[ENH] BEP022 - Magnetic Resonance Spectroscopy

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
 skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
 builtin = clear,rare
-ignore-words-list = nd
+ignore-words-list = nd,TE

.gitignore

@@ -12,4 +12,6 @@ env/
 
 *.asv
 
-site/
+site/
+
+.vscode

dataset_listing.tsv

@@ -2,7 +2,7 @@ name description link to full data maintained by datatypes suffixes
 eeg_matchingpennies Offline data of BCI experiment decoding left vs. right hand movement. BrainVision data format (.eeg, .vhdr, .vmrk) [link](https://doi.org/10.17605/OSF.IO/CJ2DR) [@sappelhoff](https://github.com/sappelhoff) eeg channels, eeg, events
 eeg_rishikesh Mind wandering experiment. EEG data in Biosemi (.bdf) format [link](https://openneuro.org/datasets/ds001787) [@arnodelorme](https://github.com/arnodelorme) eeg channels, eeg, events
 eeg_face13 Deconstructing the early visual electrocortical response to face and house stimuli. EDF format [@andesha](https://github.com/andesha) eeg channels, coordsystem, eeg, electrodes, events
-eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) eeg, beh channels, eeg, events, participants, scans
+eeg_ds003645s_hed_demo Shows usage of Hierarchical Event Descriptor (HED) in .tsv files [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) anat, beh, eeg, micr, motion KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, scans
 eeg_ds003645s_hed_library HED annotation using HED library vocabularies (schema). [link](https://openneuro.org/datasets/ds003645) [@VisLab](https://github.com/VisLab) eeg channels, eeg, events
 eeg_cbm Rest EEG. European Data Format (.edf) [@cpernet](https://github.com/cpernet) eeg channels, eeg, events, scans
 ieeg_filtered_speech recordings of three seizures [@choldgraf](https://github.com/choldgraf) ieeg channels, coordsystem, electrodes, events, ieeg, photo
@@ -57,7 +57,7 @@ pet003 T1w, PET, blood [@mnoergaard](https://github.com/mnoergaard) anat, pet T
 pet004 PET, blood [@mnoergaard](https://github.com/mnoergaard) pet blood, pet
 pet005 T1w, PET [@mnoergaard](https://github.com/mnoergaard) anat, pet T1w, events, pet
 micr_SEM Example SEM dataset in PNG format with 1 sample imaged over 2 sessions [link](https://doi.org/10.5281/zenodo.5498378) [@jcohenadad](https://github.com/jcohenadad) micr SEM, photo, samples, sessions
-micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions [@TheChymera](https://github.com/TheChymera) micr SEM, samples, sessions
+micr_SEMzarr Example SEM dataset in PNG and OME-ZARR format with 1 sample imaged over 2 sessions [@TheChymera](https://github.com/TheChymera) micr SEM, SPIM, samples, sessions
 micr_SPIM Example SPIM dataset in OME-TIFF format with 2 samples from the same subject with 4 chunks each [link](https://doi.org/10.5281/zenodo.5517223) [@jcohenadad](https://github.com/jcohenadad) micr SPIM, photo, samples
 fnirs_tapping Example fNIRS measurement with three conditions from five subjects [link](https://doi.org/10.5281/zenodo.5529797) [@rob_luke](https://github.com/rob_luke) nirs channels, coordsystem, events, nirs, optodes, scans
 fnirs_automaticity 24 subjects performing (non-)automatic finger tapping and foot stepping [link](https://doi.org/10.34973/vesb-mh30) [@robertoostenveld](https://github.com/robertoostenveld) nirs channels, coordsystem, events, nirs, optodes, practicelogbook, scans
@@ -72,6 +72,9 @@ ieeg_epilepsy multiple sessions, tutorial [link](https://neuroimage.usc.edu/bst/
 ieeg_epilepsyNWB multiple sessions, tutorial — derivative dataset of `ieeg_epilepsy` showcasing the NWB file format alternative [link](https://neuroimage.usc.edu/bst/getupdate.php?s=tutorial_epimap_bids) [@TheChymera](https://github.com/TheChymera) anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, scans
 ieeg_epilepsy_ecog multiple sessions, tutorial [link](https://neuroimage.usc.edu/bst/getupdate.php?s=sample_ecog) [@ftadel](https://github.com/ftadel) anat, ieeg T1w, channels, coordsystem, electrodes, events, ieeg, photo, scans
 ieeg_visual_multimodal [@irisgroen](https://github.com/irisgroen) anat, fmap, func, ieeg T1w, bold, channels, coordsystem, electrodes, epi, events, ieeg, sbref
-genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, fmap, func FLAIR, T1w, bold, dwi, events, info, magnitude1, phasediff
+genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, func FLAIR, T1w, bold, dwi, events, info
 motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans
 motion_spotrotation participants rotated heading using full-body motion or joystick [link](https://openneuro.org/datasets/ds004460) [@sjeung](https://github.com/sjeung) eeg, motion channels, coordsystem, eeg, electrodes, events, motion, scans
+mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat T1w
+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 T1w
+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 T1w, events

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/README.md

@@ -0,0 +1,27 @@
+# 2D semi-LASER MRSI reproducibility dataset
+
+Contact: <[email protected]>
+
+Data availability: <https://doi.org/10.5281/zenodo.7701228>
+
+## Overview
+
+The data from this study were acquired as part of a project to validate [SLIPMAT](https://doi.org/10.1016/j.neuroimage.2023.120235), a tool to extract high-quality, tissue-specific, spectral profiles from MR spectroscopic imaging data (MRSI).
+
+Data types included are T1-weighted structural MRI images and 2D semi-LASER MRSI data. Each subject has three runs of each MRSI acquisition.
+
+## Methods
+
+### Subjects
+
+Eight healthy adults (2 females, 6 males, mean age = 21 years).
+
+### MR protocol
+
+Reproduced with slight modifications from [SLIPMAT](https://doi.org/10.1016/j.neuroimage.2023.120235):
+
+MR data were acquired using a 3T Siemens Magnetom Prisma (Siemens Healthcare, Erlangen, Germany) system using a 32-channel receiver head coil-array. A T1-weighted MRI scan was acquired with a 3D-MPRAGE sequence: FOV = 208 × 256 × 256 mm, resolution = 1 × 1 × 1 mm<sup>3</sup>, TE / TR = 2 ms / 2000 ms, inversion time = 880 ms, flip angle = 8°, GRAPPA acceleration factor = 2, 4 min 54 s scan duration. Water suppressed MRSI data were acquired with 2D phase-encoding: FOV = 160 × 160 × 15 mm<sup>3</sup>, nominal voxel resolution 10 × 10 × 15 mm<sup>3</sup>, TE / TR = 40 ms / 2000 ms, complex data points = 1024, sampling frequency = 2000 Hz. The MRSI slice was aligned axially in the subcallosal plane with an approximately 1 mm gap from the upper surface of the corpus callosum. The semi-LASER method ([Scheenen et al., 2008](https://doi.org/10.1002/mrm.21302)) was used localize a 100 × 100 × 15 mm VOI, central to the FOV, four saturation regions were placed around the VOI prescribing a 100 × 100 mm interior, and an additional four saturation regions were positioned to intersect the four corners of the semi-LASER VOI to provide additional scalp lipid suppression. The total acquisition time for a single MRSI scan was 5 min and 6 s, and three MRSI datasets were acquired sequentially during the same session to assess technical repeatability.
+
+### Experimental location
+
+Centre for Human Brain Health, University of Birmingham, Birmingham, UK.

mrs_2dmrsi/dataset_description.json

@@ -0,0 +1,21 @@
+{
+ "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
+}