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Merge pull request #425 from markmikkelsen/bep022
[ENH] BEP022 - Magnetic Resonance Spectroscopy
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‎.codespellrc‎

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

‎.github/workflows/validate_datasets.yml‎

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fi
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shell: bash
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- name: Skip MRS validation for legacy validator
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run: for DS in mrs_*; do touch $DS/.SKIP_VALIDATION; done
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if: "matrix.bids-validator != 'master-deno'"
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shell: bash
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- name: Validate all BIDS datasets using bids-validator
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run: |
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cat ./run_tests.sh

‎README.md‎

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‎dataset_listing.tsv‎

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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
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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
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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
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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
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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, motion, photo, samples, scans
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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
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eeg_cbm Rest EEG. European Data Format (.edf) [@cpernet](https://github.com/cpernet) eeg channels, eeg, events, scans
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ieeg_filtered_speech recordings of three seizures [@choldgraf](https://github.com/choldgraf) ieeg channels, coordsystem, electrodes, events, ieeg, photo
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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
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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
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motion_systemvalidation Example dataset of two different motion captured system recorded almost simultaneously, but no brain data [link](https://doi.org/10.6084/m9.figshare.20238006.v2) [@JuliusWelzel](https://github.com/JuliusWelzel) motion channels, motion, scans
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ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task [link](https://openneuro.org/datasets/ds000117/) [@RikHenson](https://github.com/RikHenson) anat, beh, dwi, fmap, func, meg FLASH, T1w, beh, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans
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ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ChannelGroupSet, ClassFile, MarkerFile, T1w, channels, coordsystem, default, headshape, meg, params, photo, processing, scans
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ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg ClassFile, T1w, bad, channels, coordsystem, default, headshape, meg, params, processing, scans
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ds000117 A multi-subject, multi-modal human neuroimaging dataset of 19 subjects on a MEG visual task [link](https://openneuro.org/datasets/ds000117/) [@RikHenson](https://github.com/RikHenson) anat, beh, dwi, fmap, func, meg FLASH, T1w, bold, channels, coordsystem, dwi, events, headshape, magnitude1, magnitude2, meg, phasediff, scans
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ds000246 Auditory dataset used for Brainstorm’s general online tutorial [link](https://openneuro.org/datasets/ds000246/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, photo, scans
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ds000247 Five minutes, eyes-open, resting-state MEG data from 5 subjects. This is a sample from The Open MEG Archive (OMEGA). [link](https://openneuro.org/datasets/ds000247/versions/00001) [@guiomar](https://github.com/guiomar) anat, meg T1w, channels, coordsystem, headshape, meg, scans
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ds000248 MNE sample data: Data with visual and auditory stimuli [link](https://openneuro.org/datasets/ds000248/versions/00001) [@agramfort](https://github.com/agramfort) anat, meg FLASH, T1w, channels, coordsystem, events, meg, scans
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eeg_ds000117 Multimodal (fMRI, MEG, EEG) stripped down to EEG with MRI anatomical scan and electrode coordinates. EEGLAB data format (.set, .fdt) [link](https://openneuro.org/datasets/ds000117/) [@robertoostenveld](https://github.com/robertoostenveld) anat, eeg T1w, channels, coordsystem, eeg, electrodes, events
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eeg_rest_fmri Resting state with simultaneous fMRI. BrainVision data format (.eeg, .vhdr, .vmrk) [@cpernet](https://github.com/cpernet) anat, dwi, eeg, func T1w, bold, dwi, eeg
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genetics_ukbb multiple tasks, T1w, DTI, BOLD, genetic info [@cpernet](https://github.com/cpernet) anat, dwi, func FLAIR, T1w, bold, dwi, events, info
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motion_dualtask older and younger participants walking while performing discrimination task [@sjeung](https://github.com/sjeung) eeg, motion channels, eeg, events, motion, scans
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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
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mrs_2dmrsi 2D sLASER MRSI data from 8 subjects [link](https://zenodo.org/records/7701228) [@markmikkelsen](https://github.com/markmikkelsen) anat, mrs T1w, mrsi
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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
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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

‎mrs_2dmrsi/CHANGES‎

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

‎mrs_2dmrsi/README.md‎

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# 2D semi-LASER MRSI reproducibility dataset
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Contact: <[email protected]>
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Data availability: <https://doi.org/10.5281/zenodo.7701228>
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Publications:
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- <https://doi.org/10.1016/j.neuroimage.2023.120235>
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## Overview
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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).
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Data types included are T1-weighted structural MRI images and 2D semi-LASER MRSI data. Each subject has three runs of each MRSI acquisition.
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## Methods
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### Subjects
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Eight healthy adults (2 females, 6 males, mean age = 21 years).
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### MR protocol
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Reproduced with slight modifications from [SLIPMAT](https://doi.org/10.1016/j.neuroimage.2023.120235):
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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.
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### Experimental location
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Centre for Human Brain Health, University of Birmingham, Birmingham, UK.

‎mrs_2dmrsi/dataset_description.json‎

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

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

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

‎mrs_2dmrsi/sub-01/anat/sub-01_T1w.nii.gz‎

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

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

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