[ENH] BEP022 - Magnetic Resonance Spectroscopy

README.md

@@ -248,6 +248,19 @@ DO NOT EDIT DIRECTLY.
 | [ieeg_visual_multimodal](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal) | n/a                                                                                         | anat, fmap, func, ieeg          | T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref                                       | n/a                                                            | [@irisgroen](https://github.com/irisgroen) |
 | [synthetic](https://github.com/bids-standard/bids-examples/tree/master/synthetic)                           | A synthetic dataset                                                                         | anat, beh, func                 | T1w, beh, bold, events, physio, scans, sessions, stim                                                        | n/a                                                            | [@effigies](https://github.com/effigies)   |
 
+### MRS
+
+<!--
+TABLE BELOW IS GENERATED AUTOMATICALLY.
+DO NOT EDIT DIRECTLY.
+-->
+
+| name                                                                                  | description                                                                            | datatypes   | suffixes              | link to full data                                | maintained by                                      |
+|:--------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------|:------------|:----------------------|:-------------------------------------------------|:---------------------------------------------------|
+| [mrs_2dmrsi](https://github.com/bids-standard/bids-examples/tree/master/mrs_2dmrsi)   | 2D sLASER MRSI data from 8 subjects                                                    | anat, mrs   | T1w, mrsi             | [link](https://zenodo.org/records/7701228)       | [@markmikkelsen](https://github.com/markmikkelsen) |
+| [mrs_biggaba](https://github.com/bids-standard/bids-examples/tree/master/mrs_biggaba) | MEGA-PRESS and PRESS MRS data from 12 subjects from one site from the Big GABA project | anat, mrs   | T1w, svs, ref         | [link](https://www.nitrc.org/projects/biggaba)   | [@markmikkelsen](https://github.com/markmikkelsen) |
+| [mrs_fmrs](https://github.com/bids-standard/bids-examples/tree/master/mrs_fmrs)       | Functional MRS data involving a pain stimulus task from 15 subjects                    | anat, mrs   | T1w, svs, ref, events | [link](https://www.nitrc.org/projects/fmrs_2020) | [@markmikkelsen](https://github.com/markmikkelsen) |
+
 ### NIRS
 
 <!--

mrs_2dmrsi/CHANGES

@@ -0,0 +1,5 @@
+1.0.1 2023-11-28
+  - Edits for inclusion into https://github.com/bids-standard/bids-examples
+
+1.0.0 2022-10-06
+  - Initial release

mrs_2dmrsi/dataset_description.json

@@ -0,0 +1,19 @@
+{
+    "Name": "mrs_2dmrsi",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "raw",
+    "License": "Creative Commons Attribution 4.0 International License",
+    "Authors": [
+        "Martin Wilson",
+        "Olivia Vella"
+    ],
+    "ReferencesAndLinks": "doi:10.1016/j.neuroimage.2023.120235",
+    "DatasetDOI": "doi:10.5281/zenodo.7701228",
+    "SourceDatasets": [
+        {
+            "URL": "https://zenodo.org/records/7701228",
+            "DOI": "doi:10.5281/zenodo.7701228",
+            "Version": "v4"
+        }
+    ]
+}

mrs_2dmrsi/sub-01/anat/sub-01_T1w.json

@@ -0,0 +1,72 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.252,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionName": "CHBH",
+	"InstitutionalDepartmentName": "CHBH",
+	"InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA",
+	"DeviceSerialNumber": "166100",
+	"StationName": "AWP166100",
+	"BodyPartExamined": "BRAIN",
+	"PatientPosition": "HFS",
+	"SoftwareVersions": "syngo MR E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T1_vol_MPR_v1",
+	"ProtocolName": "T1_vol_MPR_v1",
+	"ScanningSequence": "GR\\IR",
+	"SequenceVariant": "SK\\SP\\MP\\OSP",
+	"ScanOptions": "IR",
+	"SequenceName": "*tfl3d1_16ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+	"SeriesNumber": 7,
+	"AcquisitionNumber": 1,
+	"SliceThickness": 1,
+	"SAR": 0.0560902,
+	"EchoTime": 0.00203,
+	"RepetitionTime": 2,
+	"SpoilingState": true,
+	"InversionTime": 0.88,
+	"FlipAngle": 8,
+	"PartialFourier": 1,
+	"BaseResolution": 256,
+	"ShimSetting": [
+		-6825,
+		-3922,
+		3512,
+		392,
+		-104,
+		-143,
+		93,
+		30	],
+	"TxRefAmp": 252.801,
+	"PhaseResolution": 1,
+	"PhaseOversampling": 0.05,
+	"ReceiveCoilName": "Head_32",
+	"ReceiveCoilActiveElements": "HEA;HEP",
+	"PulseSequenceDetails": "%SiemensSeq%\\tfl",
+	"RefLinesPE": 24,
+	"CoilCombinationMethod": "Adaptive Combine",
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"MatrixCoilMode": "GRAPPA",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"PhaseEncodingSteps": 269,
+	"AcquisitionMatrixPE": 256,
+	"ReconMatrixPE": 256,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 240,
+	"DwellTime": 8.2e-06,
+	"ImageOrientationPatientDICOM": [
+		-0.0456605,
+		0.996282,
+		0.0730621,
+		0.00408772,
+		0.0733241,
+		-0.9973	],
+	"ImageOrientationText": "Sag>Cor(-2.6)>Tra(-0.4)",
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20211006"
+}

mrs_2dmrsi/sub-01/mrs/sub-01_run-1_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252145,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-01/mrs/sub-01_run-2_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252145,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-01/mrs/sub-01_run-3_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252145,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-02/anat/sub-02_T1w.json

@@ -0,0 +1,72 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.252,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionName": "CHBH",
+	"InstitutionalDepartmentName": "CHBH",
+	"InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA",
+	"DeviceSerialNumber": "166100",
+	"StationName": "AWP166100",
+	"BodyPartExamined": "BRAIN",
+	"PatientPosition": "HFS",
+	"SoftwareVersions": "syngo MR E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T1_vol_MPR_v1",
+	"ProtocolName": "T1_vol_MPR_v1",
+	"ScanningSequence": "GR\\IR",
+	"SequenceVariant": "SK\\SP\\MP\\OSP",
+	"ScanOptions": "IR",
+	"SequenceName": "*tfl3d1_16ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+	"SeriesNumber": 7,
+	"AcquisitionNumber": 1,
+	"SliceThickness": 1,
+	"SAR": 0.0585647,
+	"EchoTime": 0.00203,
+	"RepetitionTime": 2,
+	"SpoilingState": true,
+	"InversionTime": 0.88,
+	"FlipAngle": 8,
+	"PartialFourier": 1,
+	"BaseResolution": 256,
+	"ShimSetting": [
+		-6840,
+		-3919,
+		3485,
+		447,
+		20,
+		-145,
+		82,
+		18	],
+	"TxRefAmp": 229.74,
+	"PhaseResolution": 1,
+	"PhaseOversampling": 0.05,
+	"ReceiveCoilName": "Head_32",
+	"ReceiveCoilActiveElements": "HEA;HEP",
+	"PulseSequenceDetails": "%SiemensSeq%\\tfl",
+	"RefLinesPE": 24,
+	"CoilCombinationMethod": "Adaptive Combine",
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"MatrixCoilMode": "GRAPPA",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"PhaseEncodingSteps": 269,
+	"AcquisitionMatrixPE": 256,
+	"ReconMatrixPE": 256,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 240,
+	"DwellTime": 8.2e-06,
+	"ImageOrientationPatientDICOM": [
+		-0.0374318,
+		0.997236,
+		0.0641811,
+		-0.0117369,
+		0.063783,
+		-0.997895	],
+	"ImageOrientationText": "Sag>Cor(-2.2)>Tra(0.5)",
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20211006"
+}

mrs_2dmrsi/sub-02/mrs/sub-02_run-1_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252157,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-02/mrs/sub-02_run-2_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252157,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-02/mrs/sub-02_run-3_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252157,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-03/anat/sub-03_T1w.json

@@ -0,0 +1,72 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.252,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionName": "CHBH",
+	"InstitutionalDepartmentName": "CHBH",
+	"InstitutionAddress": "Pritchatts Road CHBH,Birmingham,District,GB,B152RA",
+	"DeviceSerialNumber": "166100",
+	"StationName": "AWP166100",
+	"BodyPartExamined": "BRAIN",
+	"PatientPosition": "HFS",
+	"SoftwareVersions": "syngo MR E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T1_vol_MPR_v1",
+	"ProtocolName": "T1_vol_MPR_v1",
+	"ScanningSequence": "GR\\IR",
+	"SequenceVariant": "SK\\SP\\MP\\OSP",
+	"ScanOptions": "IR",
+	"SequenceName": "*tfl3d1_16ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+	"SeriesNumber": 7,
+	"AcquisitionNumber": 1,
+	"SliceThickness": 1,
+	"SAR": 0.0475148,
+	"EchoTime": 0.00203,
+	"RepetitionTime": 2,
+	"SpoilingState": true,
+	"InversionTime": 0.88,
+	"FlipAngle": 8,
+	"PartialFourier": 1,
+	"BaseResolution": 256,
+	"ShimSetting": [
+		-6847,
+		-3888,
+		3457,
+		547,
+		-77,
+		-31,
+		-198,
+		42	],
+	"TxRefAmp": 219.992,
+	"PhaseResolution": 1,
+	"PhaseOversampling": 0.05,
+	"ReceiveCoilName": "Head_32",
+	"ReceiveCoilActiveElements": "HEA;HEP",
+	"PulseSequenceDetails": "%SiemensSeq%\\tfl",
+	"RefLinesPE": 24,
+	"CoilCombinationMethod": "Adaptive Combine",
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"MatrixCoilMode": "GRAPPA",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"PhaseEncodingSteps": 269,
+	"AcquisitionMatrixPE": 256,
+	"ReconMatrixPE": 256,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 240,
+	"DwellTime": 8.2e-06,
+	"ImageOrientationPatientDICOM": [
+		0.0813511,
+		0.975376,
+		0.204994,
+		0.028976,
+		0.203275,
+		-0.978693	],
+	"ImageOrientationText": "Sag>Cor(4.9)>Tra(-0.7)",
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20211006"
+}

mrs_2dmrsi/sub-03/mrs/sub-03_run-1_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252185,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-03/mrs/sub-03_run-2_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252185,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}

mrs_2dmrsi/sub-03/mrs/sub-03_run-3_mrsi.json

@@ -0,0 +1,13 @@
+{
+  "SpectrometerFrequency": 123.252185,
+  "ResonantNucleus": "1H",
+  "SpectralWidth": 2000,
+  "NumberOfSpectralPoints": 1024,
+  "AcquisitionVoxelSize": [10, 10, 15],
+  "ChemicalShiftOffset": 4.65,
+  "EchoTime": 0.04,
+  "RepetitionTime": 2,
+  "FlipAngle": 90,
+  "SequenceName": "%SiemensSeq%\\csi_slaser",
+  "ChemicalShiftReference": 2
+}