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Add example dataset for MRI chunk entity
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valosekj committed Aug 29, 2023
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2 changes: 2 additions & 0 deletions mri_chunk/README.md
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Example dataset with empty images containing magnetic resonance imaging (MRI) data to illustrate BIDS chunk entity.
The dataset contains a T2w image from a single subject. T2w image has two chunks -- brain and spinal cord.
9 changes: 9 additions & 0 deletions mri_chunk/dataset_description.json
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{
"Name": "mri_chunk",
"Authors": [
"Jan Valosek",
"Julien Cohen-Adad"
],
"BIDSVersion": "BIDS 1.8.0",
"DatasetType": "raw"
}
6 changes: 6 additions & 0 deletions mri_chunk/participants.json
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{
"participant_id": {
"Description": "Unique Participant ID",
"LongName": "Participant ID"
}
}
2 changes: 2 additions & 0 deletions mri_chunk/participants.tsv
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participant_id
sub-001
69 changes: 69 additions & 0 deletions mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json
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{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.197,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Verio",
"PatientPosition": "HFS",
"ProcedureStepDescription": "TEST_VC^SPINE",
"SoftwareVersions": "syngo MR B17",
"MRAcquisitionType": "3D",
"SeriesDescription": "SC_tse_spc_1mm_3palliers_fov256_nopat",
"ProtocolName": "SC_tse_spc_1mm_3palliers_fov256_nopat_1",
"ScanningSequence": "SE",
"SequenceVariant": "SK\\SP\\OSP",
"ScanOptions": "PFP",
"SequenceName": "*spcR3d1_103",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"],
"NonlinearGradientCorrection": true,
"SeriesNumber": 8,
"AcquisitionTime": "10:33:32.162500",
"AcquisitionNumber": 1,
"SliceThickness": 1,
"SAR": 0.269146,
"NumberOfAverages": 2,
"EchoTime": 0.124,
"RepetitionTime": 1.5,
"SpoilingState": true,
"FlipAngle": 110,
"AveragesDouble": 1.4,
"PartialFourier": 1,
"BaseResolution": 256,
"ShimSetting": [
-5956,
12936,
-12143,
-17,
-26,
51,
158,
-40 ],
"TxRefAmp": 491.928,
"PhaseResolution": 1.0098,
"PhaseOversampling": 0.197917,
"ReceiveCoilName": "NeckMatrix",
"CoilString": "C:HEP;NE1,2",
"PulseSequenceDetails": "%SiemensSeq%\\tse_vfl",
"CoilCombinationMethod": "Adaptive Combine",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100.98,
"EchoTrainLength": 103,
"PhaseEncodingSteps": 237,
"AcquisitionMatrixPE": 259,
"ReconMatrixPE": 256,
"PixelBandwidth": 610,
"DwellTime": 3.2e-06,
"PhaseEncodingDirection": "j-",
"ImageOrientationPatientDICOM": [
0,
1,
-2.05103e-10,
0,
-2.05103e-10,
-1 ],
"ImageOrientationText": "Sag",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720"
}
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69 changes: 69 additions & 0 deletions mri_chunk/sub-001/anat/sub-001_chunk-2_T1w.json
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{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.197,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Verio",
"PatientPosition": "HFS",
"ProcedureStepDescription": "TEST_VC^SPINE",
"SoftwareVersions": "syngo MR B17",
"MRAcquisitionType": "3D",
"SeriesDescription": "SC_tse_spc_1mm_3palliers_fov256_nopat",
"ProtocolName": "SC_tse_spc_1mm_3palliers_fov256_nopat_2",
"ScanningSequence": "SE",
"SequenceVariant": "SK\\SP\\OSP",
"ScanOptions": "PFP",
"SequenceName": "*spcR3d1_103",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"],
"NonlinearGradientCorrection": true,
"SeriesNumber": 9,
"AcquisitionTime": "10:40:6.177500",
"AcquisitionNumber": 1,
"SliceThickness": 1,
"SAR": 0.978482,
"NumberOfAverages": 2,
"EchoTime": 0.124,
"RepetitionTime": 1.5,
"SpoilingState": true,
"FlipAngle": 110,
"AveragesDouble": 1.4,
"PartialFourier": 1,
"BaseResolution": 256,
"ShimSetting": [
-5956,
12936,
-12143,
-17,
-26,
51,
158,
-40 ],
"TxRefAmp": 491.928,
"PhaseResolution": 1.0098,
"PhaseOversampling": 0.197917,
"ReceiveCoilName": "NeckMatrix",
"CoilString": "C:NE1,2;SP1,2",
"PulseSequenceDetails": "%SiemensSeq%\\tse_vfl",
"CoilCombinationMethod": "Adaptive Combine",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100.98,
"EchoTrainLength": 103,
"PhaseEncodingSteps": 237,
"AcquisitionMatrixPE": 259,
"ReconMatrixPE": 256,
"PixelBandwidth": 610,
"DwellTime": 3.2e-06,
"PhaseEncodingDirection": "j-",
"ImageOrientationPatientDICOM": [
0,
1,
-2.05103e-10,
0,
-2.05103e-10,
-1 ],
"ImageOrientationText": "Sag",
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220720"
}
Binary file added mri_chunk/sub-001/anat/sub-001_chunk-2_T1w.nii.gz
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