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Merge branch 'master' into trt
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‎.github/workflows/validate_datasets.yml‎

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if: matrix.bids-validator == 'legacy'
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uses: actions/setup-node@v4
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with:
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node-version: 18
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node-version: 22
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- name: Set cache name
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if: matrix.bids-validator == 'legacy'
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run:
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echo "MONTH=$( date +%Y%m )" >> $GITHUB_ENV
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- name: Load npm cache
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if: matrix.bids-validator == 'legacy'
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uses: actions/cache@v4
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with:
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path: ~/.npm
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key: npm-${{ runner.os }}-${{ env.MONTH }}
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- uses: denoland/setup-deno@v2
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if: matrix.bids-validator != 'legacy'
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fi
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- name: Skip legacy validation for post-legacy datasets
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run: for DS in mrs_* dwi_deriv pheno004 fmaps; do touch $DS/.SKIP_VALIDATION; done
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run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing fmaps; do touch $DS/.SKIP_VALIDATION; done
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if: matrix.bids-validator == 'legacy'
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- name: Skip stable validation for datasets with unreleased validator features

‎README.md‎

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| [genetics_ukbb](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) | multiple tasks, T1w, DTI, BOLD, genetic info | anat, dwi, func | FLAIR, T1w, bold, dwi, events, info | n/a | [@cpernet](https://github.com/cpernet) |
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| [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) |
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| [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) |
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| [volume_timing](https://github.com/bids-standard/bids-examples/tree/master/volume_timing) | Sparse BOLD acquisitions | func | bold | n/a | [@effigies](https://github.com/effigies) |
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### MRS
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‎dataset_listing.tsv‎

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@@ -33,6 +33,7 @@ ds116 multiple tasks, multiple runs [link](https://openneuro.org/datasets/ds0001
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ds210 multiple tasks, multiple runs [link](https://openneuro.org/datasets/ds000210/versions/00002) func bold, physio
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hcp_example_bids [link](https://bit.ly/2H0Z6Qt) [@robertoostenveld](https://github.com/robertoostenveld) anat, fmap T1w, T2w, magnitude1, magnitude2, phasediff
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synthetic A synthetic dataset [@effigies](https://github.com/effigies) anat, beh, func T1w, beh, bold, events, physio, scans, sessions, stim
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volume_timing Sparse BOLD acquisitions [@effigies](https://github.com/effigies) func bold
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fmap A synthetic fieldmap-only dataset [@effigies](https://github.com/effigies) fmap, func epi
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ds000001-fmriprep Common derivatives example [link](https://openneuro.org/datasets/ds000001/versions/1.0.0) [@effigies](https://github.com/effigies) n/a n/a
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ds004332 Anat dataset with task entity [link](https://openneuro.org/datasets/ds004332/versions/1.0.2) [@Remi-Gau](https://github.com/Remi-Gau) anat FLAIR, T1w, T2starw, T2w
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xeeg_hed_score EEG and iEEG data with annotations of artifacts, seizures and modulators using HED-SCORE [@dorahermes](https://github.com/dorahermes) anat, eeg, ieeg T1w, channels, coordsystem, eeg, electrodes, events, ieeg
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dwi_deriv exemplifies the storage of diffusion MRI derivates that may be generated on the Siemens XA platform. dwi dwi
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pheno004 Minimal dataset with subjects with imaging and/or phenotype data [@ericearl](https://github.com/ericearl) phenotype, anat T1w
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mri_chunk Example MRI dataset to illustrate BIDS chunk entity. A single subject, two chunks. [@valosekj](https://github.com/valosekj) anat T1w

‎mri_chunk/README.md‎

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Example dataset with empty images containing magnetic resonance imaging (MRI) data to illustrate BIDS chunk entity.
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The dataset contains a T2w image from a single subject. T2w image has two chunks -- brain and spinal cord.

‎mri_chunk/dataset_description.json‎

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{
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"Name": "mri_chunk",
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"Authors": [
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"Jan Valosek",
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"Julien Cohen-Adad"
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],
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"BIDSVersion": "1.9.0",
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"DatasetType": "raw"
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}

‎mri_chunk/participants.json‎

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{
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"participant_id": {
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"Description": "Unique Participant ID",
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"LongName": "Participant ID"
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}
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}

‎mri_chunk/participants.tsv‎

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participant_id
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sub-001

‎mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.json‎

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.197,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "Verio",
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"PatientPosition": "HFS",
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"ProcedureStepDescription": "TEST_VC^SPINE",
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"SoftwareVersions": "syngo MR B17",
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"MRAcquisitionType": "3D",
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"SeriesDescription": "SC_tse_spc_1mm_3palliers_fov256_nopat",
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"ProtocolName": "SC_tse_spc_1mm_3palliers_fov256_nopat_1",
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"ScanningSequence": "SE",
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"SequenceVariant": "SK\\SP\\OSP",
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"ScanOptions": "PFP",
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"SequenceName": "*spcR3d1_103",
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"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"],
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"NonlinearGradientCorrection": true,
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"SeriesNumber": 8,
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"AcquisitionTime": "10:33:32.162500",
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"AcquisitionNumber": 1,
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"SliceThickness": 1,
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"SAR": 0.269146,
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"NumberOfAverages": 2,
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"EchoTime": 0.124,
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"RepetitionTime": 1.5,
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"SpoilingState": true,
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"FlipAngle": 110,
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"AveragesDouble": 1.4,
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"PartialFourier": 1,
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"BaseResolution": 256,
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"ShimSetting": [
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"TxRefAmp": 491.928,
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"PhaseResolution": 1.0098,
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"PhaseOversampling": 0.197917,
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"ReceiveCoilName": "NeckMatrix",
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"CoilString": "C:HEP;NE1,2",
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"PulseSequenceDetails": "%SiemensSeq%\\tse_vfl",
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"CoilCombinationMethod": "Adaptive Combine",
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"MatrixCoilMode": "SENSE",
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"PercentPhaseFOV": 100,
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"PercentSampling": 100.98,
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"EchoTrainLength": 103,
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"PhaseEncodingSteps": 237,
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"AcquisitionMatrixPE": 259,
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"ReconMatrixPE": 256,
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"PixelBandwidth": 610,
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"DwellTime": 3.2e-06,
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"PhaseEncodingDirection": "j-",
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"ImageOrientationPatientDICOM": [
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0,
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1,
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-2.05103e-10,
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0,
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"ImageOrientationText": "Sag",
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"InPlanePhaseEncodingDirectionDICOM": "COL",
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20220720"
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}

‎mri_chunk/sub-001/anat/sub-001_chunk-1_T1w.nii.gz‎

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‎mri_chunk/sub-001/anat/sub-001_chunk-2_T1w.json‎

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.197,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "Verio",
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"PatientPosition": "HFS",
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"ProcedureStepDescription": "TEST_VC^SPINE",
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"SoftwareVersions": "syngo MR B17",
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"MRAcquisitionType": "3D",
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"SeriesDescription": "SC_tse_spc_1mm_3palliers_fov256_nopat",
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"ProtocolName": "SC_tse_spc_1mm_3palliers_fov256_nopat_2",
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"ScanningSequence": "SE",
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"SequenceVariant": "SK\\SP\\OSP",
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"ScanOptions": "PFP",
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"SequenceName": "*spcR3d1_103",
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"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"],
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"NonlinearGradientCorrection": true,
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"SeriesNumber": 9,
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"AcquisitionTime": "10:40:6.177500",
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"AcquisitionNumber": 1,
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"SliceThickness": 1,
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"SAR": 0.978482,
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"NumberOfAverages": 2,
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"EchoTime": 0.124,
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"RepetitionTime": 1.5,
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"SpoilingState": true,
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"FlipAngle": 110,
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"AveragesDouble": 1.4,
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"PartialFourier": 1,
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"BaseResolution": 256,
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"ShimSetting": [
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"TxRefAmp": 491.928,
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"PhaseResolution": 1.0098,
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"PhaseOversampling": 0.197917,
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"ReceiveCoilName": "NeckMatrix",
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"CoilString": "C:NE1,2;SP1,2",
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"PulseSequenceDetails": "%SiemensSeq%\\tse_vfl",
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"CoilCombinationMethod": "Adaptive Combine",
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"MatrixCoilMode": "SENSE",
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"PercentPhaseFOV": 100,
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"PercentSampling": 100.98,
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"EchoTrainLength": 103,
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"PhaseEncodingSteps": 237,
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"AcquisitionMatrixPE": 259,
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"ReconMatrixPE": 256,
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"PixelBandwidth": 610,
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"DwellTime": 3.2e-06,
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"PhaseEncodingDirection": "j-",
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"ImageOrientationPatientDICOM": [
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"ImageOrientationText": "Sag",
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"InPlanePhaseEncodingDirectionDICOM": "COL",
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20220720"
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}

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