From 31cfaeec69f0846076b0a4752a0562bfa3898a6c Mon Sep 17 00:00:00 2001 From: aptinis Date: Fri, 30 Aug 2024 15:39:12 -0400 Subject: [PATCH 1/5] Add Siemens 2D MB PCASL example --- 2d_mb_pcasl/README | 1 + 2d_mb_pcasl/dataset_description.json | 10 + 2d_mb_pcasl/sub-1/anat/sub-1_T1w.json | 74 +++ 2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz | 0 2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json | 144 ++++++ .../sub-1/fmap/sub-1_dir-AP_epi.nii.gz | 0 2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.json | 144 ++++++ .../sub-1/fmap/sub-1_dir-PA_epi.nii.gz | 0 2d_mb_pcasl/sub-1/perf/sub-1_asl.json | 426 ++++++++++++++++++ 2d_mb_pcasl/sub-1/perf/sub-1_asl.nii.gz | 0 2d_mb_pcasl/sub-1/perf/sub-1_aslcontext.tsv | 91 ++++ 11 files changed, 890 insertions(+) create mode 100644 2d_mb_pcasl/README create mode 100644 2d_mb_pcasl/dataset_description.json create mode 100644 2d_mb_pcasl/sub-1/anat/sub-1_T1w.json create mode 100644 2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz create mode 100644 2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json create mode 100644 2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.nii.gz create mode 100644 2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.json create mode 100644 2d_mb_pcasl/sub-1/fmap/sub-1_dir-PA_epi.nii.gz create mode 100644 2d_mb_pcasl/sub-1/perf/sub-1_asl.json create mode 100644 2d_mb_pcasl/sub-1/perf/sub-1_asl.nii.gz create mode 100644 2d_mb_pcasl/sub-1/perf/sub-1_aslcontext.tsv diff --git a/2d_mb_pcasl/README b/2d_mb_pcasl/README new file mode 100644 index 000000000..719af13de --- /dev/null +++ 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 new file mode 100644 index 000000000..94016fb5d --- /dev/null +++ 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 new file mode 100644 index 000000000..8f5183923 --- /dev/null +++ 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" +} \ No newline at end of file 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 new file mode 100644 index 000000000..e69de29bb 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 new file mode 100644 index 000000000..3f8de5bdb --- /dev/null +++ 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, + 4.5225, + 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" + ] +} \ No newline at end of file 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 new file mode 100644 index 000000000..e69de29bb 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 new file mode 100644 index 000000000..a525a0fde --- /dev/null +++ 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, + 0.5325, + 4.655, + 0.665, + 4.7875, + 0.7975, + 4.92, + 0.93, + 5.0525, + 1.0625, + 5.185, + 1.1975, + 5.32, + 1.33, + 5.4525, + 1.4625, + 5.585, + 1.595, + 5.7175, + 1.7275, + 5.85, + 1.8625, + 5.985, + 1.995, + 6.1175, + 2.1275, + 6.25, + 2.26, + 6.3825, + 2.3925, + 6.515, + 2.525, + 6.65, + 2.66, + 6.7825, + 2.7925, + 6.915, + 2.925, + 7.0475, + 3.0575, + 7.18, + 3.19, + 7.315, + 3.325, + 7.4475, + 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" + ] +} \ No newline at end of file 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 new file mode 100644 index 000000000..e69de29bb diff --git a/2d_mb_pcasl/sub-1/perf/sub-1_asl.json b/2d_mb_pcasl/sub-1/perf/sub-1_asl.json new file mode 100644 index 000000000..3cb06a261 --- /dev/null +++ b/2d_mb_pcasl/sub-1/perf/sub-1_asl.json @@ -0,0 +1,426 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.249, + "Manufacturer": "Siemens", + "ManufacturersModelName": "Prisma_fit", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR E11", + "MRAcquisitionType": "2D", + "SeriesDescription": "mbPCASLhr_PA", + "ProtocolName": "mbPCASLhr_PA", + "ScanningSequence": "EP", + "SequenceVariant": "SK", + "ScanOptions": "PFP\\FS", + "SequenceName": "mbPCASL2d1_86", + "ImageType": [ + "ORIGINAL", + "PRIMARY", + "M", + "ND", + "MOSAIC" + ], + "SeriesNumber": 40, + "AcquisitionNumber": 1, + "SliceThickness": 2.27, + "SpacingBetweenSlices": 2.497, + "SAR": 0.398268, + "EchoTime": 0.019, + "RepetitionTime": 3.58, + "FlipAngle": 90, + "PartialFourier": 0.75, + "BaseResolution": 86, + "ShimSetting": [ + 4722, + 5675, + 763, + 454, + 110, + 176, + 8, + -58 + ], + "TxRefAmp": 252.904, + "PhaseResolution": 1, + "ReceiveCoilName": "Head_32", + "ReceiveCoilActiveElements": "HEA;HEP", + "PulseSequenceDetails": "%CustomerSeq%\\PCASL_C2P_XFL", + "RefLinesPE": 12, + "CoilCombinationMethod": "Sum of Squares", + "ConsistencyInfo": "N4_VE11E_LATEST_20181129", + "MultibandAccelerationFactor": 6, + "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": [ + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325, + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325, + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325, + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325, + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325, + 0, + 0.06, + 0.1175, + 0.1775, + 0.2375, + 0.295, + 0.355, + 0.4125, + 0.4725, + 0.5325 + ], + "ImageOrientationPatientDICOM": [ + 0.998106, + 0.0407013, + 0.0461229, + -0.0395646, + 0.998897, + -0.0252958 + ], + "ImageOrientationText": "Tra>Sag(2.7)>Cor(-1.3)", + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20211006", + "B0FieldSource": "pepolar_b0s", + "RepetitionTimePreparation": [ + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 3.58, + 8.0, + 8.0 + ], + "ArterialSpinLabelingType": "PCASL", + "PostLabelingDelay": [ + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.2, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 0.7, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.2, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 1.7, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 2.2, + 0.0, + 0.0, + 0.0, + 0.0 + ], + "BackgroundSuppression": false, + "M0Type": "Included", + "TotalAcquiredPairs": 43, + "AcquisitionVoxelSize": [ + 2.5, + 2.5, + 2.497 + ], + "LabelingDuration": [ + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 1.5, + 0.0, + 0.0, + 0.0, + 0.0 + ] +} \ No newline at end of file diff --git a/2d_mb_pcasl/sub-1/perf/sub-1_asl.nii.gz b/2d_mb_pcasl/sub-1/perf/sub-1_asl.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/2d_mb_pcasl/sub-1/perf/sub-1_aslcontext.tsv b/2d_mb_pcasl/sub-1/perf/sub-1_aslcontext.tsv new file mode 100644 index 000000000..e21ba3ff2 --- /dev/null +++ b/2d_mb_pcasl/sub-1/perf/sub-1_aslcontext.tsv @@ -0,0 +1,91 @@ +volume_type +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +label +control +noRF +noRF +m0scan +m0scan From 62151765144402a40702e7dc20fc2722c9c9408b Mon Sep 17 00:00:00 2001 From: aptinis Date: Fri, 30 Aug 2024 15:53:50 -0400 Subject: [PATCH 2/5] Add CITATION to suffixes to remove in dataset listing script --- tools/print_dataset_listing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/print_dataset_listing.py b/tools/print_dataset_listing.py index 9841c2353..49b7efbb3 100644 --- a/tools/print_dataset_listing.py +++ b/tools/print_dataset_listing.py @@ -10,7 +10,7 @@ from bids import BIDSLayout folders_to_skip = ["docs", ".git", ".github", "tools", "env", "site", ".vscode"] -suffixes_to_remove = ["README", "description", "participants"] +suffixes_to_remove = ["README", "description", "participants", "CITATION"] column_order = [ "name", "description", From a54b674baa935026e91c2ed87dd46e8e103bfa15 Mon Sep 17 00:00:00 2001 From: aptinis Date: Fri, 30 Aug 2024 15:55:10 -0400 Subject: [PATCH 3/5] Update docs for 2d_mb_pcasl --- README.md | 15 ++++++++------- dataset_listing.tsv | 1 + 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 5fd612af7..a92a20a52 100644 --- a/README.md +++ b/README.md @@ -127,13 +127,14 @@ TABLE BELOW IS GENERATED AUTOMATICALLY. DO NOT EDIT DIRECTLY. --> -| name | description | datatypes | suffixes | link to full data | maintained by | -|:----------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:-----------------|:------------------------------------------|:------------------------------|:-----------------------------------------| -| [asl001](https://github.com/bids-standard/bids-examples/tree/master/asl001) | T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries | anat, perf | T1w, asl, aslcontext, asllabeling | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | -| [asl002](https://github.com/bids-standard/bids-examples/tree/master/asl002) | T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | -| [asl003](https://github.com/bids-standard/bids-examples/tree/master/asl003) | T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | -| [asl004](https://github.com/bids-standard/bids-examples/tree/master/asl004) | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach | anat, fmap, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | -| [asl005](https://github.com/bids-standard/bids-examples/tree/master/asl005) | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | +| name | description | datatypes | suffixes | link to full data | maintained by | +|:--------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------|:-----------------|:------------------------------------------|:------------------------------|:-----------------------------------------| +| [2d_mb_pcasl](https://github.com/bids-standard/bids-examples/tree/master/2d_mb_pcasl) | Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) | anat, fmap, perf | T1w, asl, aslcontext, epi | [link](https://osf.io/xrkc4/) | [@aptinis](https://github.com/aptinis) | +| [asl001](https://github.com/bids-standard/bids-examples/tree/master/asl001) | T1w, asl (GE, PCASL, 3D_SPIRAL), m0scan within timeseries | anat, perf | T1w, asl, aslcontext, asllabeling | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | +| [asl002](https://github.com/bids-standard/bids-examples/tree/master/asl002) | T1w, asl (Philips, PCASL, 2D_EPI), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | +| [asl003](https://github.com/bids-standard/bids-examples/tree/master/asl003) | T1w, asl (Siemens, PASL, multiTI), M0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | +| [asl004](https://github.com/bids-standard/bids-examples/tree/master/asl004) | T1w, asl (Siemens, PCASL, multiPLD with pepolar), m0scan separate scans with pepolar approach | anat, fmap, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | +| [asl005](https://github.com/bids-standard/bids-examples/tree/master/asl005) | T1w, asl (Siemens, PCASL, singleTI, 3D_GRASE), m0scan as separate scan | anat, perf | T1w, asl, aslcontext, asllabeling, m0scan | [link](https://osf.io/yru2q/) | [@patsycle](https://github.com/patsycle) | ### EEG diff --git a/dataset_listing.tsv b/dataset_listing.tsv index f3540c073..8e592369a 100644 --- a/dataset_listing.tsv +++ b/dataset_listing.tsv @@ -79,3 +79,4 @@ motion_spotrotation participants rotated heading using full-body motion or joyst mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsi mrs_biggaba MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project [link](https://www.nitrc.org/projects/biggaba) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsref, svs mrs_fmrs Functional MRS data involving a pain stimulus task from 15 subjects [link](https://www.nitrc.org/projects/fmrs_2020) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, events, mrsref, svs +2d_mb_pcasl Siemens 2D MultiBand Multi-delay PCASL (m0 and noRF included within timeseries) [link](https://osf.io/xrkc4/) [@aptinis](https://github.com/aptinis) anat, fmap, perf T1w, asl, aslcontext, epi From 6e79b9ec620f7cc6463203e43355c7a7863996b9 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 30 Aug 2024 16:13:44 -0400 Subject: [PATCH 4/5] Use schema from bids-standard/bids-specification#1884 --- .github/workflows/validate_datasets.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index 55073f3a1..9ff0a768c 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -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 From 17847111251d7fc40dd38dd8832d027f927f8428 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 5 Sep 2024 13:34:36 -0400 Subject: [PATCH 5/5] Update .github/workflows/validate_datasets.yml --- .github/workflows/validate_datasets.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index 9ff0a768c..55073f3a1 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -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--1884.org.readthedocs.build/en/1884/schema.json + BIDS_SCHEMA: https://bids-specification.readthedocs.io/en/latest/schema.json