 | dwi<br>(dwi bvec bval)                                                                         | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                          |                | OPTIONAL                 | OPTIONAL      |                        |                |                     | OPTIONAL       |                       |                 |

From 3c222d1b883e9cd6473e9d551145bca06a3a42ec Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 18 May 2020 11:26:58 -0400
Subject: [PATCH 08/33] Fix entity order (part goes after run).

---
 .../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 18675cb5f0..d57b2539f3 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
@@ -112,7 +112,7 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_part-<mag|phase>][_run-<index>]_<modality_label>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<mag|phase>]_<modality_label>.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 

From 908bdba46cdd65badcf38baf837b2f2ec0aeb55a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Sat, 20 Jun 2020 18:47:47 -0400
Subject: [PATCH 09/33] Fix 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 aa1e53453c..c17bf0d3a5 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
@@ -280,7 +280,7 @@ integer) of the echo not the echo time value which needs to be stored in the
 field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
-For BOLD data, there are separate suffices for magnitude (`_bold`) and phase
+For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
 (`_phase`) data.
 For other contrasts (e.g., `_sbref` or `_cbv`), each file shares the same
 name with the exception of the `part-<mag|phase>` key/value. For example:

From 3ca97631e3c424076c677e77aca581e680ceada1 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Aug 2020 13:22:24 -0400
Subject: [PATCH 10/33] Incorporate part into schema.

---
 src/99-appendices/04-entity-table.md | 21 +++++++++++----------
 src/schema/datatypes/anat.yaml       |  1 +
 src/schema/datatypes/dwi.yaml        |  2 ++
 src/schema/datatypes/func.yaml       | 23 ++++++++++++++++++++---
 src/schema/entities.yaml             | 11 +++++++++++
 5 files changed, 45 insertions(+), 13 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 704e6020a9..9766f1eab1 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -13,16 +13,17 @@ A general introduction to entities is given in the section on
 
 ## Magnetic Resonance Imaging
 
-| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent   | Reconstruction   | Phase-Encoding Direction   | Run           | Corresponding Modality   | Echo           | Recording           |
-|------------------------------------------------------------------------------------------------|---------------|---------------|----------------|---------------|----------------------------|------------------|----------------------------|---------------|--------------------------|----------------|---------------------|
-| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`               | `rec-<label>`    | `dir-<label>`              | `run-<index>` | `mod-<label>`            | `echo-<index>` | `recording-<label>` |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      |                          |                |                     |
-| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      | OPTIONAL                 |                |                     |
-| dwi<br>(dwi sbref)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  | OPTIONAL                   | OPTIONAL      |                          |                |                     |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  |                            | OPTIONAL      |                          |                |                     |
-| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   |                  | REQUIRED                   | OPTIONAL      |                          |                |                     |
-| func<br>(bold cbv phase sbref events)                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     |
-| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                            | OPTIONAL         |                            | OPTIONAL      |                          |                | OPTIONAL            |
+| Entity                                                                                         | Subject       | Session       | Task           | Acquisition   | Contrast Enhancing Agent   | Reconstruction   | Phase-Encoding Direction   | Run           | Corresponding Modality   | Echo           | Recording           | Part           |
+|------------------------------------------------------------------------------------------------|---------------|---------------|----------------|---------------|----------------------------|------------------|----------------------------|---------------|--------------------------|----------------|---------------------|----------------|
+| Format                                                                                         | `sub-<label>` | `ses-<label>` | `task-<label>` | `acq-<label>` | `ce-<label>`               | `rec-<label>`    | `dir-<label>`              | `run-<index>` | `mod-<label>`            | `echo-<index>` | `recording-<label>` | `part-<label>` |
+| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      |                          |                |                     | OPTIONAL       |
+| anat<br>(defacemask)                                                                           | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   | OPTIONAL         |                            | OPTIONAL      | OPTIONAL                 |                |                     |                |
+| dwi<br>(dwi sbref)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  | OPTIONAL                   | OPTIONAL      |                          |                |                     | OPTIONAL       |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  |                            | OPTIONAL      |                          |                |                     |                |
+| fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   |                  | REQUIRED                   | OPTIONAL      |                          |                |                     |                |
+| func<br>(cbv sbref)                                                                            | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     | OPTIONAL       |
+| func<br>(bold phase events)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     |                |
+| func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                            | OPTIONAL         |                            | OPTIONAL      |                          |                | OPTIONAL            |                |
 
 ## Encephalography (EEG, iEEG, and MEG)
 
diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index bae17648ce..e0b8bad9fb 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -26,6 +26,7 @@
     acq: optional
     ce: optional
     rec: optional
+    part: optional
 # Second group
 - suffixes:
     - defacemask
diff --git a/src/schema/datatypes/dwi.yaml b/src/schema/datatypes/dwi.yaml
index 26f78761cf..291db298e9 100644
--- a/src/schema/datatypes/dwi.yaml
+++ b/src/schema/datatypes/dwi.yaml
@@ -14,6 +14,7 @@
     acq: optional
     dir: optional
     run: optional
+    part: optional
 # Second group
 - suffixes:
     - sbref
@@ -27,3 +28,4 @@
     acq: optional
     dir: optional
     run: optional
+    part: optional
diff --git a/src/schema/datatypes/func.yaml b/src/schema/datatypes/func.yaml
index 62a26b60b8..0196800327 100644
--- a/src/schema/datatypes/func.yaml
+++ b/src/schema/datatypes/func.yaml
@@ -2,9 +2,7 @@
 # First group
 - suffixes:
     - bold
-    - cbv
     - phase
-    - sbref
   extensions:
     - .nii.gz
     - .nii
@@ -20,6 +18,25 @@
     run: optional
     echo: optional
 # Second group
+- suffixes:
+    - cbv
+    - sbref
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    task: required
+    acq: optional
+    ce: optional
+    rec: optional
+    dir: optional
+    run: optional
+    echo: optional
+    part: optional
+# Third group
 - suffixes:
     - events
   extensions:
@@ -35,7 +52,7 @@
     dir: optional
     run: optional
     echo: optional
-# Third group
+# Fourth group
 - suffixes:
     - physio
     - stim
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 10cf4cfbe7..66f45768f6 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -104,6 +104,17 @@ recording:
     In such case use different labels.
     For example: `_recording-contrast`, `_recording-saturation`.
   format: label
+part:
+  name: Part
+  description: |
+    Complex-valued data MUST be split into one file for each data type.
+    Each file shares the same name with the exception of the `part-<mag|phase>`
+    key/value.
+
+    In cases where both magnitude and phase data are not reconstructed, the
+    `part-<mag|phase>` key/value is OPTIONAL.
+    If the key/value is not provided, data are assumed to be magnitude.
+  format: label
 proc:
   name: Processed (on device)
   description: |

From f566cf420a2eb98dff1920210076bda832753511 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Aug 2020 13:29:45 -0400
Subject: [PATCH 11/33] Update definition and examples to match BEP001.

---
 .../01-magnetic-resonance-imaging-data.md     | 31 +++++++++++++++----
 src/schema/entities.yaml                      | 18 +++++++----
 2 files changed, 37 insertions(+), 12 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 1fe377d4cf..f6888b0873 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
@@ -177,13 +177,32 @@ JSON file, with the same label.
 
 #### The `part` entity
 
-Complex-valued data MUST be split into one file for each data type.
-Each file shares the same name with the exception of the `part-<mag|phase>`
-key/value.
+This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data.
+The `part-<label>` key/value pair is associated with the DICOM tag `0008,9208`.
+Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or `real/imag` pairs.
+For example:
+
+```
+sub-01_part-mag_T1w.nii.gz
+sub-01_part-mag_T1w.json
+sub-01_part-phase_T1w.nii.gz
+sub-01_part-phase_T1w.json
+```
+
+Phase images MAY be in radians or in arbitrary units.
+The sidecar JSON file MUST include the units of the `phase` image.
+The possible options are: `radians` or `a.u.` for grayscale images.
+For example:
+
+sub-01_part-phase.json
+
+```
+{
+   "Units": "radians"
+}
+```
 
-In cases where both magnitude and phase data are not reconstructed, the
-`part-<mag|phase>` key/value is OPTIONAL.
-If the key/value is not provided, data are assumed to be magnitude.
+If the `part` key/value pair is absent from a filename, the image SHOULD be a magnitude image.
 
 Some meta information about the acquisition MAY be provided in an additional
 JSON file. See [Common metadata fields](#common-metadata-fields) for a
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 66f45768f6..7b56d2db2f 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -107,13 +107,19 @@ recording:
 part:
   name: Part
   description: |
-    Complex-valued data MUST be split into one file for each data type.
-    Each file shares the same name with the exception of the `part-<mag|phase>`
-    key/value.
+    This entity is used to indicate which component of the complex
+    representation of the MRI signal is represented in voxel data.
+    The `part-<label>` key/value pair is associated with the DICOM tag
+    `0008,9208`.
+    Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+    which are typically used in `mag/phase` or `real/imag` pairs.
+
+    Phase images MAY be in radians or in arbitrary units.
+    The sidecar JSON file MUST include the units of the `phase` image.
+    The possible options are: `radians` or `a.u.` for grayscale images.
 
-    In cases where both magnitude and phase data are not reconstructed, the
-    `part-<mag|phase>` key/value is OPTIONAL.
-    If the key/value is not provided, data are assumed to be magnitude.
+    If the `part` key/value pair is absent from a filename, the image SHOULD be
+    a magnitude image.
   format: label
 proc:
   name: Processed (on device)

From d6dc2ac01e746b381f4afd4cf2c150887822922d Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Aug 2020 13:35:13 -0400
Subject: [PATCH 12/33] Fix code snippets.

---
 .../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 f6888b0873..6e619972cd 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
@@ -182,7 +182,7 @@ The `part-<label>` key/value pair is associated with the DICOM tag `0008,9208`.
 Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or `real/imag` pairs.
 For example:
 
-```
+```Text
 sub-01_part-mag_T1w.nii.gz
 sub-01_part-mag_T1w.json
 sub-01_part-phase_T1w.nii.gz
@@ -196,7 +196,7 @@ For example:
 
 sub-01_part-phase.json
 
-```
+```Text
 {
    "Units": "radians"
 }

From 8db0dea2590712d1b6eaeeb28f51e506e4a7a59f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 24 Aug 2020 13:44:32 -0400
Subject: [PATCH 13/33] Fix filename patterns now that real/imag is supported.

---
 .../01-magnetic-resonance-imaging-data.md      | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 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 6e619972cd..a12ecd475b 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
@@ -114,7 +114,7 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     anat/
-        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<mag|phase>]_<modality_label>.nii[.gz]
+        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<modality_label>.nii[.gz]
         sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
 ```
 
@@ -235,8 +235,8 @@ sub-<label>/[ses-<label>/]
     func/
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_phase.nii[.gz]
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<mag|phase>]_cbv.nii[.gz]
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<mag|phase>]_sbref.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.nii[.gz]
 ```
 
 Imaging data acquired during functional imaging (i.e. imaging which supports
@@ -415,12 +415,12 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     dwi/
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_dwi.nii[.gz]
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_dwi.bval
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_dwi.bvec
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_dwi.json
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_sbref.nii[.gz]
-       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>]_sbref.json
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bval
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bvec
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.json
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.nii[.gz]
+       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.json
 ```
 
 Diffusion-weighted imaging data acquired for that participant. The OPTIONAL

From 85957a37a3dfff9a26a845d9b2660b8d8e5c467a Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 1 Sep 2020 14:17:01 -0400
Subject: [PATCH 14/33] Apply suggestions from code review

- Change radians to rad.
- Treat `part` like `run`. Can only be omitted if only magnitude image is provided.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../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 a12ecd475b..c0ae6b45d3 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
@@ -191,18 +191,18 @@ sub-01_part-phase_T1w.json
 
 Phase images MAY be in radians or in arbitrary units.
 The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are: `radians` or `a.u.` for grayscale images.
+The possible options are: `rad` or `a.u.` for grayscale images.
 For example:
 
-sub-01_part-phase.json
+sub-01_part-phase_T1w.json
 
 ```Text
 {
-   "Units": "radians"
+   "Units": "rad"
 }
 ```
 
-If the `part` key/value pair is absent from a filename, the image SHOULD be a magnitude image.
+When there is only a magnitude image of a given type, the `part` key MAY be omitted.
 
 Some meta information about the acquisition MAY be provided in an additional
 JSON file. See [Common metadata fields](#common-metadata-fields) for a

From 0a889985a4e7ca69c5df376521a22fa77e4cbce3 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 1 Sep 2020 14:28:46 -0400
Subject: [PATCH 15/33] Support part with BOLD and update entity table.

---
 .../01-magnetic-resonance-imaging-data.md     | 21 +++++++++++--------
 src/99-appendices/04-entity-table.md          |  4 ++--
 src/schema/datatypes/func.yaml                |  8 +++----
 src/schema/entities.yaml                      |  6 +++---
 4 files changed, 21 insertions(+), 18 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 c0ae6b45d3..a2514df376 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
@@ -191,7 +191,7 @@ sub-01_part-phase_T1w.json
 
 Phase images MAY be in radians or in arbitrary units.
 The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are: `rad` or `a.u.` for grayscale images.
+The possible options are `rad` or `a.u.`.
 For example:
 
 sub-01_part-phase_T1w.json
@@ -233,7 +233,7 @@ Template:
 ```Text
 sub-<label>/[ses-<label>/]
     func/
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_bold.nii[.gz]
+        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_bold.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_phase.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.nii[.gz]
@@ -300,17 +300,20 @@ field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
 For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data.
-For other contrasts (e.g., `_sbref` or `_cbv`), each file shares the same
-name with the exception of the `part-<mag|phase>` key/value. For example:
+(`_phase`) data, but the `_phase` suffix is considered a legacy suffix
+(i.e., still supported in the specification, but to be deprecated later).
+For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.
+When the `_phase` suffix is not used, each file shares the same
+name with the exception of the `part-<mag|phase>` or `part-<real|imag>` key/value.
+For example:
 
 ```Text
 sub-01/
    func/
-      sub-01_task-cuedSGT_bold.nii.gz
-      sub-01_task-cuedSGT_bold.json
-      sub-01_task-cuedSGT_phase.nii.gz
-      sub-01_task-cuedSGT_phase.json
+      sub-01_task-cuedSGT_part-mag_bold.nii.gz
+      sub-01_task-cuedSGT_part-mag_bold.json
+      sub-01_task-cuedSGT_part-phase_bold.nii.gz
+      sub-01_task-cuedSGT_part-phase_bold.json
       sub-01_task-cuedSGT_part-mag_sbref.nii.gz
       sub-01_task-cuedSGT_part-mag_sbref.nii.gz
       sub-01_task-cuedSGT_part-phase_sbref.nii.gz
diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 9766f1eab1..190d912579 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -21,8 +21,8 @@ A general introduction to entities is given in the section on
 | dwi<br>(dwi sbref)                                                                             | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  | OPTIONAL                   | OPTIONAL      |                          |                |                     | OPTIONAL       |
 | fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED      | OPTIONAL      |                | OPTIONAL      |                            |                  |                            | OPTIONAL      |                          |                |                     |                |
 | fmap<br>(epi)                                                                                  | REQUIRED      | OPTIONAL      |                | OPTIONAL      | OPTIONAL                   |                  | REQUIRED                   | OPTIONAL      |                          |                |                     |                |
-| func<br>(cbv sbref)                                                                            | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     | OPTIONAL       |
-| func<br>(bold phase events)                                                                    | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     |                |
+| func<br>(bold cbv sbref)                                                                       | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     | OPTIONAL       |
+| func<br>(phase events)                                                                         | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      | OPTIONAL                   | OPTIONAL         | OPTIONAL                   | OPTIONAL      |                          | OPTIONAL       |                     |                |
 | func<br>(physio stim)                                                                          | REQUIRED      | OPTIONAL      | REQUIRED       | OPTIONAL      |                            | OPTIONAL         |                            | OPTIONAL      |                          |                | OPTIONAL            |                |
 
 ## Encephalography (EEG, iEEG, and MEG)
diff --git a/src/schema/datatypes/func.yaml b/src/schema/datatypes/func.yaml
index 0196800327..8c99a3689d 100644
--- a/src/schema/datatypes/func.yaml
+++ b/src/schema/datatypes/func.yaml
@@ -2,7 +2,8 @@
 # First group
 - suffixes:
     - bold
-    - phase
+    - cbv
+    - sbref
   extensions:
     - .nii.gz
     - .nii
@@ -17,10 +18,10 @@
     dir: optional
     run: optional
     echo: optional
+    part: optional
 # Second group
 - suffixes:
-    - cbv
-    - sbref
+    - phase
   extensions:
     - .nii.gz
     - .nii
@@ -35,7 +36,6 @@
     dir: optional
     run: optional
     echo: optional
-    part: optional
 # Third group
 - suffixes:
     - events
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 7b56d2db2f..093d571732 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -116,10 +116,10 @@ part:
 
     Phase images MAY be in radians or in arbitrary units.
     The sidecar JSON file MUST include the units of the `phase` image.
-    The possible options are: `radians` or `a.u.` for grayscale images.
+    The possible options are `rad` or `a.u.`.
 
-    If the `part` key/value pair is absent from a filename, the image SHOULD be
-    a magnitude image.
+    When there is only a magnitude image of a given type, the `part` key MAY be
+    omitted.
   format: label
 proc:
   name: Processed (on device)

From 08a0934645b8fccc053164127f50c7d462866d7f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 1 Sep 2020 14:36:33 -0400
Subject: [PATCH 16/33] 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 a2514df376..e9ae6f5777 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
@@ -315,9 +315,9 @@ sub-01/
       sub-01_task-cuedSGT_part-phase_bold.nii.gz
       sub-01_task-cuedSGT_part-phase_bold.json
       sub-01_task-cuedSGT_part-mag_sbref.nii.gz
-      sub-01_task-cuedSGT_part-mag_sbref.nii.gz
-      sub-01_task-cuedSGT_part-phase_sbref.nii.gz
+      sub-01_task-cuedSGT_part-mag_sbref.json
       sub-01_task-cuedSGT_part-phase_sbref.nii.gz
+      sub-01_task-cuedSGT_part-phase_sbref.json
 ```
 
 Some meta information about the acquisition MUST be provided in an additional

From c46715fd4ee7e4962adffd56d0711c08227c43d5 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 8 Sep 2020 11:18:34 -0400
Subject: [PATCH 17/33] Update entity table and entity definitions.

---
 src/99-appendices/04-entity-table.md | 21 +++++++++++----------
 src/99-appendices/09-entities.md     | 20 ++++++++++++++++++++
 2 files changed, 31 insertions(+), 10 deletions(-)

diff --git a/src/99-appendices/04-entity-table.md b/src/99-appendices/04-entity-table.md
index 9f3002bf33..f9ae4bd520 100644
--- a/src/99-appendices/04-entity-table.md
+++ b/src/99-appendices/04-entity-table.md
@@ -18,16 +18,17 @@ while entity definitions are in [Appendix IX](09-entities.md).
 
 ## Magnetic Resonance Imaging
 
-| Entity                                                                                         | Subject                             | Session                             | Task                                  | Acquisition                         | Contrast Enhancing Agent          | Reconstruction                      | Phase-Encoding Direction            | Run                                 | Corresponding Modality              | Echo                                  | Recording                                       |
-|------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------------------|
-| Format                                                                                         | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`ce-<label>`](09-entities.md#ce) | [`rec-<label>`](09-entities.md#rec) | [`dir-<label>`](09-entities.md#dir) | [`run-<index>`](09-entities.md#run) | [`mod-<label>`](09-entities.md#mod) | [`echo-<index>`](09-entities.md#echo) | [`recording-<label>`](09-entities.md#recording) |
-| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                                 |
-| anat<br>(defacemask)                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            | OPTIONAL                            |                                       |                                                 |
-| dwi<br>(dwi sbref)                                                                             | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     | OPTIONAL                            | OPTIONAL                            |                                     |                                       |                                                 |
-| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     |                                     | OPTIONAL                            |                                     |                                       |                                                 |
-| fmap<br>(epi)                                                                                  | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          |                                     | REQUIRED                            | OPTIONAL                            |                                     |                                       |                                                 |
-| func<br>(bold cbv phase sbref events)                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                                 |
-| func<br>(physio stim)                                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            |                                   | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | OPTIONAL                                        |
+| Entity                                                                                         | Subject                             | Session                             | Task                                  | Acquisition                         | Contrast Enhancing Agent          | Reconstruction                      | Phase-Encoding Direction            | Run                                 | Corresponding Modality              | Echo                                  | Recording                                       | Part                                  |
+|------------------------------------------------------------------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------|-----------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|-------------------------------------|---------------------------------------|-------------------------------------------------|---------------------------------------|
+| Format                                                                                         | [`sub-<label>`](09-entities.md#sub) | [`ses-<label>`](09-entities.md#ses) | [`task-<label>`](09-entities.md#task) | [`acq-<label>`](09-entities.md#acq) | [`ce-<label>`](09-entities.md#ce) | [`rec-<label>`](09-entities.md#rec) | [`dir-<label>`](09-entities.md#dir) | [`run-<index>`](09-entities.md#run) | [`mod-<label>`](09-entities.md#mod) | [`echo-<index>`](09-entities.md#echo) | [`recording-<label>`](09-entities.md#recording) | [`part-<label>`](09-entities.md#part) |
+| anat<br>(T1w T2w T1rho T1map T2map T2star FLAIR FLASH PD PDmap PDT2 inplaneT1 inplaneT2 angio) | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       |                                                 | OPTIONAL                              |
+| anat<br>(defacemask)                                                                           | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            |                                     | OPTIONAL                            | OPTIONAL                            |                                       |                                                 |                                       |
+| dwi<br>(dwi sbref)                                                                             | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     | OPTIONAL                            | OPTIONAL                            |                                     |                                       |                                                 | OPTIONAL                              |
+| fmap<br>(phasediff phase1 phase2 magnitude1 magnitude2 magnitude fieldmap)                     | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            |                                   |                                     |                                     | OPTIONAL                            |                                     |                                       |                                                 |                                       |
+| fmap<br>(epi)                                                                                  | REQUIRED                            | OPTIONAL                            |                                       | OPTIONAL                            | OPTIONAL                          |                                     | REQUIRED                            | OPTIONAL                            |                                     |                                       |                                                 |                                       |
+| func<br>(bold cbv sbref)                                                                       | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                                 | OPTIONAL                              |
+| func<br>(phase events)                                                                         | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            | OPTIONAL                          | OPTIONAL                            | OPTIONAL                            | OPTIONAL                            |                                     | OPTIONAL                              |                                                 |                                       |
+| func<br>(physio stim)                                                                          | REQUIRED                            | OPTIONAL                            | REQUIRED                              | OPTIONAL                            |                                   | OPTIONAL                            |                                     | OPTIONAL                            |                                     |                                       | OPTIONAL                                        |                                       |
 
 ## Encephalography (EEG, iEEG, and MEG)
 
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 4695ccd8b8..1cb98abd4e 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -151,6 +151,26 @@ sampling frequencies).
 In such case use different labels.
 For example: `_recording-contrast`, `_recording-saturation`.
 
+## part
+
+Full name: Part
+
+Format: `part-<label>`
+
+Definition: This entity is used to indicate which component of the complex
+representation of the MRI signal is represented in voxel data.
+The `part-<label>` key/value pair is associated with the DICOM tag
+`0008,9208`.
+Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+which are typically used in `mag/phase` or `real/imag` pairs.
+
+Phase images MAY be in radians or in arbitrary units.
+The sidecar JSON file MUST include the units of the `phase` image.
+The possible options are `rad` or `a.u.`.
+
+When there is only a magnitude image of a given type, the `part` key MAY be
+omitted.
+
 ## proc
 
 Full name: Processed (on device)

From 44a1a3577aaef745bc55b7fa0dd997db4cfb1dfc Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 8 Sep 2020 11:19:58 -0400
Subject: [PATCH 18/33] Add link in text.

---
 .../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 74452d2787..92316c12f8 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
@@ -176,7 +176,7 @@ JSON file, with the same label.
 #### The `part` entity
 
 This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data.
-The `part-<label>` key/value pair is associated with the DICOM tag `0008,9208`.
+The [`part-<label>`](../99-appendices/09-entities.md#part) key/value pair is associated with the DICOM tag `0008,9208`.
 Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or `real/imag` pairs.
 For example:
 

From 8561f4abd1feea18ac43fce2bc637be1cb89b051 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 8 Sep 2020 11:22:43 -0400
Subject: [PATCH 19/33] Remove section header.

---
 .../01-magnetic-resonance-imaging-data.md                       | 2 --
 1 file changed, 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 92316c12f8..90546a9858 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
@@ -173,8 +173,6 @@ sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
 JSON file, with the same label.
 
-#### The `part` entity
-
 This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data.
 The [`part-<label>`](../99-appendices/09-entities.md#part) key/value pair is associated with the DICOM tag `0008,9208`.
 Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or `real/imag` pairs.

From 78aad5a38785aa9de0edc53b917e76d73f111cb4 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 18 Sep 2020 09:54:22 -0400
Subject: [PATCH 20/33] Address review.

---
 .../01-magnetic-resonance-imaging-data.md     | 27 ++++++++++---------
 1 file changed, 15 insertions(+), 12 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 90546a9858..505ff579da 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
@@ -173,9 +173,21 @@ sequences using different contrast enhanced images. The label is the name of the
 contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
 JSON file, with the same label.
 
-This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data.
-The [`part-<label>`](../99-appendices/09-entities.md#part) key/value pair is associated with the DICOM tag `0008,9208`.
-Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `mag/phase` or `real/imag` pairs.
+Some meta information about the acquisition MAY be provided in an additional
+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:
+
+| Field name              | Definition                                                                                                                                         |
+| -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
+
+The [`part-<label>`](../99-appendices/09-entities.md#part) key/value pair is
+used to indicate which component of the complex representation of the MRI
+signal is represented in voxel data.
+This entity is associated with the DICOM tag `0008,9208`.
+Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
+which are typically used in `mag/phase` or `real/imag` pairs.
 For example:
 
 ```Text
@@ -200,15 +212,6 @@ sub-01_part-phase_T1w.json
 
 When there is only a magnitude image of a given type, the `part` key MAY be omitted.
 
-Some meta information about the acquisition MAY be provided in an additional
-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:
-
-| Field name              | Definition                                                                                                                                         |
-| -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
-| ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
-
 Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
 key/value can be used to distinguish
 different reconstruction algorithms (for example ones using motion correction).

From eb1f95f4b30486c7be9cdcec185433a6e1c254ca Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 2 Oct 2020 20:33:37 -0400
Subject: [PATCH 21/33] 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 37c0271fd3..fde42d2b46 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
@@ -211,7 +211,7 @@ sub-01_part-phase_T1w.json
 
 Phase images MAY be in radians or in arbitrary units.
 The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are `rad` or `a.u.`.
+The possible options are `rad` or `arbitrary`.
 For example:
 
 sub-01_part-phase_T1w.json

From e0ffe8427291c00941cd750dca5b6beeaec8a518 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:12:19 -0400
Subject: [PATCH 22/33] Deprecate phase suffix.

---
 .../01-magnetic-resonance-imaging-data.md                    | 5 +++--
 1 file changed, 3 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 fde42d2b46..e502fb4602 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
@@ -316,8 +316,9 @@ field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
 For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data, but the `_phase` suffix is considered a legacy suffix
-(i.e., still supported in the specification, but to be deprecated later).
+(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles#Definitions).
+Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed
+from the specification in the next major release.
 For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.
 When the `_phase` suffix is not used, each file shares the same
 name with the exception of the `part-<mag|phase>` or `part-<real|imag>` key/value.

From d800c09a514334208b2df56642b1deba6d14a2d5 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:15:22 -0400
Subject: [PATCH 23/33] Fix link.

---
 .../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 e502fb4602..52d775e67c 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
@@ -316,7 +316,7 @@ field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
 For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles#Definitions).
+(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles.md#Definitions).
 Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed
 from the specification in the next major release.
 For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.

From 90273340c3a9535fdeeb5a3e85aac89d2b2d66da Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:18:12 -0400
Subject: [PATCH 24/33] Fix link again.

---
 .../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 52d775e67c..d9c93047f0 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
@@ -316,7 +316,7 @@ field EchoTime of the separate JSON file.
 
 Complex-valued data MUST be split into one file for each data type.
 For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles.md#Definitions).
+(`_phase`) data, but the `_phase` suffix is [deprecated](../02-common-principles.md#definitions).
 Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed
 from the specification in the next major release.
 For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.

From a8f54a1c736264e0a7bc8aab63d137e11c02f26c Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:25:43 -0400
Subject: [PATCH 25/33] Include deprecation in table.

---
 .../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 d9c93047f0..cfb7069a6e 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
@@ -236,7 +236,7 @@ Currently supported image contrasts include:
 |---------- | ---------------- | ---------------------------------------------------------------------------------------------------- |
 | BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                   |
 | CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images) |
-| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast                      |
+| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions).         |
 
 Template:
 

From f04f195134641b383aef3f758f0baf5b1689f736 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:26:41 -0400
Subject: [PATCH 26/33] Fix table.

---
 .../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 cfb7069a6e..8833cc0afb 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
@@ -232,11 +232,11 @@ different reconstruction algorithms (for example ones using motion correction).
 
 Currently supported image contrasts include:
 
-| **Name**  | `contrast_label` | **Description**                                                                                      |
-|---------- | ---------------- | ---------------------------------------------------------------------------------------------------- |
-| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                   |
-| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images) |
-| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions).         |
+| **Name**  | `contrast_label` | **Description**                                                                                                                        |
+|---------- | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------- |
+| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                     |
+| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                   |
+| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions). |
 
 Template:
 

From 72800d1eb5af1f499828c00c9fb55298402150b8 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Oct 2020 17:36:52 -0400
Subject: [PATCH 27/33] Update 01-magnetic-resonance-imaging-data.md

---
 .../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 8833cc0afb..98de870865 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
@@ -232,11 +232,11 @@ different reconstruction algorithms (for example ones using motion correction).
 
 Currently supported image contrasts include:
 
-| **Name**  | `contrast_label` | **Description**                                                                                                                        |
-|---------- | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------- |
-| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                     |
-| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                   |
-| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions). |
+| **Name**  | `contrast_label` | **Description**                                                                                                                                                                                                     |
+|---------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                  |
+| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                |
+| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions). [`part-phase`](../99-appendices/09-entities.md#part) should be used instead. |
 
 Template:
 

From 28abc54937f96a88a79c13a44c82512e6b4afc35 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 16 Nov 2020 17:22:11 -0500
Subject: [PATCH 28/33] Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../01-magnetic-resonance-imaging-data.md                    | 5 ++---
 src/schema/entities.yaml                                     | 2 +-
 2 files changed, 3 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 98de870865..e9133d33cb 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
@@ -232,11 +232,11 @@ different reconstruction algorithms (for example ones using motion correction).
 
 Currently supported image contrasts include:
 
-| **Name**  | `contrast_label` | **Description**                                                                                                                                                                                                     |
+| **Name**  | `suffix` | **Description**                                                                                                                                                                                                     |
 |---------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                  |
 | CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                |
-| Phase     | phase            | Phase information associated with magnitude information stored in BOLD contrast. [Deprecated](../02-common-principles.md#definitions). [`part-phase`](../99-appendices/09-entities.md#part) should be used instead. |
+| Phase     | phase            | [DEPRECATED](../02-common-principles.md#definitions). Phase information associated with magnitude information stored in BOLD contrast. This suffix should be replaced by the [`part-phase`](../99-appendices/09-entities.md#part) in conjunction with the `bold` suffix. |
 
 Template:
 
@@ -244,7 +244,6 @@ Template:
 sub-<label>/[ses-<label>/]
     func/
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_bold.nii[.gz]
-        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_phase.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.nii[.gz]
         sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.nii[.gz]
 ```
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index c596813ac9..96555dc1eb 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -127,7 +127,7 @@ part:
 
     Phase images MAY be in radians or in arbitrary units.
     The sidecar JSON file MUST include the units of the `phase` image.
-    The possible options are `rad` or `a.u.`.
+    The possible options are `rad` or `arbitrary`.
 
     When there is only a magnitude image of a given type, the `part` key MAY be
     omitted.

From 5903d5d0c9d52a4de395e071b679f9378d83ab89 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 16 Nov 2020 17:26:30 -0500
Subject: [PATCH 29/33] Add entity field.

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

diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index 96555dc1eb..f004cff162 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -117,6 +117,7 @@ recording:
   format: label
 part:
   name: Part
+  entity: part
   description: |
     This entity is used to indicate which component of the complex
     representation of the MRI signal is represented in voxel data.

From 21aed29b8de9dd39845d429a69a779e56936336f Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 16 Nov 2020 17:27:53 -0500
Subject: [PATCH 30/33] Fix bug and generate appendix.

---
 src/99-appendices/09-entities.md | 26 +++++++++++++++-----------
 tools/bids_schema.py             |  4 +++-
 2 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index 1c5af8dc5e..eddbfb7178 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -40,7 +40,8 @@ several visits (for example fMRI on one day followed by DWI the day after)
 those can be grouped in one session.
 Defining multiple sessions is appropriate when several identical or similar
 data acquisitions are planned and performed on all -or most- subjects,
-often in the case of some intervention between sessions (for example, training).
+often in the case of some intervention between sessions
+(for example, training).
 
 ## task
 
@@ -69,11 +70,12 @@ In such case two files could have the following names:
 `sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however
 the user is free to choose any other label than highres and lowres as long
 as they are consistent across subjects and sessions.
-In case different sequences are used to record the same modality (for example, RARE
-and FLASH for T1w) this field can also be used to make that distinction.
-At what level of detail to make the distinction (for example, just between RARE and
-FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the
-discretion of the researcher.
+In case different sequences are used to record the same modality
+(for example, RARE and FLASH for T1w)
+this field can also be used to make that distinction.
+At what level of detail to make the distinction (for example,
+just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled)
+remains at the discretion of the researcher.
 
 ## ce
 
@@ -104,7 +106,8 @@ Full name: Phase-Encoding Direction
 Format: `dir-<label>`
 
 Definition: The `dir-<label>` key/value can be set to an arbitrary alphanumeric label
-(for example, `dir-LR` or `dir-AP`) to distinguish different phase-encoding directions.
+(for example, `dir-LR` or `dir-AP`) to distinguish different phase-encoding
+directions.
 
 ## run
 
@@ -166,7 +169,7 @@ which are typically used in `mag/phase` or `real/imag` pairs.
 
 Phase images MAY be in radians or in arbitrary units.
 The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are `rad` or `a.u.`.
+The possible options are `rad` or `arbitrary`.
 
 When there is only a magnitude image of a given type, the `part` key MAY be
 omitted.
@@ -180,9 +183,10 @@ Format: `proc-<label>`
 Definition: The proc label is analogous to rec for MR and denotes a variant of a file
 that was a result of particular processing performed on the device.
 This is useful for files produced in particular by Elekta’s MaxFilter
-(for example, sss, tsss, trans, quat or mc), which some installations impose to
-be run on raw data because of active shielding software corrections before
-the MEG data can actually be exploited.
+(for example, sss, tsss, trans, quat or mc),
+which some installations impose to be run on raw data because of active
+shielding software corrections before the MEG data can actually be
+exploited.
 
 ## space
 
diff --git a/tools/bids_schema.py b/tools/bids_schema.py
index fa139c8e44..5c1423f7c9 100755
--- a/tools/bids_schema.py
+++ b/tools/bids_schema.py
@@ -224,7 +224,9 @@ def save_entities(schema_path, out_file):
             fo.write('\n\n')
             fo.write('Full name: {}'.format(entity_info['name']))
             fo.write('\n\n')
-            fo.write('Format: `{}-<{}>`'.format(entity, entity_info['format']))
+            fo.write('Format: `{}-<{}>`'.format(
+                entity_info['entity'], entity_info['format'])
+            )
             fo.write('\n\n')
             fo.write('Definition: {}'.format(entity_info['description']))
 

From e914b91586befa3b690e056bf76b9afb2227f163 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 16 Nov 2020 20:59:26 -0500
Subject: [PATCH 31/33] Fix table.

---
 .../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 0efff4e590..c39cf1ac6d 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
@@ -233,10 +233,10 @@ different reconstruction algorithms (for example ones using motion correction).
 
 Currently supported image contrasts include:
 
-| **Name**  | `suffix` | **Description**                                                                                                                                                                                                     |
-|---------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                  |
-| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                |
+| **Name**  | `suffix`         | **Description**                                                                                                                                                                                                                                                          |
+|---------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                                                                       |
+| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                                                                     |
 | Phase     | phase            | [DEPRECATED](../02-common-principles.md#definitions). Phase information associated with magnitude information stored in BOLD contrast. This suffix should be replaced by the [`part-phase`](../99-appendices/09-entities.md#part) in conjunction with the `bold` suffix. |
 
 Template:

From 903324b53bc13fa6a56e24a581e091ac74b69679 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 17 Nov 2020 10:17:35 -0500
Subject: [PATCH 32/33] 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              | 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 c39cf1ac6d..b71401795d 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
@@ -233,11 +233,11 @@ different reconstruction algorithms (for example ones using motion correction).
 
 Currently supported image contrasts include:
 
-| **Name**  | `suffix`         | **Description**                                                                                                                                                                                                                                                          |
-|---------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| BOLD      | bold             | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                                                                       |
-| CBV       | cbv              | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                                                                     |
-| Phase     | phase            | [DEPRECATED](../02-common-principles.md#definitions). Phase information associated with magnitude information stored in BOLD contrast. This suffix should be replaced by the [`part-phase`](../99-appendices/09-entities.md#part) in conjunction with the `bold` suffix. |
+| **Name**  | `suffix` | **Description**                                                                                                                                                                                                                                                          |
+|---------- | -------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| BOLD      | bold     | Blood-Oxygen-Level Dependent contrast (specialized T2\* weighting)                                                                                                                                                                                                       |
+| CBV       | cbv      | Cerebral Blood Volume contrast (specialized T2\* weighting or difference between T1 weighted images)                                                                                                                                                                     |
+| Phase     | phase    | [DEPRECATED](../02-common-principles.md#definitions). Phase information associated with magnitude information stored in BOLD contrast. This suffix should be replaced by the [`part-phase`](../99-appendices/09-entities.md#part) in conjunction with the `bold` suffix. |
 
 Template:
 

From 78e70ef7135d3ec0d1b0d28ca1f398117103e6f0 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Tue, 17 Nov 2020 12:59:19 -0500
Subject: [PATCH 33/33] Improve part definition.

---
 .../01-magnetic-resonance-imaging-data.md                      | 3 ++-
 src/99-appendices/09-entities.md                               | 3 ++-
 src/schema/entities.yaml                                       | 3 ++-
 3 files changed, 6 insertions(+), 3 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 b71401795d..5b7312a47b 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
@@ -200,7 +200,8 @@ used to indicate which component of the complex representation of the MRI
 signal is represented in voxel data.
 This entity is associated with the DICOM tag `0008,9208`.
 Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
-which are typically used in `mag/phase` or `real/imag` pairs.
+which are typically used in `part-mag`/`part-phase` or `part-real`/`part-imag`
+pairs of files.
 For example:
 
 ```Text
diff --git a/src/99-appendices/09-entities.md b/src/99-appendices/09-entities.md
index eddbfb7178..937bf35ce5 100644
--- a/src/99-appendices/09-entities.md
+++ b/src/99-appendices/09-entities.md
@@ -165,7 +165,8 @@ representation of the MRI signal is represented in voxel data.
 The `part-<label>` key/value pair is associated with the DICOM tag
 `0008,9208`.
 Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
-which are typically used in `mag/phase` or `real/imag` pairs.
+which are typically used in `part-mag`/`part-phase` or
+`part-real`/`part-imag` pairs of files.
 
 Phase images MAY be in radians or in arbitrary units.
 The sidecar JSON file MUST include the units of the `phase` image.
diff --git a/src/schema/entities.yaml b/src/schema/entities.yaml
index eca2dad23d..54382c21cb 100644
--- a/src/schema/entities.yaml
+++ b/src/schema/entities.yaml
@@ -127,7 +127,8 @@ part:
     The `part-<label>` key/value pair is associated with the DICOM tag
     `0008,9208`.
     Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
-    which are typically used in `mag/phase` or `real/imag` pairs.
+    which are typically used in `part-mag`/`part-phase` or
+    `part-real`/`part-imag` pairs of files.
 
     Phase images MAY be in radians or in arbitrary units.
     The sidecar JSON file MUST include the units of the `phase` image.