Updated version of MRIAcquisition for v5 by Alixbonard · Pull Request #43 · openMetadataInitiative/openMINDS_neuroimaging

Alixbonard · 2026-01-26T12:50:52Z

Major changes:

Add core:File to input*
Add output
Update required field

19/02/2026:

rename MRIacquisition to staticMRIAcquisition
add new properties coming from dynamicMRIAcquisition ( distortion correction, motion correction, registration data)
core:File is removed from inputs

…in MRIAcquisition

Co-authored-by: Laura Morel <44158117+lauramble@users.noreply.github.com>

lzehl · 2026-02-13T11:01:23Z

@Alixbonard @apdavison since we are asking now for potential input files (used for correction , etc) explicitly in the device usage and in the activity (at least for fMRI) I think File should be removed from input and input should only handle the specimen.

And I checked: distortion correction, motion correction, and registration data are special inputs also for structural MRI (should be optional there). So they could move in here and be removed from fMRI acquisition which extends this one here.
For fMRI: Distortion + motion + registration = standard preprocessing inputs.
For sMRI: Same exists, but are optional.
NOTE: I think we can stick to allowing them to be defined as inputs in these acquisition schemas as short cut, however they are actually always performed as postprocessing of the scan and not as part of the scan (so they normally would be handled by computation).

Otherwise I think this looks good and could be merged from my side. To be considered for the future are potentially the additional parameters identified for activity in #22 (such as: additional contrast agent parameters (e.g. timing after injection), motion and physiology handling parameters, artifact control parameters (maybe, when dependent on specimen))

maybe rename schema to staticMRIAcquisition

lzehl · 2026-02-20T11:38:48Z

+  ],
+  "properties": {
+    "contrastAgent": {
+      "_instruction": "Add the contrast agent used for this scan.",


Suggested change

"_instruction": "Add the contrast agent used for this scan.",

"_instruction": "Add the contrast agent(s) administered for this acquisition, including for each the agent identity and administered amount; if no contrast agent was used, leave this field null. Include all agents given prior to or during the scan.",

expected value number is 1-N (so needs to become an array)

lzehl · 2026-02-20T11:42:33Z

+      ]
+    },
+    "device": {
+      "_instruction": "Add the MRI machine setting used for this scan.",


Suggested change

"_instruction": "Add the MRI machine setting used for this scan.",

"_instruction": "Add the magnetic resonance imaging (MRI) scanner used for this acquisition. This reference should identify the specific device configuration under which the scan was performed.",

lzehl · 2026-02-20T11:45:00Z

+      ]
+    },
+    "distortionCorrection": {
+      "_instruction": "Add the calibration file corresponding to images or field maps used for correction of inhomogeneities in B0 field of this acquisition.",


Suggested change

"_instruction": "Add the calibration file corresponding to images or field maps used for correction of inhomogeneities in B0 field of this acquisition.",

"_instruction": "Add the distortion correction data used for this acquisition, linking to the calibration files applied during image reconstruction or post-processing. If no distortion correction was performed, leave this field null.",

the expected values here are 1-N so needs to become an array

lzehl · 2026-02-20T11:49:53Z

+      ]
+    },
+    "motionCorrection": {
+      "_instruction": "Add the calibration file used for motion correction, corresponding to single-band reference image, for this volume.",


Suggested change

"_instruction": "Add the calibration file used for motion correction, corresponding to single-band reference image, for this volume.",

"_instruction": "Add the motion correction data used for this acquisition, linking to the calibration files or reference images applied during image reconstruction or post-processing. If no motion correction was performed, leave this field null.",

the expected values here are 1-N so needs to become an array

lzehl · 2026-02-20T11:54:31Z

+      ]
+    },
+    "output":{
+      "_instruction": "Add the file generated during this session.",


Suggested change

"_instruction": "Add the file generated during this session.",

"_instruction": "Add the output data generated by this acquisition by linking to one or more files containing the primary imaging outputs and/or, if applicable, any secondary reconstructed or corrected outputs produced during post-processing.",

the expected values here are 1-N so needs to become an array

lzehl · 2026-02-20T11:59:42Z

+      ]
+    },
+    "registrationData": {
+      "_instruction": "Add the registration file corresponding to structural MRI relevant for this acquisition.",


Suggested change

"_instruction": "Add the registration file corresponding to structural MRI relevant for this acquisition.",

"_instruction": "Add the registration data used for this acquisition, linking to the transformation and/or reference files applied during image alignment in post-processing. If no registration was performed, leave this field null.",

the expected values here are 1-N so needs to become an array

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

…rection, registrationData

apdavison and others added 6 commits September 2, 2024 15:17

Update webhook to only trigger the dev pipeline

bbfcff7

Fix JSON sent by curl in openMINDS_upstream.yml

c58facd

Merge branch 'openMetadataInitiative:v1' into dev-MRIAquisition

a0956c5

Add core:FIle to input in MRIAcquisition

e61234c

Add output to MRIAcquisition

61c88f6

Update required with input, device, speciementOrientation and output …

352d719

…in MRIAcquisition

Alixbonard mentioned this pull request Jan 26, 2026

Proposed changes v5: MRIAcquisition schema #21

Closed

lauramble added major update most likely causes a new version v5.0 candidate labels Jan 27, 2026

lauramble reviewed Feb 2, 2026

View reviewed changes

Comment thread schemas/activity/MRIAcquisition.schema.tpl.json Outdated

Alixbonard and others added 3 commits February 2, 2026 12:55

Update schemas/activity/MRIAcquisition.schema.tpl.json

74a77c2

Co-authored-by: Laura Morel <44158117+lauramble@users.noreply.github.com>

Move required fields in MRIAcquisition schema

19fe330

Reorder specimenOrientation and output fields in MRIAcquisition schema

f8f62fd

Alixbonard marked this pull request as ready for review February 2, 2026 12:05

Alixbonard requested review from apdavison and lzehl February 12, 2026 15:19

lzehl mentioned this pull request Feb 13, 2026

Updated version of dynamicMRIAcquisition for v5 #34

Merged

abonard added 3 commits February 17, 2026 11:57

Remove file from input

05b2f4e

Add distortionCorrection, motionCorrection, registrationData

a208b13

Rename MRIAcquisition by staticMRIAcquisition

4d0062b

Alixbonard changed the title ~~Updated version of MRIAcquisition for v5~~ Updated version of staticMRIAcquisition for v5 Feb 20, 2026

lzehl requested changes Feb 20, 2026

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Alixbonard and others added 7 commits February 20, 2026 13:23

Apply suggestion from @lzehl

c529478

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

e6e0892

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

3898a70

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

dce2b03

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

6ea8691

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

77ea5ce

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Apply suggestion from @lzehl

8e7ede4

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Alixbonard and others added 4 commits February 20, 2026 13:25

Apply suggestion from @lzehl

2713736

Co-authored-by: Lyuba Zehl <lyuba.zehl@ebrains.eu>

Add "type": "array" to contrastAgent, distortionCorrection, motionCor…

debc490

…rection, registrationData

Add targetAnatomy property

76098b5

fix typo

963742d

lzehl approved these changes Feb 20, 2026

View reviewed changes

lzehl requested changes Feb 20, 2026

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Comment thread schemas/activity/MRIAcquisition.schema.tpl.json

Alixbonard changed the title ~~Updated version of staticMRIAcquisition for v5~~ Updated version of MRIAcquisition for v5 Feb 20, 2026

Rename MRIAcquisition instead of staticMRIAcquisition

53963c7

lzehl approved these changes Feb 20, 2026

View reviewed changes

lzehl merged commit 1ecffce into openMetadataInitiative:dev Feb 20, 2026
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	"_instruction": "Add the contrast agent used for this scan.",
	"_instruction": "Add the contrast agent(s) administered for this acquisition, including for each the agent identity and administered amount; if no contrast agent was used, leave this field null. Include all agents given prior to or during the scan.",

	"_instruction": "Add the MRI machine setting used for this scan.",
	"_instruction": "Add the magnetic resonance imaging (MRI) scanner used for this acquisition. This reference should identify the specific device configuration under which the scan was performed.",

	"_instruction": "Add the calibration file corresponding to images or field maps used for correction of inhomogeneities in B0 field of this acquisition.",
	"_instruction": "Add the distortion correction data used for this acquisition, linking to the calibration files applied during image reconstruction or post-processing. If no distortion correction was performed, leave this field null.",

	"_instruction": "Add the calibration file used for motion correction, corresponding to single-band reference image, for this volume.",
	"_instruction": "Add the motion correction data used for this acquisition, linking to the calibration files or reference images applied during image reconstruction or post-processing. If no motion correction was performed, leave this field null.",

	"_instruction": "Add the file generated during this session.",
	"_instruction": "Add the output data generated by this acquisition by linking to one or more files containing the primary imaging outputs and/or, if applicable, any secondary reconstructed or corrected outputs produced during post-processing.",

	"_instruction": "Add the registration file corresponding to structural MRI relevant for this acquisition.",
	"_instruction": "Add the registration data used for this acquisition, linking to the transformation and/or reference files applied during image alignment in post-processing. If no registration was performed, leave this field null.",

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Alixbonard commented Jan 26, 2026 •

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lzehl commented Feb 13, 2026 •

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