From 766f7db108e2b8402b892051ccd8f98639d4558d Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 22 Apr 2022 14:53:57 -0400
Subject: [PATCH 1/4] ENH elaborate description of rec entity to mention proc,
 and adjust _proc to not make analogous to _rec

I think it is actually misleading to equate _proc to _rec of MRI.  _rec should
be specific about data reconstruction (specific to MR) and _proc to incorporate
any possible processing performed on the hardware.  I do not think it is
productive to make _rec ambigously absorb any possible preprocessing, whenever
there is a true process of "reconstruction" involved.

Eventually, we might even have _rec used again for ultrasound or some other
modality needing "reconstruction" from data "acquisition" domain into data
"output" domain.  Could even be for EEG inverse problem solving if some
hardware would do any of that LORETA dance etc.  But again, postprocessing
(smoothing etc) would be a separate step
---
 src/modality-specific-files/magnetoencephalography.md | 5 ++---
 src/schema/objects/entities.yaml                      | 4 +++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
index 9548f84ee3..7b1990d198 100644
--- a/src/modality-specific-files/magnetoencephalography.md
+++ b/src/modality-specific-files/magnetoencephalography.md
@@ -74,9 +74,8 @@ For example: `sub-01_task-nback_markers.sqd`
 Please refer to the [MEG File Formats Appendix](../appendices/meg-file-formats.md)
 for general information on how to deal with such manufacturer specifics and to see more examples.
 
-The [`proc-<label>`](../appendices/entities.md#proc) entity is analogous to the
-[`rec-<label>`](../appendices/entities.md#rec) entity for MRI,
-and denotes a variant of a file that was a result of particular processing performed on the device.
+The [`proc-<label>`](../appendices/entities.md#proc) entity
+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 Neuromag/Elekta/MEGIN's MaxFilter
 (for example, sss, tsss, trans, quat, mc),
 which some installations impose to be run on raw data prior to analysis.
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index e26b793c44..8a992ff942 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -215,7 +215,7 @@ processing:
   name: proc
   display_name: Processed (on device)
   description: |
-    The proc label is analogous to rec for MR and denotes a variant of
+    The proc label 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 Neuromag/Elekta/MEGIN's
@@ -231,6 +231,8 @@ reconstruction:
   description: |
     The `rec-<label>` entity can be used to distinguish different reconstruction algorithms
     (for example, `MoCo` for the ones using motion correction).
+    Also consider `proc-<label>` entity to represent additional processing performed on the data
+    after initial reconstruction (for example, spatial smoothing).
   type: string
   format: label
 recording:

From 24947f28d062784d4c6b4de7d383c9c365c41bc6 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 16 Dec 2022 16:55:38 -0500
Subject: [PATCH 2/4] [DATALAD RUNCMD] compliment each reconstruction with
 processing entity

=== Do not change lines below ===
{
 "chain": [
  "e58542b95bdb7551638ee0e2bf337583cec55c07"
 ],
 "cmd": "git grep -l 'reconstruction: opt' | xargs sed -e 's,^\\( *\\)\\(reconstruction: optional\\),\\1\\2\\n\\1processing: optional,g' -i ",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "src"
}
^^^ Do not change lines above ^^^
---
 src/schema/rules/files/raw/anat.yaml | 9 +++++++++
 src/schema/rules/files/raw/dwi.yaml  | 2 ++
 src/schema/rules/files/raw/fmap.yaml | 5 +++++
 src/schema/rules/files/raw/func.yaml | 2 ++
 src/schema/rules/files/raw/perf.yaml | 3 +++
 src/schema/rules/files/raw/pet.yaml  | 2 ++
 src/schema/rules/files/raw/task.yaml | 4 ++++
 7 files changed, 27 insertions(+)

diff --git a/src/schema/rules/files/raw/anat.yaml b/src/schema/rules/files/raw/anat.yaml
index 54edaccc22..addd0289c0 100644
--- a/src/schema/rules/files/raw/anat.yaml
+++ b/src/schema/rules/files/raw/anat.yaml
@@ -26,6 +26,7 @@ nonparametric:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     part: optional
 
@@ -61,6 +62,7 @@ parametric:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
 
 defacemask:
@@ -79,6 +81,7 @@ defacemask:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     modality: optional
 
@@ -99,6 +102,7 @@ multiecho:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: required
     part: optional
@@ -119,6 +123,7 @@ multiflip:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: optional
     flip: required
@@ -140,6 +145,7 @@ multiinversion:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     inversion: required
     part: optional
@@ -160,6 +166,7 @@ mp2rage:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: optional
     flip: optional
@@ -183,6 +190,7 @@ vfamt:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: optional
     flip: required
@@ -205,6 +213,7 @@ mtr:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     mtransfer: required
     part: optional
diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 98840ef6a1..a03cbf68e7 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -15,6 +15,7 @@ dwi:
     session: optional
     acquisition: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
     part: optional
@@ -33,6 +34,7 @@ sbref:
     session: optional
     acquisition: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
     part: optional
diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml
index 8f5e66a508..f9b27bc289 100644
--- a/src/schema/rules/files/raw/fmap.yaml
+++ b/src/schema/rules/files/raw/fmap.yaml
@@ -53,6 +53,7 @@ TB1DAM:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     flip: required
     inversion: optional
@@ -73,6 +74,7 @@ TB1EPI:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: required
     flip: required
@@ -97,6 +99,7 @@ RFFieldMaps:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: optional
     flip: optional
@@ -118,6 +121,7 @@ TB1SRGE:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
     echo: optional
     flip: required
@@ -140,4 +144,5 @@ parametric:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     run: optional
diff --git a/src/schema/rules/files/raw/func.yaml b/src/schema/rules/files/raw/func.yaml
index 589d187444..226b9d049e 100644
--- a/src/schema/rules/files/raw/func.yaml
+++ b/src/schema/rules/files/raw/func.yaml
@@ -17,6 +17,7 @@ func:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
     echo: optional
@@ -38,6 +39,7 @@ phase:
     acquisition: optional
     ceagent: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
     echo: optional
diff --git a/src/schema/rules/files/raw/perf.yaml b/src/schema/rules/files/raw/perf.yaml
index 61cbc24721..b158e5c745 100644
--- a/src/schema/rules/files/raw/perf.yaml
+++ b/src/schema/rules/files/raw/perf.yaml
@@ -14,6 +14,7 @@ asl:
     session: optional
     acquisition: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
 
@@ -30,6 +31,7 @@ aslcontext:
     session: optional
     acquisition: optional
     reconstruction: optional
+    processing: optional
     direction: optional
     run: optional
 
@@ -45,4 +47,5 @@ asllabeling:
     session: optional
     acquisition: optional
     reconstruction: optional
+    processing: optional
     run: optional
diff --git a/src/schema/rules/files/raw/pet.yaml b/src/schema/rules/files/raw/pet.yaml
index a94cb9addd..b00e561857 100644
--- a/src/schema/rules/files/raw/pet.yaml
+++ b/src/schema/rules/files/raw/pet.yaml
@@ -14,6 +14,7 @@ pet:
     task: optional
     tracer: optional
     reconstruction: optional
+    processing: optional
     run: optional
 
 blood:
@@ -30,5 +31,6 @@ blood:
     task: optional
     tracer: optional
     reconstruction: optional
+    processing: optional
     run: optional
     recording: required
diff --git a/src/schema/rules/files/raw/task.yaml b/src/schema/rules/files/raw/task.yaml
index 1767814eb9..d8f52ae88b 100644
--- a/src/schema/rules/files/raw/task.yaml
+++ b/src/schema/rules/files/raw/task.yaml
@@ -49,6 +49,7 @@ events__mri:
     $ref: rules.files.raw.task.events.entities
     ceagent: optional
     reconstruction: optional
+    processing: optional
     direction: optional
 
 events__pet:
@@ -62,6 +63,7 @@ events__pet:
     task: required
     tracer: optional
     reconstruction: optional
+    processing: optional
     run: optional
 
 timeseries__mri:
@@ -72,6 +74,7 @@ timeseries__mri:
   entities:
     $ref: rules.files.raw.task.timeseries.entities
     reconstruction: optional
+    processing: optional
     direction: optional
 
 timeseries__func:
@@ -101,5 +104,6 @@ timeseries__pet:
     task: required
     tracer: optional
     reconstruction: optional
+    processing: optional
     run: optional
     recording: optional

From 5aa12fc00a5e694761803a244200d0974d573d0a Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Fri, 16 Dec 2022 17:04:37 -0500
Subject: [PATCH 3/4] RF: make MEG channels less special (give processing to
 all datatypes channels)

---
 src/schema/rules/files/raw/channels.yaml | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml
index 88c8e79aa8..ca0acab2b6 100644
--- a/src/schema/rules/files/raw/channels.yaml
+++ b/src/schema/rules/files/raw/channels.yaml
@@ -8,22 +8,15 @@ channels:
   datatypes:
     - eeg
     - ieeg
+    - meg
     - nirs
   entities:
     subject: required
     session: optional
     task: required
     acquisition: optional
-    run: optional
-
-# MEG has an additional entity available
-channels__meg:
-  $ref: rules.files.raw.channels.channels
-  datatypes:
-    - meg
-  entities:
-    $ref: rules.files.raw.channels.channels.entities
     processing: optional
+    run: optional
 
 coordsystem:
   suffixes:

From 16bade398de9b03e6fd8247f8a5d9cabde71d354 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Sun, 18 Dec 2022 13:02:05 -0500
Subject: [PATCH 4/4] Add processing to eeg,ieeg,nirs data files

---
 src/schema/rules/files/raw/eeg.yaml  | 1 +
 src/schema/rules/files/raw/ieeg.yaml | 1 +
 src/schema/rules/files/raw/nirs.yaml | 1 +
 3 files changed, 3 insertions(+)

diff --git a/src/schema/rules/files/raw/eeg.yaml b/src/schema/rules/files/raw/eeg.yaml
index 676d66dc1b..270bbab17e 100644
--- a/src/schema/rules/files/raw/eeg.yaml
+++ b/src/schema/rules/files/raw/eeg.yaml
@@ -18,4 +18,5 @@ eeg:
     session: optional
     task: required
     acquisition: optional
+    processing: optional
     run: optional
diff --git a/src/schema/rules/files/raw/ieeg.yaml b/src/schema/rules/files/raw/ieeg.yaml
index 587f9bcbb8..ac7b76d77a 100644
--- a/src/schema/rules/files/raw/ieeg.yaml
+++ b/src/schema/rules/files/raw/ieeg.yaml
@@ -19,4 +19,5 @@ ieeg:
     session: optional
     task: required
     acquisition: optional
+    processing: optional
     run: optional
diff --git a/src/schema/rules/files/raw/nirs.yaml b/src/schema/rules/files/raw/nirs.yaml
index 8dfc41e861..5bd7b430fb 100644
--- a/src/schema/rules/files/raw/nirs.yaml
+++ b/src/schema/rules/files/raw/nirs.yaml
@@ -12,4 +12,5 @@ nirs:
     session: optional
     task: required
     acquisition: optional
+    processing: optional
     run: optional