From 05faf641cc377a5fa5d4c333bc305a6ca181e8bb Mon Sep 17 00:00:00 2001 From: valosekj Date: Tue, 29 Aug 2023 13:28:14 -0400 Subject: [PATCH] Add example dataset for MRI chunk entity --- mri_chunk/README.md | 2 + mri_chunk/dataset_description.json | 9 +++ mri_chunk/participants.json | 6 ++ mri_chunk/participants.tsv | 2 + .../sub-001/anat/sub-001_chunk-1_T1w.json | 69 ++++++++++++++++++ .../sub-001/anat/sub-001_chunk-1_T1w.nii.gz | Bin 0 -> 29936 bytes .../sub-001/anat/sub-001_chunk-2_T1w.json | 69 ++++++++++++++++++ .../sub-001/anat/sub-001_chunk-2_T1w.nii.gz | Bin 0 -> 29939 bytes 8 files changed, 157 insertions(+) create mode 100644 mri_chunk/README.md create mode 100644 mri_chunk/dataset_description.json create mode 100644 mri_chunk/participants.json create mode 100644 mri_chunk/participants.tsv create mode 100644 mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json create mode 100644 mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.nii.gz create mode 100644 mri_chunk/sub-001/anat/sub-001_chunk-2_T1w.json create mode 100644 mri_chunk/sub-001/anat/sub-001_chunk-2_T1w.nii.gz diff --git a/mri_chunk/README.md b/mri_chunk/README.md new file mode 100644 index 000000000..64341e36b --- /dev/null +++ b/mri_chunk/README.md @@ -0,0 +1,2 @@ +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. diff --git a/mri_chunk/dataset_description.json b/mri_chunk/dataset_description.json new file mode 100644 index 000000000..0928a2c0e --- /dev/null +++ b/mri_chunk/dataset_description.json @@ -0,0 +1,9 @@ +{ + "Name": "mri_chunk", + "Authors": [ + "Jan Valosek", + "Julien Cohen-Adad" + ], + "BIDSVersion": "BIDS 1.8.0", + "DatasetType": "raw" +} diff --git a/mri_chunk/participants.json b/mri_chunk/participants.json new file mode 100644 index 000000000..71cdaefa2 --- /dev/null +++ b/mri_chunk/participants.json @@ -0,0 +1,6 @@ +{ + "participant_id": { + "Description": "Unique Participant ID", + "LongName": "Participant ID" + } +} diff --git a/mri_chunk/participants.tsv b/mri_chunk/participants.tsv new file mode 100644 index 000000000..c8f899b83 --- /dev/null +++ b/mri_chunk/participants.tsv @@ -0,0 +1,2 @@ +participant_id +sub-001 \ No newline at end of file diff --git a/mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json b/mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json new file mode 100644 index 000000000..644ed1d20 --- /dev/null +++ b/mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json @@ -0,0 +1,69 @@ +{ + "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": 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