Merge pull request #425 from markmikkelsen/bep022

[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

.github/workflows/validate_datasets.yml

@@ -98,6 +98,11 @@ jobs:
         fi
       shell: bash
 
+    - name: Skip MRS validation for legacy validator
+      run: for DS in mrs_*; do touch $DS/.SKIP_VALIDATION; done
+      if: "matrix.bids-validator != 'master-deno'"
+      shell: bash
+
     - name: Validate all BIDS datasets using bids-validator
       run: |
         cat ./run_tests.sh

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)	anat, beh, eeg, micr, motion	KSSSleep, SPIM, beh, channels, coordsystem, defacemask, eeg, electrodes, events, headshape, motion, photo, samples, 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, 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
@@ -63,9 +63,9 @@ micr_XPCTzarr	Example XPCT dataset in OME-ZARR format with 1 sample imaged	[link
 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
 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
-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
-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
-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
+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
+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
+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
 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
 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
 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
@@ -76,3 +76,6 @@ ieeg_visual_multimodal			[@irisgroen](https://github.com/irisgroen)	anat, fmap,
 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, 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

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 +1,31 @@
+# 2D semi-LASER MRSI reproducibility dataset
+
+Contact: <[email protected]>
+
+Data availability: <https://doi.org/10.5281/zenodo.7701228>
+
+Publications:
+
+- <https://doi.org/10.1016/j.neuroimage.2023.120235>
+
+## 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
+}