Merge pull request #466 from aptinis/add-2d-mb-pcasl

Add Siemens 2D MB PCASL example
bids-standard · Nov 5, 2024 · 38e3467 · 38e3467
2 parents dc0b73d + d21a4e9
commit 38e3467
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diff --git a/2d_mb_pcasl/README b/2d_mb_pcasl/README
@@ -0,0 +1 @@
+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.
diff --git a/2d_mb_pcasl/dataset_description.json b/2d_mb_pcasl/dataset_description.json
@@ -0,0 +1,10 @@
+{
+  "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."
+}
diff --git a/2d_mb_pcasl/sub-1/anat/sub-1_T1w.json b/2d_mb_pcasl/sub-1/anat/sub-1_T1w.json
@@ -0,0 +1,74 @@
+{
+  "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": [
+    4722,
+    5694,
+    766,
+    494,
+    81,
+    212,
+    -39,
+    -17
+  ],
+  "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,
+  "ParallelReductionFactorInPlane": 2,
+  "PixelBandwidth": 220,
+  "DwellTime": 7.1e-06,
+  "ImageOrientationPatientDICOM": [
+    0,
+    1,
+    0,
+    0,
+    0,
+    -1
+  ],
+  "ImageOrientationText": "Sag",
+  "InPlanePhaseEncodingDirectionDICOM": "ROW",
+  "ConversionSoftware": "dcm2niix",
+  "ConversionSoftwareVersion": "v1.0.20211006"
+}
diff --git a/2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz b/2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz
diff --git a/2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json b/2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json
@@ -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_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,
+  "EchoTime": 0.04,
+  "RepetitionTime": 8,
+  "FlipAngle": 90,
+  "PartialFourier": 0.75,
+  "BaseResolution": 86,
+  "ShimSetting": [
+    4723,
+    5691,
+    765,
+    492,
+    87,
+    207,
+    -41,
+    -18
+  ],
+  "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,
+  "PixelBandwidth": 2325,
+  "DwellTime": 2.5e-06,
+  "PhaseEncodingDirection": "j-",
+  "SliceTiming": [
+    3.99,
+    0,
+    4.1225,
+    0.1325,
+    4.255,
+    0.2675,
+    4.39,
+    0.4,
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+    0.5325,
+    4.655,
+    0.665,
+    4.7875,
+    0.7975,
+    4.92,
+    0.9325,
+    5.055,
+    1.065,
+    5.1875,
+    1.1975,
+    5.32,
+    1.33,
+    5.4525,
+    1.4625,
+    5.585,
+    1.5975,
+    5.72,
+    1.73,
+    5.8525,
+    1.8625,
+    5.985,
+    1.995,
+    6.1175,
+    2.1275,
+    6.25,
+    2.2625,
+    6.385,
+    2.395,
+    6.5175,
+    2.5275,
+    6.65,
+    2.66,
+    6.7825,
+    2.7925,
+    6.915,
+    2.925,
+    7.05,
+    3.06,
+    7.1825,
+    3.1925,
+    7.315,
+    3.325,
+    7.4475,
+    3.4575,
+    7.58,
+    3.59,
+    7.715,
+    3.725,
+    7.8475,
+    3.8575
+  ],
+  "ImageOrientationPatientDICOM": [
+    0.998104,
+    0.0407458,
+    0.0461261,
+    -0.0250904,
+    0.953743,
+    -0.299574
+  ],
+  "ImageOrientationText": "Tra>Cor(-17.4)>Sag(3.2)",
+  "InPlanePhaseEncodingDirectionDICOM": "COL",
+  "ConversionSoftware": "dcm2niix",
+  "ConversionSoftwareVersion": "v1.0.20211006",
+  "B0FieldIdentifier": "pepolar_b0s",
+  "IntendedFor": [
+    "perf/sub-1_asl.nii.gz"
+  ]
+}
diff --git a/2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.nii.gz b/2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.nii.gz
diff --git a/2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.json b/2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.json
@@ -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": [
+    "ORIGINAL",
+    "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": [
+    4723,
+    5691,
+    765,
+    492,
+    87,
+    207,
+    -41,
+    -18
+  ],
+  "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,
+  "PixelBandwidth": 2325,
+  "DwellTime": 2.5e-06,
+  "PhaseEncodingDirection": "j",
+  "SliceTiming": [
+    3.99,
+    0,
+    4.1225,
+    0.1325,
+    4.255,
+    0.265,
+    4.3875,
+    0.3975,
+    4.52,
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+    0.7975,
+    4.92,
+    0.93,
+    5.0525,
+    1.0625,
+    5.185,
+    1.1975,
+    5.32,
+    1.33,
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+    1.4625,
+    5.585,
+    1.595,
+    5.7175,
+    1.7275,
+    5.85,
+    1.8625,
+    5.985,
+    1.995,
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+    2.1275,
+    6.25,
+    2.26,
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+    2.3925,
+    6.515,
+    2.525,
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+    2.66,
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+    2.7925,
+    6.915,
+    2.925,
+    7.0475,
+    3.0575,
+    7.18,
+    3.19,
+    7.315,
+    3.325,
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+    3.4575,
+    7.58,
+    3.59,
+    7.7125,
+    3.7225,
+    7.845,
+    3.855
+  ],
+  "ImageOrientationPatientDICOM": [
+    0.998104,
+    0.0407458,
+    0.0461261,
+    -0.0250904,
+    0.953743,
+    -0.299574
+  ],
+  "ImageOrientationText": "Tra>Cor(-17.4)>Sag(3.2)",
+  "InPlanePhaseEncodingDirectionDICOM": "COL",
+  "ConversionSoftware": "dcm2niix",
+  "ConversionSoftwareVersion": "v1.0.20211006",
+  "B0FieldIdentifier": "pepolar_b0s",
+  "IntendedFor": [
+    "perf/sub-1_asl.nii.gz"
+  ]
+}
diff --git a/2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.nii.gz b/2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.nii.gz
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		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.