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Add Siemens 2D MB PCASL example #466

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merged 7 commits into from
Nov 5, 2024
Merged

Add Siemens 2D MB PCASL example #466

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31cfaee
Add Siemens 2D MB PCASL example
aptinis Aug 30, 2024
6215176
Add CITATION to suffixes to remove in dataset listing script
aptinis Aug 30, 2024
a54b674
Update docs for 2d_mb_pcasl
aptinis Aug 30, 2024
6e79b9e
Use schema from bids-standard/bids-specification#1884
effigies Aug 30, 2024
1784711
Update .github/workflows/validate_datasets.yml
effigies Sep 5, 2024
6de210a
Merge branch 'master' into add-2d-mb-pcasl
effigies Nov 5, 2024
d21a4e9
Merge branch 'master' into add-2d-mb-pcasl
effigies Nov 5, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/validate_datasets.yml
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Expand Up @@ -111,4 +111,4 @@ jobs:
env:
# When proposing new features, schema changes may be necessary.
# Update this URL to the schema.json from PRs to the spec, when needed.
BIDS_SCHEMA: https://bids-specification.readthedocs.io/en/latest/schema.json
BIDS_SCHEMA: https://bids-specification--1884.org.readthedocs.build/en/1884/schema.json
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unrelated to this PR but this little 'trick' to test a version of the schema related to a PR in the spec should be mentioned in our doc, so that BEP leads know how to start testing their datasets

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#1864 was merged so this PR should be updated

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1 change: 1 addition & 0 deletions 2d_mb_pcasl/README
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This dataset is an example of the Siemens 2D MultiBand Multi-delay PCASL sequence with noRF and m0 volumes included within the timeseries (HCP Aging ASL sequence). It also contains corresponding PEPOLAR fmaps and a T1w scan.
10 changes: 10 additions & 0 deletions 2d_mb_pcasl/dataset_description.json
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{
"Name": "ASL_Siemens_MultiPLD_2DMB_PCASL",
"BIDSVersion": "1.9.0",
"DatasetType": "raw",
"Authors": [
"Ashley Ptinis",
"Nicole Coverdale"
],
"HowToAcknowledge": "If you reference this dataset in your publications, please acknowledge its authors."
}
74 changes: 74 additions & 0 deletions 2d_mb_pcasl/sub-1/anat/sub-1_T1w.json
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{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.249,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "3D",
"SeriesDescription": "T1w_MPR",
"ProtocolName": "T1w_MPR",
"ScanningSequence": "GR\\IR",
"SequenceVariant": "SK\\SP\\MP",
"ScanOptions": "IR\\WE",
"SequenceName": "*tfl3d1_16ns",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"NORM"
],
"SeriesNumber": 3,
"AcquisitionNumber": 1,
"SliceThickness": 0.8,
"SAR": 0.042424,
"EchoTime": 0.00222,
"RepetitionTime": 2.5,
"SpoilingState": true,
"InversionTime": 1,
"FlipAngle": 8,
"PartialFourier": 1,
"BaseResolution": 320,
"ShimSetting": [
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],
"TxRefAmp": 252.904,
"PhaseResolution": 1,
"ReceiveCoilName": "Head_32",
"ReceiveCoilActiveElements": "HEA;HEP",
"PulseSequenceDetails": "%SiemensSeq%\\tfl",
"RefLinesPE": 32,
"CoilCombinationMethod": "Adaptive Combine",
"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
"MatrixCoilMode": "GRAPPA",
"PercentPhaseFOV": 93.75,
"PercentSampling": 100,
"PhaseEncodingSteps": 299,
"AcquisitionMatrixPE": 300,
"ReconMatrixPE": 300,
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"DwellTime": 7.1e-06,
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"ImageOrientationText": "Sag",
"InPlanePhaseEncodingDirectionDICOM": "ROW",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20211006"
}
Empty file added 2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz
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144 changes: 144 additions & 0 deletions 2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json
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{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.249,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "PCASLhr_SpinEchoFieldMap_AP",
"ProtocolName": "PCASLhr_SpinEchoFieldMap_AP",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "PFP\\FS",
"SequenceName": "epse2d1_86",
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"ND",
"MOSAIC"
],
"SeriesNumber": 41,
"AcquisitionNumber": 1,
"SliceThickness": 2.27,
"SpacingBetweenSlices": 2.497,
"SAR": 0.135571,
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"ReceiveCoilName": "Head_32",
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"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
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"EchoTrainLength": 65,
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"AcquisitionMatrixPE": 86,
"ReconMatrixPE": 86,
"BandwidthPerPixelPhaseEncode": 20.4,
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"ConversionSoftwareVersion": "v1.0.20211006",
"B0FieldIdentifier": "pepolar_b0s",
"IntendedFor": [
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]
}
Empty file added 2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.nii.gz
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144 changes: 144 additions & 0 deletions 2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.json
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@@ -0,0 +1,144 @@
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.249,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"BodyPartExamined": "BRAIN",
"PatientPosition": "HFS",
"SoftwareVersions": "syngo MR E11",
"MRAcquisitionType": "2D",
"SeriesDescription": "PCASLhr_SpinEchoFieldMap_PA",
"ProtocolName": "PCASLhr_SpinEchoFieldMap_PA",
"ScanningSequence": "EP",
"SequenceVariant": "SK",
"ScanOptions": "PFP\\FS",
"SequenceName": "epse2d1_86",
"ImageType": [
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"PRIMARY",
"M",
"ND",
"MOSAIC"
],
"SeriesNumber": 42,
"AcquisitionNumber": 1,
"SliceThickness": 2.27,
"SpacingBetweenSlices": 2.497,
"SAR": 0.135571,
"EchoTime": 0.04,
"RepetitionTime": 8,
"FlipAngle": 90,
"PartialFourier": 0.75,
"BaseResolution": 86,
"ShimSetting": [
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"TxRefAmp": 252.904,
"PhaseResolution": 1,
"VendorReportedEchoSpacing": 0.00057,
"ReceiveCoilName": "Head_32",
"ReceiveCoilActiveElements": "HEA;HEP",
"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
"CoilCombinationMethod": "Sum of Squares",
"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
"MatrixCoilMode": "SENSE",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"EchoTrainLength": 65,
"PhaseEncodingSteps": 65,
"AcquisitionMatrixPE": 86,
"ReconMatrixPE": 86,
"BandwidthPerPixelPhaseEncode": 20.4,
"EffectiveEchoSpacing": 0.000569995,
"DerivedVendorReportedEchoSpacing": 0.000569995,
"TotalReadoutTime": 0.0484496,
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"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20211006",
"B0FieldIdentifier": "pepolar_b0s",
"IntendedFor": [
"perf/sub-1_asl.nii.gz"
]
}
Empty file added 2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.nii.gz
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