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* peyman-main: (69 commits) deleting MRIScannerUsageForDiffusion deleting b0 and asl _extends correction for _extends correction for extending adding tpl Update MRIScannerUsageForDiffusion.schema.tpl.json subjectOrientation Lyuba's feedback correction for space renaming to neuroimaging Forgotten Array meeting 2024-07-01 correction for linked types before meeting 27-05 Meeting 2024/05/13 Homogenizing the required fieldOfView to Categories numberOfVolumes required sorting FunctionalMRI ...
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‎CONTRIBUTING.md

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# How to contribute
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The openMINDS metadata framework is an open-source project and community contributions are highly appreciated.
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If you want to contribute please follow our :arrow_right: [**contribution guidelines**][contribution-url].
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<!-- MARKDOWN LINKS & IMAGES -->
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<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
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[contribution-url]: https://openminds-documentation.readthedocs.io/en/latest/shared/how_to_contribute.html

‎LICENSE

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MIT License
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Copyright (c) 2021 Human Brain Project
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Copyright (c) 2021, 2022 CNRS, Forschungszentrum Jülich GmbH, Universitetet i Oslo, EBRAINS AISBL
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎README.md

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# openMINDS_MRI
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A metadata model for MRI experiments; an openMINDS extension
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<a href="/img/openMINDS_MRI_logo_light.png">
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<picture>
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<source media="(prefers-color-scheme: dark)" srcset="/img/openMINDS_MRI_logo_dark.png">
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<source media="(prefers-color-scheme: light)" srcset="/img/openMINDS_MRI_logo_light.png">
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<img alt="openMINDS_MRI metadata model" src="/img/openMINDS_MRI_logo_light.png" title="Logo created by U. Schlegel, L. Zehl, C. Hagen Blixhavn" align="right" height="70">
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</picture>
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</a>
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# openMINDS_core
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[![GitHub][license-shield]][license-url]
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[![GitHub contributors][contributors-shield]][contributors-url]
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The **openMINDS_MRI** repository hosts one of the metadata models of the **openMINDS metadata framework**. It defines modular metadata schemas for describing magnetic resonance imaging (MRI) experiments.
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To generally learn more about the openMINDS metadata framework please go to :arrow_right: [**ReadTheDocs**][docu-url].
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Or explore directly the metadata schemas of the openMINDS_MRI metadata model under :arrow_right: [**schema specifications**][docu-MRI-url].
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## How to contribute
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The openMINDS metadata framework is an open-source project and community contributions are highly appreciated.
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If you want to contribute please follow our :arrow_right: [**contribution guidelines**][contribution-url].
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<!-- MARKDOWN LINKS & IMAGES -->
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<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
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[contribution-url]: https://openminds-documentation.readthedocs.io/en/latest/shared/contribution_guidelines.html
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[contributors-url]: https://github.com/openMetadataInitiative/openMINDS_MRI/graphs/contributors
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[contributors-shield]: https://img.shields.io/github/contributors/openMetadataInitiative/openMINDS_MRI
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[docu-url]: https://openminds-documentation.readthedocs.io
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[docu-MRI-url]: https://openminds-documentation.readthedocs.io/en/v3.0/schema_specifications/mri.html
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[license-url]: https://raw.githubusercontent.com/openMetadataInitiative/openMINDS_MRI/v1/LICENSE
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[license-shield]: https://img.shields.io/github/license/openMetadataInitiative/openMINDS_MRI

‎schemas/activity/MRIAcquisition.schema.tpl.json

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{
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"_extends": "/core/schemas/research/ExperimentalActivity.schema.tpl.json",
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"properties": {
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"contrastAgent": {
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"_instruction": "Add the contrast agent used for this scan.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/chemicals/AmountOfChemical"
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]
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},
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"device": {
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"_instruction": "Add the MRI machine setting used for this scan.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/neuroimaging/MRIScannerUsage"
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]
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},
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"input": {
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"_instruction": "Add the state of the subject or tissue sample before this session.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/SubjectState",
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"https://openminds.ebrains.eu/core/TissueSampleState"
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]
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},
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"specimenOrientation": {
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"_instruction": "Add the anatomical orientation of the specimen in the scanner.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation"
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]
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}
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},
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"required": [
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"device"
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]
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}

‎schemas/activity/functionalMRIAcquisition.schema.tpl.json

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{
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"_extends": "activity/MRIAcquisition.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/FunctionalMRIAcquisition",
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"properties": {
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"acquisitionDuration": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter duration of volume acquisition."
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},
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"behavioralProtocol": {
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"_instruction": "Add all behavioral protocols that were performed during this session.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/BehavioralProtocol"
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],
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"minItems": 1,
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"type": "array",
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"uniqueItems": true
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},
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"delayAfterTrigger": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the duration from trigger delivery to scan onset (only the first volum)."
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},
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"delayTime": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the arbitrary delay time set by user before each volume acquisition."
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},
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"fieldMap": {
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"_instruction": "Add the images or field maps used for correction of inhemogenties in B0 field of this aquisition.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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],
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"minItems": 1,
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"type": "array"
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},
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"numberOfVolumesDiscardedByUser": {
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"_instruction": "Enter number of volumes discarded by user before the first volume.",
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"type": "number"
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},
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"repetitionTime": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the echo time of this aquisition (TR)."
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},
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"sbref": {
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"_instruction": "Add the single-band reference image for this volume.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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]
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},
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"structuralMRI": {
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"_instruction": "Add the structural MRI relavent for this aquisition.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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]
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},
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"volumeTiming": {
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"_instruction": "Enter aquisition times of each vloume.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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]
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}
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}
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}

‎schemas/activity/structuralMRIAcquisition.schema.tpl.json

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{
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"_extends": "activity/MRIAcquisition.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/StructuralMRIAcquisition"
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}

‎schemas/device/MRIScanner.schema.tpl.json

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{
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"_extends": "/core/schemas/products/device.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/MRIScanner",
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"properties": {
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"magneticFieldStrength": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the nominal field strength of MR magnet in Tesla."
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}
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}
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}

‎schemas/device/MRIScannerUsage.schema.tpl.json

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{
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"_extends": "/core/schemas/research/deviceUsage.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/MRIScannerUsage",
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"properties": {
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"bValues": {
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"_instruction": "Add the b values coresponding to this aquisition.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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]
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},
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"bVectors": {
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"_instruction": "Add the b vectors coresponding to this aquisition.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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]
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},
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"dwellTime": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the dewell time of this aquistion."
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},
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"echoTime": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the echo times of this aquisition (TE).",
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"minItems": 1,
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"type": "array",
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"uniqueItems": true
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},
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"fieldOfView": {
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"_instruction": "Add the field of view of this image.",
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"_linkedCategories": [
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"mathematicalShapes"
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]
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},
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"flipAngle": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the flip angle of this scan (preferred units: degrees)."
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},
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"interSliceGap": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue",
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"https://openminds.ebrains.eu/core/QuantitativeValueRange"
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],
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"_instruction": "Enter the inter slice distance of this scan."
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},
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"mRAcquisitionType": {
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"_instruction": "Add the type of sequence readout (2D or 3D).",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/MRAcquisitionType"
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]
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},
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"mTState": {
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"_instruction": "Boolean stating whether the magnetization transfer pulse is applied.",
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"type": "boolean"
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},
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"nonlinearGradientCorrection": {
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"_instruction": "Has this scan, been corrected for gradient nonlinearities by the scanner sequence?",
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"type": "boolean"
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},
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"numberOfVolumesDiscardedByScanner": {
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"_instruction": "Enter number of volumes discarded by scanner before the first volume.",
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"type": "number"
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},
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"parallelAcquisitionTechnique": {
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"_ instruction": "Enter the parallel acquisition technique sequance name for this scan. 'GRAPPA' for most Siemens machines and 'SENSE' for most Philips machines.",
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"type": "string"
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},
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"phaseEncodingDirection": {
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"_instruction": "Add the direction along which phase is modulated which may result in visible distortions.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/CartesianDirectionVector"
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]
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},
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"pulseSequenceType": {
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"_instruction": "Add the type pulse sequence used for this scan.",
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"_linkedType": [
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"https://openminds.ebrains.eu/controlledTerms/MRIPulseSequence"
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]
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},
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"radiofrequencyCoilType": {
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"_instruction": "Add the type of radiofrequency coil.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/MRIRadiofrequencyCoilType"
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]
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},
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"sliceOrder": {
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"_instruction": "Enter the time in which each slice have been aquired within each volume.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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]
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},
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"sliceThickness": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue",
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"https://openminds.ebrains.eu/core/QuantitativeValueRange"
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],
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"_instruction": "Enter the slice thickness of this MR image."
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},
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"sliceTiming": {
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"_instruction": "Enter the time in which each slice have been aquired within each volume.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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]
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},
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"spoilingState": {
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"_instruction": "Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.",
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"type": "boolean"
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},
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"voxelSize": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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],
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"_instruction": "Enter voxel size this image: in this order x,y,z."
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}
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}
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}

‎schemas/entity/image.schema.tpl.json

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{
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"_type": "https://openminds.ebrains.eu/neuroimaging/Image",
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"properties": {
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"additionalRemarks": {
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"_instruction": "Enter any additional remarks concerning this image.",
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"type": "string"
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},
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"capturedWith": {
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"_instruction": "Add the device used to captured this image.",
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"_linkedCategories": [
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"deviceUsage"
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]
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},
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"colorDepth": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the number of bits used to represent the color of each pixel."
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},
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"coordinateSpace": {
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"_instruction": "Add the coordinate space in which this image exists.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/sands/CustomCoordinateSpace"
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]
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},
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"dataLocation": {
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"_instruction": "Add the location of the file or file bundle in which the image is stored.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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]
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},
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"dimension": {
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"_instruction": "Enter the dimension of this image in pixels.",
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"items": {
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"type": "integer"
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},
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"maxItems": 2,
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"minItems": 2,
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"type": "array"
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},
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"name": {
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"_instruction": "Enter a descriptive name for this image.",
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"type": "string"
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},
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"pixelSize": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the physical pixel size for this image (in x,y order).",
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"maxItems": 2,
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"minItems": 2,
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"type": "array"
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}
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},
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"required": [
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"dataLocation",
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"pixelSize",
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"dimension",
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"coordinateSpace"
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]
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}

‎schemas/entity/imageSequence.schema.tpl.json

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{
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"_extends": "entity/image.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/ImageSequence",
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"properties": {
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"numberOfImages": {
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"_instruction": "Enter the total number of images in this sequence (at least two).",
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"minimum": 2,
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"type": "integer"
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},
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"temporalResolution": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the temporal resolution of this sequence."
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}
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},
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"required": [
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"numberOfImages"
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]
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}

‎schemas/entity/imageStack.schema.tpl.json

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{
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"_extends": "entity/image.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/ImageStack",
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"properties": {
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"numberOfImages": {
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"_instruction": "Enter the total number of images in this stack (at least two).",
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"minimum": 2,
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"type": "integer"
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},
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"sliceThickness": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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],
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"_instruction": "Enter the thickness of each image slice in the stack."
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}
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},
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"required": [
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"numberOfImages"
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]
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}

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