From bbfcff78113efbc4db03b726a567d41b3ddb25e6 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 2 Sep 2024 15:17:13 +0200 Subject: [PATCH 01/23] Update webhook to only trigger the dev pipeline --- .github/workflows/openMINDS_upstream.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openMINDS_upstream.yml b/.github/workflows/openMINDS_upstream.yml index e08af99..fea76eb 100644 --- a/.github/workflows/openMINDS_upstream.yml +++ b/.github/workflows/openMINDS_upstream.yml @@ -10,4 +10,4 @@ jobs: steps: - name: Trigger central repository run: | - curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}' + curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build-dev.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}' From c58facdb4a051498a9b309da6f0c161590314091 Mon Sep 17 00:00:00 2001 From: Andrew Davison Date: Mon, 31 Mar 2025 16:44:44 +0200 Subject: [PATCH 02/23] Fix JSON sent by curl in openMINDS_upstream.yml --- .github/workflows/openMINDS_upstream.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/openMINDS_upstream.yml b/.github/workflows/openMINDS_upstream.yml index fea76eb..5061430 100644 --- a/.github/workflows/openMINDS_upstream.yml +++ b/.github/workflows/openMINDS_upstream.yml @@ -10,4 +10,4 @@ jobs: steps: - name: Trigger central repository run: | - curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build-dev.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}' + curl -XPOST -u "${{secrets.PAT_USERNAME}}:${{secrets.PAT_TOKEN}}" -H "Accept: application/vnd.github.everest-preview+json" -H "Content-Type: application/json" https://api.github.com/repos/openMetadataInitiative/openMINDS/actions/workflows/build-dev.yml/dispatches --data '{"ref": "pipeline", "inputs": {"branch": "${{github.ref_name}}", "repository": "${{ github.repository }}"}}' From e61234cb34ba6af72827cd0836bdde19b7d7f2ee Mon Sep 17 00:00:00 2001 From: abonard Date: Mon, 26 Jan 2026 13:48:09 +0100 Subject: [PATCH 03/23] Add core:FIle to input in MRIAcquisition --- schemas/activity/MRIAcquisition.schema.tpl.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 5968032..3b975ec 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -17,7 +17,8 @@ "_instruction": "Add the state of the subject or tissue sample before this session.", "_linkedTypes": [ "core:SubjectState", - "core:TissueSampleState" + "core:TissueSampleState", + "core:File" ] }, "specimenOrientation": { From 61c88f6558a91d87722909deb3e17ae55c155284 Mon Sep 17 00:00:00 2001 From: abonard Date: Mon, 26 Jan 2026 13:48:38 +0100 Subject: [PATCH 04/23] Add output to MRIAcquisition --- schemas/activity/MRIAcquisition.schema.tpl.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 3b975ec..04642c5 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -26,6 +26,13 @@ "_linkedTypes": [ "controlledTerms:AnatomicalAxesOrientation" ] + }, + "output":{ + "_instruction": "Add the file generated during this session.", + "_linkedTypes": [ + "core:File" + ] + } }, "required": [ From 352d7192ea2b421c156af55b2caa5236e6cc4103 Mon Sep 17 00:00:00 2001 From: abonard Date: Mon, 26 Jan 2026 13:49:19 +0100 Subject: [PATCH 05/23] Update required with input, device, speciementOrientation and output in MRIAcquisition --- schemas/activity/MRIAcquisition.schema.tpl.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 04642c5..2b8bc0d 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -36,6 +36,9 @@ } }, "required": [ - "device" + "input", + "device", + "specimenOrientation", + "output" ] } From 74a77c2be03ed3bc1b10fe80bd8907d3cbe2b1f3 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Mon, 2 Feb 2026 12:55:34 +0100 Subject: [PATCH 06/23] Update schemas/activity/MRIAcquisition.schema.tpl.json Co-authored-by: Laura Morel <44158117+lauramble@users.noreply.github.com> --- schemas/activity/MRIAcquisition.schema.tpl.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 2b8bc0d..618bce9 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -36,9 +36,9 @@ } }, "required": [ - "input", "device", - "specimenOrientation", - "output" + "input", + "output", + "specimenOrientation" ] } From 19fe33076e85cab93913e655c297a3ef3b72ba8f Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Mon, 2 Feb 2026 12:58:50 +0100 Subject: [PATCH 07/23] Move required fields in MRIAcquisition schema --- schemas/activity/MRIAcquisition.schema.tpl.json | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 618bce9..1a4a6ba 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -1,5 +1,11 @@ { "_extends": "/core/schemas/research/experimentalActivity.schema.tpl.json", + "required": [ + "device", + "input", + "output", + "specimenOrientation" + ], "properties": { "contrastAgent": { "_instruction": "Add the contrast agent used for this scan.", @@ -34,11 +40,5 @@ ] } - }, - "required": [ - "device", - "input", - "output", - "specimenOrientation" - ] + } } From f8f62fd5af1a9bd8ba465b9904c207215b432ab6 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Mon, 2 Feb 2026 13:02:46 +0100 Subject: [PATCH 08/23] Reorder specimenOrientation and output fields in MRIAcquisition schema --- schemas/activity/MRIAcquisition.schema.tpl.json | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 1a4a6ba..1468632 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -27,18 +27,17 @@ "core:File" ] }, - "specimenOrientation": { - "_instruction": "Add the anatomical orientation of the specimen in the scanner.", - "_linkedTypes": [ - "controlledTerms:AnatomicalAxesOrientation" - ] - }, "output":{ "_instruction": "Add the file generated during this session.", "_linkedTypes": [ "core:File" ] - + }, + "specimenOrientation": { + "_instruction": "Add the anatomical orientation of the specimen in the scanner.", + "_linkedTypes": [ + "controlledTerms:AnatomicalAxesOrientation" + ] } } } From 05b2f4ebc28e7b056f4fb96310e1e6f8d0fd0c63 Mon Sep 17 00:00:00 2001 From: abonard Date: Tue, 17 Feb 2026 11:57:44 +0100 Subject: [PATCH 09/23] Remove file from input --- schemas/activity/MRIAcquisition.schema.tpl.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 1468632..521b88e 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -23,8 +23,7 @@ "_instruction": "Add the state of the subject or tissue sample before this session.", "_linkedTypes": [ "core:SubjectState", - "core:TissueSampleState", - "core:File" + "core:TissueSampleState" ] }, "output":{ From a208b13abbaa85d8a21bf1be4d882f60711a602c Mon Sep 17 00:00:00 2001 From: abonard Date: Tue, 17 Feb 2026 12:19:24 +0100 Subject: [PATCH 10/23] Add distortionCorrection, motionCorrection, registrationData --- .../activity/MRIAcquisition.schema.tpl.json | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json index 521b88e..df010f0 100644 --- a/schemas/activity/MRIAcquisition.schema.tpl.json +++ b/schemas/activity/MRIAcquisition.schema.tpl.json @@ -19,6 +19,14 @@ "neuroimaging:MRIScannerUsage" ] }, + "distortionCorrection": { + "_instruction": "Add the calibration file corresponding to images or field maps used for correction of inhomogeneities in B0 field of this acquisition.", + "_linkedTypes": [ + "core:File" + ], + "minItems": 1, + "type": "array" + }, "input": { "_instruction": "Add the state of the subject or tissue sample before this session.", "_linkedTypes": [ @@ -26,12 +34,24 @@ "core:TissueSampleState" ] }, + "motionCorrection": { + "_instruction": "Add the calibration file used for motion correction, corresponding to single-band reference image, for this volume.", + "_linkedTypes": [ + "core:File" + ] + }, "output":{ "_instruction": "Add the file generated during this session.", "_linkedTypes": [ "core:File" ] }, + "registrationData": { + "_instruction": "Add the registration file corresponding to structural MRI relevant for this acquisition.", + "_linkedTypes": [ + "core:File" + ] + }, "specimenOrientation": { "_instruction": "Add the anatomical orientation of the specimen in the scanner.", "_linkedTypes": [ From 4d0062babd73176b2b800dc3de05540ce043af15 Mon Sep 17 00:00:00 2001 From: abonard Date: Wed, 18 Feb 2026 03:47:24 +0100 Subject: [PATCH 11/23] Rename MRIAcquisition by staticMRIAcquisition --- ...ition.schema.tpl.json => staticMRIAcquisition.schema.tpl.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename schemas/activity/{MRIAcquisition.schema.tpl.json => staticMRIAcquisition.schema.tpl.json} (100%) diff --git a/schemas/activity/MRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json similarity index 100% rename from schemas/activity/MRIAcquisition.schema.tpl.json rename to schemas/activity/staticMRIAcquisition.schema.tpl.json From c5294785b71fbfe28771f6477dfd3ee16c14cc78 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:23:28 +0100 Subject: [PATCH 12/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index df010f0..2563215 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -8,7 +8,7 @@ ], "properties": { "contrastAgent": { - "_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.", "_linkedTypes": [ "chemicals:AmountOfChemical" ] From e6e08928d90057baf36206e0c73d75134bf96581 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:23:44 +0100 Subject: [PATCH 13/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 2563215..9ba6baf 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -14,7 +14,7 @@ ] }, "device": { - "_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.", "_linkedTypes": [ "neuroimaging:MRIScannerUsage" ] From 3898a707cc1444d2d6d1d9f814aeb9bd62559671 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:24:10 +0100 Subject: [PATCH 14/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 9ba6baf..bcc980e 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -20,7 +20,7 @@ ] }, "distortionCorrection": { - "_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.", "_linkedTypes": [ "core:File" ], From dce2b03579a250c19d2fbeda1c36658e53624145 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:24:18 +0100 Subject: [PATCH 15/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index bcc980e..a44c6d5 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -28,7 +28,7 @@ "type": "array" }, "input": { - "_instruction": "Add the state of the subject or tissue sample before this session.", + "_instruction": "Add the specimen (subject or tissue sample) in the physical and biological state in which it was scanned, referencing the corresponding specimen record at the time of imaging.", "_linkedTypes": [ "core:SubjectState", "core:TissueSampleState" From 6ea8691d75baa1ed6a9af572be41860574bf8401 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:24:26 +0100 Subject: [PATCH 16/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index a44c6d5..2a3d909 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -35,7 +35,7 @@ ] }, "motionCorrection": { - "_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.", "_linkedTypes": [ "core:File" ] From 77ea5cefdc2ab8edc8b29bcbbc73f876a45b643b Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:24:41 +0100 Subject: [PATCH 17/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 2a3d909..56e83fe 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -41,7 +41,7 @@ ] }, "output":{ - "_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.", "_linkedTypes": [ "core:File" ] From 8e7ede4fd5943883296d1a9eb2ebed30b7ab1797 Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:24:54 +0100 Subject: [PATCH 18/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 56e83fe..d07d993 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -47,7 +47,7 @@ ] }, "registrationData": { - "_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.", "_linkedTypes": [ "core:File" ] From 2713736c801245dfacdc7db243165e4ba8f3477e Mon Sep 17 00:00:00 2001 From: Alix Bonard <117838894+Alixbonard@users.noreply.github.com> Date: Fri, 20 Feb 2026 13:25:06 +0100 Subject: [PATCH 19/23] Apply suggestion from @lzehl Co-authored-by: Lyuba Zehl --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index d07d993..6758363 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -53,7 +53,7 @@ ] }, "specimenOrientation": { - "_instruction": "Add the anatomical orientation of the specimen in the scanner.", + "_instruction": "Add the specimen orientation as the anatomical directions corresponding to the scanner X, Y, and Z axes, describing the alignment of the specimen’s anatomy with the scanner coordinate system. Note that this orientation may differ from the prescribed slice orientation, especially in nonstandard specimen positioning.", "_linkedTypes": [ "controlledTerms:AnatomicalAxesOrientation" ] From debc4907c6af5aaf4e2a8cfb999a2998ed027d55 Mon Sep 17 00:00:00 2001 From: abonard Date: Fri, 20 Feb 2026 15:49:05 +0100 Subject: [PATCH 20/23] Add "type": "array" to contrastAgent, distortionCorrection, motionCorrection, registrationData --- .../staticMRIAcquisition.schema.tpl.json | 24 +++++++++++++++---- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 6758363..9cc8b65 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -11,7 +11,10 @@ "_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.", "_linkedTypes": [ "chemicals:AmountOfChemical" - ] + ], + "minItems": 1, + "type": "array", + "uniqueItems": true }, "device": { "_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.", @@ -25,7 +28,8 @@ "core:File" ], "minItems": 1, - "type": "array" + "type": "array", + "uniqueItems": true }, "input": { "_instruction": "Add the specimen (subject or tissue sample) in the physical and biological state in which it was scanned, referencing the corresponding specimen record at the time of imaging.", @@ -38,19 +42,29 @@ "_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.", "_linkedTypes": [ "core:File" - ] + ], + "minItems": 1, + "type": "array", + "uniqueItems": true }, "output":{ "_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.", "_linkedTypes": [ "core:File" - ] + ], + "minItems": 1, + "type": "array", + "uniqueItems": true }, "registrationData": { "_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.", "_linkedTypes": [ "core:File" - ] + ], + "minItems": 1, + "type": "array", + "uniqueItems": true + }, "specimenOrientation": { "_instruction": "Add the specimen orientation as the anatomical directions corresponding to the scanner X, Y, and Z axes, describing the alignment of the specimen’s anatomy with the scanner coordinate system. Note that this orientation may differ from the prescribed slice orientation, especially in nonstandard specimen positioning.", From 76098b55a3d6f7057a30559aadc2eb6da36299b0 Mon Sep 17 00:00:00 2001 From: abonard Date: Fri, 20 Feb 2026 15:49:25 +0100 Subject: [PATCH 21/23] Add targetAnatomy property --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 9cc8b65..879fa2f 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -71,6 +71,12 @@ "_linkedTypes": [ "controlledTerms:AnatomicalAxesOrientation" ] + }, + "targetAnatomy": { + "_instruction": "Add the target anatomy, indicating the primary anatomical structure or region intended to be imaged in this acquisition. This field describes the imaging objective (for example, organ, tissue, or structure) and may be derived from the acquisition protocol description.", + "_linkedCategories": [ + "anatomicalLocation" + ] } } } From 963742d76cd8e628156d0636db57ef76eb5ea242 Mon Sep 17 00:00:00 2001 From: abonard Date: Fri, 20 Feb 2026 16:40:17 +0100 Subject: [PATCH 22/23] fix typo --- schemas/activity/staticMRIAcquisition.schema.tpl.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/staticMRIAcquisition.schema.tpl.json index 879fa2f..90405b7 100644 --- a/schemas/activity/staticMRIAcquisition.schema.tpl.json +++ b/schemas/activity/staticMRIAcquisition.schema.tpl.json @@ -67,7 +67,7 @@ }, "specimenOrientation": { - "_instruction": "Add the specimen orientation as the anatomical directions corresponding to the scanner X, Y, and Z axes, describing the alignment of the specimen’s anatomy with the scanner coordinate system. Note that this orientation may differ from the prescribed slice orientation, especially in nonstandard specimen positioning.", + "_instruction": "Add the specimen orientation as the anatomical directions corresponding to the scanner X, Y, and Z axes, describing the alignment of the specimen's anatomy with the scanner coordinate system. Note that this orientation may differ from the prescribed slice orientation, especially in nonstandard specimen positioning.", "_linkedTypes": [ "controlledTerms:AnatomicalAxesOrientation" ] From 53963c725c8b732b6854cae5d302536a110fc2cc Mon Sep 17 00:00:00 2001 From: abonard Date: Fri, 20 Feb 2026 17:41:08 +0100 Subject: [PATCH 23/23] Rename MRIAcquisition instead of staticMRIAcquisition --- ...Acquisition.schema.tpl.json => MRIAcquisition.schema.tpl.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename schemas/activity/{staticMRIAcquisition.schema.tpl.json => MRIAcquisition.schema.tpl.json} (100%) diff --git a/schemas/activity/staticMRIAcquisition.schema.tpl.json b/schemas/activity/MRIAcquisition.schema.tpl.json similarity index 100% rename from schemas/activity/staticMRIAcquisition.schema.tpl.json rename to schemas/activity/MRIAcquisition.schema.tpl.json