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‎.github/workflows/deploy.yml

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@@ -5,9 +5,8 @@ concurrency:
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cancel-in-progress: true
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on:
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push:
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branches:
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- master
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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permissions:
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contents: write

‎.github/workflows/validate_datasets.yml

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@@ -21,7 +21,7 @@ jobs:
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fail-fast: false
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matrix:
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platform: [ubuntu-latest, macos-latest, windows-latest]
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bids-validator: [master, stable, master-deno]
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bids-validator: [stable, main, dev, legacy]
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runs-on: ${{ matrix.platform }}
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@@ -33,53 +33,50 @@ jobs:
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- uses: actions/checkout@v4
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- name: Set up Node.js
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if: "matrix.bids-validator == 'stable' || matrix.bids-validator == 'master'"
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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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- name: Install BIDS validator (stable)
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if: "matrix.bids-validator == 'stable'"
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run: |
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npm install -g bids-validator
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- uses: denoland/setup-deno@v2
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if: matrix.bids-validator != 'legacy'
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with:
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deno-version: v2.x
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- name: Install BIDS validator (master)
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if: "matrix.bids-validator == 'master'"
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- name: Install BIDS validator (stable)
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if: matrix.bids-validator == 'stable'
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run: |
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pushd ..
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# Get npm 7+
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npm install -g npm
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git clone --depth 1 https://github.com/bids-standard/bids-validator
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cd bids-validator
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# Generate the full development node_modules
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npm clean-install
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# Build & bundle the bids-validator CLI package
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npm -w bids-validator run build
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# Generate a package to install globally
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npm -w bids-validator pack
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# Install the package globally
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bash -c "npm install -g bids-validator-*.tgz"
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popd
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- uses: denoland/setup-deno@v1
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if: "matrix.bids-validator == 'master-deno'"
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with:
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deno-version: v1.x
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deno install -Agf -n bids-validator jsr:@bids/validator
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shell: bash
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- name: Install BIDS validator (master deno build)
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if: "matrix.bids-validator == 'master-deno'"
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- name: Install BIDS validator (main)
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if: matrix.bids-validator == 'main'
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run: |
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# If unmerged validator PRs are needed for testing, you can use
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# https://github.com/<FORK>/bids-validator/raw/<BRANCH>/bids-validator/src/bids-validator.ts
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deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
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shell: bash
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- name: Install BIDS validator (dev)
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if: matrix.bids-validator == 'dev'
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run: |
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git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
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cd ../bids-validator
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deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
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shell: bash
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- name: Install BIDS validator (legacy)
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if: "matrix.bids-validator == 'legacy'"
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run: |
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npm install -g bids-validator
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- name: Display versions and environment information
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run: |
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echo $TZ
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date
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echo "npm"; npm --version
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echo "node"; node --version
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which deno && echo "deno\n----" && deno --version || true
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echo "node\n----"; node --version
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echo "npm\n----"; npm --version
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echo "bids-validator"; bids-validator --version
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shell: bash
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@@ -98,17 +95,26 @@ jobs:
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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
103-
if: "matrix.bids-validator != 'master-deno'"
98+
- name: Skip legacy validation for post-legacy datasets
99+
run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
100+
if: matrix.bids-validator == 'legacy'
101+
shell: bash
102+
103+
- name: Skip stable validation for datasets with unreleased features
104+
run: for DS in dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
105+
if: matrix.bids-validator != 'dev'
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shell: bash
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- name: Set BIDS_SCHEMA variable for dev version
109+
if: matrix.bids-validator == 'dev'
110+
# When proposing new features, schema changes may be necessary.
111+
# Update this URL to the schema.json from PRs to the spec, when needed.
112+
# If this variable is unset, dev will generally track the latest development
113+
# release of https://jsr.io/@bids/schema
114+
run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
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- name: Validate all BIDS datasets using bids-validator
107117
run: |
108118
cat ./run_tests.sh
109119
./run_tests.sh
110120
shell: bash
111-
env:
112-
# When proposing new features, schema changes may be necessary.
113-
# Update this URL to the schema.json from PRs to the spec, when needed.
114-
BIDS_SCHEMA: https://bids-specification.readthedocs.io/en/latest/schema.json

‎2d_mb_pcasl/README

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This dataset is an example of the Siemens 2D MultiBand Multi-delay PCASL sequence with noRF and m0 volumes included within the timeseries (HCP Aging ASL sequence). It also contains corresponding PEPOLAR fmaps and a T1w scan.

‎2d_mb_pcasl/dataset_description.json

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{
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"Name": "ASL_Siemens_MultiPLD_2DMB_PCASL",
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"BIDSVersion": "1.9.0",
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"DatasetType": "raw",
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"Authors": [
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"Ashley Ptinis",
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"Nicole Coverdale"
8+
],
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"HowToAcknowledge": "If you reference this dataset in your publications, please acknowledge its authors."
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}

‎2d_mb_pcasl/sub-1/anat/sub-1_T1w.json

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.249,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "Prisma_fit",
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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": "T1w_MPR",
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"ProtocolName": "T1w_MPR",
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"ScanningSequence": "GR\\IR",
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"SequenceVariant": "SK\\SP\\MP",
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"ScanOptions": "IR\\WE",
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"SequenceName": "*tfl3d1_16ns",
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"ImageType": [
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"ORIGINAL",
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"PRIMARY",
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"M",
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"ND",
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"NORM"
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],
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"SeriesNumber": 3,
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"AcquisitionNumber": 1,
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"SliceThickness": 0.8,
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"SAR": 0.042424,
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"EchoTime": 0.00222,
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"RepetitionTime": 2.5,
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"SpoilingState": true,
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"InversionTime": 1,
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"FlipAngle": 8,
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"PartialFourier": 1,
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"BaseResolution": 320,
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"ShimSetting": [
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],
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"TxRefAmp": 252.904,
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"PhaseResolution": 1,
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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": 32,
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"CoilCombinationMethod": "Adaptive Combine",
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"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
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"MatrixCoilMode": "GRAPPA",
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"PercentPhaseFOV": 93.75,
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"PercentSampling": 100,
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"PhaseEncodingSteps": 299,
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"AcquisitionMatrixPE": 300,
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"ReconMatrixPE": 300,
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"ParallelReductionFactorInPlane": 2,
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"PixelBandwidth": 220,
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"DwellTime": 7.1e-06,
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"ImageOrientationText": "Sag",
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"InPlanePhaseEncodingDirectionDICOM": "ROW",
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20211006"
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}

‎2d_mb_pcasl/sub-1/anat/sub-1_T1w.nii.gz

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‎2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.json

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.249,
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"Manufacturer": "Siemens",
6+
"ManufacturersModelName": "Prisma_fit",
7+
"BodyPartExamined": "BRAIN",
8+
"PatientPosition": "HFS",
9+
"SoftwareVersions": "syngo MR E11",
10+
"MRAcquisitionType": "2D",
11+
"SeriesDescription": "PCASLhr_SpinEchoFieldMap_AP",
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"ProtocolName": "PCASLhr_SpinEchoFieldMap_AP",
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"ScanningSequence": "EP",
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"SequenceVariant": "SK",
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"ScanOptions": "PFP\\FS",
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"SequenceName": "epse2d1_86",
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"ImageType": [
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"ORIGINAL",
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"PRIMARY",
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"M",
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"ND",
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"MOSAIC"
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],
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"AcquisitionNumber": 1,
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"SliceThickness": 2.27,
27+
"SpacingBetweenSlices": 2.497,
28+
"SAR": 0.135571,
29+
"EchoTime": 0.04,
30+
"RepetitionTime": 8,
31+
"FlipAngle": 90,
32+
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"TxRefAmp": 252.904,
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"ReceiveCoilName": "Head_32",
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"ReceiveCoilActiveElements": "HEA;HEP",
49+
"PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
50+
"CoilCombinationMethod": "Sum of Squares",
51+
"ConsistencyInfo": "N4_VE11E_LATEST_20181129",
52+
"MatrixCoilMode": "SENSE",
53+
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54+
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55+
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56+
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57+
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58+
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60+
"EffectiveEchoSpacing": 0.000569995,
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}

‎2d_mb_pcasl/sub-1/fmap/sub-1_dir-AP_epi.nii.gz

Whitespace-only changes.

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