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lzehllzehl
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Merge pull request #5 from Raphael-Gazzotti/v2
Removal of namespace in schema files.
2 parents 6d6d871 + b153a90 commit 84192c0

10 files changed

+47
-47
lines changed

‎schemas/activity/MRIAcquisition.schema.tpl.json

+5-5
Original file line numberDiff line numberDiff line change
@@ -4,26 +4,26 @@
44
"contrastAgent": {
55
"_instruction": "Add the contrast agent used for this scan.",
66
"_linkedTypes": [
7-
"https://openminds.ebrains.eu/chemicals/AmountOfChemical"
7+
"chemicals:AmountOfChemical"
88
]
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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": [
13-
"https://openminds.ebrains.eu/neuroimaging/MRIScannerUsage"
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"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": [
19-
"https://openminds.ebrains.eu/core/SubjectState",
20-
"https://openminds.ebrains.eu/core/TissueSampleState"
19+
"core:SubjectState",
20+
"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": [
26-
"https://openminds.ebrains.eu/controlledTerms/AnatomicalAxesOrientation"
26+
"controlledTerms:AnatomicalAxesOrientation"
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]
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}
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},

‎schemas/activity/functionalMRIAcquisition.schema.tpl.json

+9-9
Original file line numberDiff line numberDiff line change
@@ -1,38 +1,38 @@
11
{
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"_extends": "activity/MRIAcquisition.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/FunctionalMRIAcquisition",
3+
"_type": "neuroimaging:FunctionalMRIAcquisition",
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"properties": {
55
"acquisitionDuration": {
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"_embeddedTypes": [
7-
"https://openminds.ebrains.eu/core/QuantitativeValue"
7+
"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": [
14-
"https://openminds.ebrains.eu/core/BehavioralProtocol"
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"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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"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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"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": [
35-
"https://openminds.ebrains.eu/core/File"
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"core:File"
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],
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"minItems": 1,
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"type": "array"
@@ -44,19 +44,19 @@
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"sbref": {
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"_instruction": "Add the single-band reference image for this volume.",
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"_linkedTypes": [
47-
"https://openminds.ebrains.eu/core/File"
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"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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"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": [
59-
"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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"core:QuantitativeValueArray"
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]
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}
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}

‎schemas/activity/structuralMRIAcquisition.schema.tpl.json

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
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{
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"_extends": "activity/MRIAcquisition.schema.tpl.json",
3-
"_type": "https://openminds.ebrains.eu/neuroimaging/StructuralMRIAcquisition"
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"_type": "neuroimaging:StructuralMRIAcquisition"
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}

‎schemas/device/MRIScanner.schema.tpl.json

+2-2
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
{
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"_extends": "/core/schemas/products/device.schema.tpl.json",
3-
"_type": "https://openminds.ebrains.eu/neuroimaging/MRIScanner",
3+
"_type": "neuroimaging:MRIScanner",
44
"properties": {
55
"magneticFieldStrength": {
66
"_embeddedTypes": [
7-
"https://openminds.ebrains.eu/core/QuantitativeValue"
7+
"core:QuantitativeValue"
88
],
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"_instruction": "Enter the nominal field strength of MR magnet in Tesla."
1010
}

‎schemas/device/MRIScannerUsage.schema.tpl.json

+17-17
Original file line numberDiff line numberDiff line change
@@ -1,28 +1,28 @@
11
{
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"_extends": "/core/schemas/research/deviceUsage.schema.tpl.json",
3-
"_type": "https://openminds.ebrains.eu/neuroimaging/MRIScannerUsage",
3+
"_type": "neuroimaging:MRIScannerUsage",
44
"properties": {
55
"bValues": {
66
"_instruction": "Add the b values coresponding to this aquisition.",
77
"_linkedTypes": [
8-
"https://openminds.ebrains.eu/core/File"
8+
"core:File"
99
]
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},
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"bVectors": {
1212
"_instruction": "Add the b vectors coresponding to this aquisition.",
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"_linkedTypes": [
14-
"https://openminds.ebrains.eu/core/File"
14+
"core:File"
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]
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},
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"dwellTime": {
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"_embeddedTypes": [
19-
"https://openminds.ebrains.eu/core/QuantitativeValue"
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"core:QuantitativeValue"
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],
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"_instruction": "Enter the dewell time of this aquistion."
2222
},
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"echoTime": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
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"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,
@@ -37,27 +37,27 @@
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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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"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": [
46-
"https://openminds.ebrains.eu/core/QuantitativeValue",
47-
"https://openminds.ebrains.eu/core/QuantitativeValueRange"
46+
"core:QuantitativeValue",
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"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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"inversionTime": {
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"_embeddedTypes": [
53-
"https://openminds.ebrains.eu/core/QuantitativeValue"
53+
"core:QuantitativeValue"
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],
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"_instruction": "Enter the inversion time of this aquistion."
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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": [
60-
"https://openminds.ebrains.eu/controlledTerms/MRAcquisitionType"
60+
"controlledTerms:MRAcquisitionType"
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]
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},
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"mTState": {
@@ -79,37 +79,37 @@
7979
"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": [
82-
"https://openminds.ebrains.eu/controlledTerms/CartesianDirectionVector"
82+
"controlledTerms:CartesianDirectionVector"
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]
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},
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"pulseSequenceType": {
8686
"_instruction": "Add the type pulse sequence used for this scan.",
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"_linkedTypes": [
88-
"https://openminds.ebrains.eu/controlledTerms/MRIPulseSequence"
88+
"controlledTerms:MRIPulseSequence"
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]
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},
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"radiofrequencyCoilType": {
9292
"_instruction": "Add the type of radiofrequency coil.",
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"_linkedTypes": [
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"https://openminds.ebrains.eu/controlledTerms/MRIRadiofrequencyCoilType"
94+
"controlledTerms:MRIRadiofrequencyCoilType"
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]
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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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"core:QuantitativeValue"
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],
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"_instruction": "Enter the echo time of this aquisition (TR)."
102102
},
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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"
106+
"core:QuantitativeValueArray"
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]
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},
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"sliceTiming": {
110110
"_instruction": "Enter the time in which each slice have been aquired within each volume.",
111111
"_linkedTypes": [
112-
"https://openminds.ebrains.eu/core/QuantitativeValueArray"
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"core:QuantitativeValueArray"
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]
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},
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"spoilingState": {
@@ -118,7 +118,7 @@
118118
},
119119
"voxelSize": {
120120
"_embeddedTypes": [
121-
"https://openminds.ebrains.eu/core/QuantitativeValueArray"
121+
"core:QuantitativeValueArray"
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],
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"_instruction": "Enter voxel size this image: in this order x,y,z."
124124
}

‎schemas/entity/image.schema.tpl.json

+4-4
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@@ -1,5 +1,5 @@
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{
2-
"_type": "https://openminds.ebrains.eu/neuroimaging/Image",
2+
"_type": "neuroimaging:Image",
33
"properties": {
44
"additionalRemarks": {
55
"_instruction": "Enter any additional remarks concerning this image.",
@@ -13,7 +13,7 @@
1313
},
1414
"colorDepth": {
1515
"_embeddedTypes": [
16-
"https://openminds.ebrains.eu/core/QuantitativeValue"
16+
"core:QuantitativeValue"
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],
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"_instruction": "Enter the number of bits used to represent the color of each pixel."
1919
},
@@ -26,7 +26,7 @@
2626
"dataLocation": {
2727
"_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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"core:File"
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]
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},
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"dimension": {
@@ -44,7 +44,7 @@
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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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"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,

‎schemas/entity/imageSequence.schema.tpl.json

+2-2
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@@ -1,6 +1,6 @@
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{
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"_extends": "entity/image.schema.tpl.json",
3-
"_type": "https://openminds.ebrains.eu/neuroimaging/ImageSequence",
3+
"_type": "neuroimaging:ImageSequence",
44
"properties": {
55
"numberOfImages": {
66
"_instruction": "Enter the total number of images in this sequence (at least two).",
@@ -9,7 +9,7 @@
99
},
1010
"temporalResolution": {
1111
"_embeddedTypes": [
12-
"https://openminds.ebrains.eu/core/QuantitativeValue"
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"core:QuantitativeValue"
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],
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"_instruction": "Enter the temporal resolution of this sequence."
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}

‎schemas/entity/imageStack.schema.tpl.json

+2-2
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@@ -1,6 +1,6 @@
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{
22
"_extends": "entity/image.schema.tpl.json",
3-
"_type": "https://openminds.ebrains.eu/neuroimaging/ImageStack",
3+
"_type": "neuroimaging:ImageStack",
44
"properties": {
55
"numberOfImages": {
66
"_instruction": "Enter the total number of images in this stack (at least two).",
@@ -9,7 +9,7 @@
99
},
1010
"sliceThickness": {
1111
"_embeddedTypes": [
12-
"https://openminds.ebrains.eu/core/QuantitativeValue"
12+
"core:QuantitativeValue"
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],
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"_instruction": "Enter the thickness of each image slice in the stack."
1515
}

‎schemas/entity/volume.schema.tpl.json

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@@ -1,5 +1,5 @@
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{
2-
"_type": "https://openminds.ebrains.eu/neuroimaging/Volume",
2+
"_type": "neuroimaging:Volume",
33
"properties": {
44
"additionalRemarks": {
55
"_instruction": "Enter any additional remarks concerning this volume.",
@@ -21,7 +21,7 @@
2121
"dataLocation": {
2222
"_instruction": "Add the location of the file or file bundle in which the volume is stored.",
2323
"_linkedTypes": [
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"https://openminds.ebrains.eu/core/File"
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"core:File"
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]
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},
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"dimension": {
@@ -43,7 +43,7 @@
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},
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"voxelSize": {
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"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
46+
"core:QuantitativeValue"
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],
4848
"_instruction": "Enter the physical voxel size for this image (in x,y,z order).",
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"maxItems": 3,

‎schemas/entity/volumeSequence.schema.tpl.json

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{
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"_extends": "entity/volume.schema.tpl.json",
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"_type": "https://openminds.ebrains.eu/neuroimaging/VolumeSequence",
3+
"_type": "neuroimaging:VolumeSequence",
44
"properties": {
55
"numberOfVolumes": {
66
"_instruction": "Enter the total number of volumes in this volume sequence (at least two).",
@@ -9,7 +9,7 @@
99
},
1010
"temporalResolution": {
1111
"_embeddedTypes": [
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"https://openminds.ebrains.eu/core/QuantitativeValue"
12+
"core:QuantitativeValue"
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],
1414
"_instruction": "Enter the temporal resolution of this sequence."
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}

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