Felix Hoffstaedter
3be8ee40fe
=== Do not change lines below ===
{
"chain": [],
"cmd": "./code/containers/scripts/singularity_cmd exec code/containers/images/bids/bids-mriqc--24.0.2.sing mriqc sourcedata/raw . participant --participant-label sub-0025 --no-datalad-get --no-sub --verbose --nprocs 1 --mem 3000 --work-dir /tmp --float32 --verbose-reports",
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"exit": 0,
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],
"inputs": [
"sourcedata/raw/sub-0025",
"sourcedata/raw/dataset_description.json"
],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
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616 lines
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<ul class="navbar-nav me-auto mb-2 mb-lg-0">
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<li class="nav-item"><a class="nav-link" href="#Basic echo-wise reports">Basic echo-wise reports</a></li>
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<li class="nav-item"><a class="nav-link" href="#Extended echo-wise reports">Extended echo-wise reports</a></li>
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<li class="nav-item"><a class="nav-link" href="#Extended reports shared across echos">Extended reports shared across echos</a></li>
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About
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<li><a class="dropdown-item" href="#errors">Errors</a></li>
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</div>
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</nav>
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<noscript>
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<h1 class="text-danger"> The navigation menu uses Javascript. Without it this report might not work as expected </h1>
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</noscript>
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<div id="Basic echo-wise reports" class="mt-5">
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<h1 class="sub-report-title pt-5 ps-4">Basic echo-wise reports</h1>
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<div id="acquisition-mb8_datatype-figures_desc-stdev_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Standard deviation of signal through time</h3><p class="elem-caption">The voxel-wise standard deviation of the signal (variability along time).</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-stdev_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-stdev_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-stdev_bold.svg</a></small>
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</div>
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<div id="acquisition-mb8_datatype-figures_desc-background_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">View of the background of the voxel-wise average of the BOLD timeseries</h3><p class="elem-caption">This panel shows a mosaic enhancing the background around the head. Artifacts usually unveil themselves in the air surrounding the head, where no signal sources are present.</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-background_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-background_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-background_bold.svg</a></small>
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</div>
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<div id="acquisition-mb8_datatype-figures_desc-zoomed_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Voxel-wise average of BOLD time-series, zoomed-in covering just the brain</h3><p class="elem-caption">This panel shows a mosaic of the brain. This mosaic is the most suitable to screen head-motion intensity inhomogeneities, global/local noise, signal leakage (for example, from the eyeballs and across the phase-encoding axis), etc.</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-zoomed_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-zoomed_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-zoomed_bold.svg</a></small>
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</div>
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<div id="acquisition-mb8_datatype-figures_desc-carpet_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Carpetplot and nuisance signals</h3><p class="elem-caption">The so-called «carpetplot» may assist in assessing head-motion derived artifacts and respiation effects.</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-carpet_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-carpet_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-carpet_bold.svg</a></small>
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</div>
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</div>
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<div id="Extended echo-wise reports" class="mt-5">
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<h1 class="sub-report-title pt-5 ps-4">Extended echo-wise reports</h1>
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<div id="acquisition-mb8_datatype-figures_desc-mean_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Voxel-wise average of BOLD time-series</h3><p class="elem-caption">The average signal calculated across the last axis (time).</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-mean_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-mean_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-mean_bold.svg</a></small>
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</div>
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</div>
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<div id="Extended reports shared across echos" class="mt-5">
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<h1 class="sub-report-title pt-5 ps-4">Extended reports shared across echos</h1>
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<div id="acquisition-mb8_datatype-figures_desc-brainmask_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Brain extraction performance</h3><p class="elem-caption">Brain mask as internally extracted by MRIQC. Defects on the brainmask could indicate problematic aspects of the image quality-wise.</p> <div class="reportlet">
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<img class="svg-reportlet" src="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-brainmask_bold.svg" style="width: 100%" />
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-brainmask_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-brainmask_bold.svg</a></small>
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</div>
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<div id="acquisition-mb8_datatype-figures_desc-norm_run-01_session-02_subject-0025_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
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<h3 class="run-title mt-3">Spatial normalization of the anatomical image</h3><p class="elem-caption">This panel shows a <em>quick-and-dirty</em> nonlinear registration into the <code>MNI152NLin2009cAsym</code> template accessed with <a href="https://templateflow.org/browse" target="_blank"><em>TemplateFlow</em></a>.</p> <div class="reportlet">
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<object class="svg-reportlet" type="image/svg+xml" data="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-norm_bold.svg" style="">
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Problem loading figure sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-norm_bold.svg. If the link below works, please try reloading the report in your browser.</object>
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</div>
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<small>Get figure file: <a href="./sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-norm_bold.svg" target="_blank">sub-0025/figures/sub-0025_ses-02_task-narratives_acq-mb8_run-01_desc-norm_bold.svg</a></small>
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</div>
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</div>
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<div id="About" class="mt-5">
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<h1 class="sub-report-title pt-5 ps-4">About</h1>
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<div id="errors" class="ps-4 pe-4 mb-2">
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<h2 class="sub-report-group mt-4">Errors</h2> <p class="alert alert-success" role="alert">No errors to report!</p>
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</div>
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<div id="meta-about-metadata" class="ps-4 pe-4 mb-2">
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<h2 class="sub-report-group mt-4">Reproducibility and provenance information</h2><p class="elem-caption">Thanks for using <em>MRIQC</em>. The following information may assist in
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reconstructing the provenance of the corresponding derivatives.
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</p> <div class="accordion accordion-flush" id="about-metadata">
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<div class="accordion-item">
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<h2 class="accordion-header" id="about-metadata-0">
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<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-0-collapse" aria-controls="about-metadata-0-collapse">
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Provenance Information
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</button>
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</h2>
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<div id="about-metadata-0-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-0-heading" data-bs-parent="#about-metadata-0">
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<div class="accordion-body metadata-table">
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<table id="about-metadata-table-0" class="table table-sm table-striped">
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<tr><td colspan=2>Execution environment</td><td>singularity</td></tr>
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<tr><td colspan=2>Input filename</td><td><BIDS root>/sub-0025/ses-02/func/sub-0025_ses-02_task-narratives_acq-mb8_run-01_bold.nii.gz</td></tr>
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<tr><td>Versions</td><td>MRIQC</td><td>24.1.0.dev0+gd5b13cb5.d20240826</td></tr>
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<tr><td>Versions</td><td>NiPype</td><td>1.8.6</td></tr>
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<tr><td>Versions</td><td>TemplateFlow</td><td>24.2.0</td></tr>
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<tr><td colspan=2>md5sum</td><td>bfa99f551d028c4efcc06ae965116738</td></tr>
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</table>
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</div>
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</div>
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</div>
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<div class="accordion-item">
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<h2 class="accordion-header" id="about-metadata-1">
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<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-1-collapse" aria-controls="about-metadata-1-collapse">
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Dataset Information
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</button>
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</h2>
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<div id="about-metadata-1-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-1-heading" data-bs-parent="#about-metadata-1">
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<div class="accordion-body metadata-table">
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<table id="about-metadata-table-1" class="table table-sm table-striped">
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<tr><td colspan=2>AcquisitionMatrixPE</td><td>82</td></tr>
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<tr><td colspan=2>AcquisitionNumber</td><td>1</td></tr>
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<tr><td colspan=2>AcquisitionTime</td><td>20:15:12.335000</td></tr>
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<tr><td colspan=2>BandwidthPerPixelPhaseEncode</td><td>24.888</td></tr>
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<tr><td colspan=2>BaseResolution</td><td>82</td></tr>
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<tr><td colspan=2>BodyPartExamined</td><td>BRAIN</td></tr>
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<tr><td colspan=2>ConsistencyInfo</td><td>N4_VE11E_LATEST_20181129</td></tr>
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<tr><td colspan=2>ConversionSoftware</td><td>dcm2niix</td></tr>
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<tr><td colspan=2>ConversionSoftwareVersion</td><td>v1.0.20201102</td></tr>
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<tr><td colspan=2>DerivedVendorReportedEchoSpacing</td><td>0.00049</td></tr>
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<tr><td colspan=2>DeviceSerialNumber</td><td>66112</td></tr>
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<tr><td colspan=2>DwellTime</td><td>2e-06</td></tr>
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<tr><td colspan=2>EchoTime</td><td>0.0272</td></tr>
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<tr><td colspan=2>EchoTrainLength</td><td>82</td></tr>
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<tr><td colspan=2>EffectiveEchoSpacing</td><td>0.00049</td></tr>
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<tr><td colspan=2>FlipAngle</td><td>44</td></tr>
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<tr><td colspan=2>ImageComments</td><td>Unaliased MB8/PE3</td></tr>
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<tr><td colspan=2>ImageOrientationPatientDICOM</td><td>[0.999796, 0.0162727, -0.011966, -0.017277, 0.995858, -0.0892672]</td></tr>
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<tr><td colspan=2>ImageType</td><td>['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']</td></tr>
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<tr><td colspan=2>ImagingFrequency</td><td>123.259</td></tr>
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<tr><td colspan=2>InPlanePhaseEncodingDirectionDICOM</td><td>COL</td></tr>
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<tr><td colspan=2>InstitutionAddress</td><td>Maynard 3,Hanover,NH,US,03755</td></tr>
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<tr><td colspan=2>InstitutionName</td><td>Dartmouth College - PBS</td></tr>
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<tr><td colspan=2>InstitutionalDepartmentName</td><td>Department</td></tr>
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<tr><td colspan=2>MRAcquisitionType</td><td>2D</td></tr>
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<tr><td colspan=2>MagneticFieldStrength</td><td>3</td></tr>
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<tr><td colspan=2>Manufacturer</td><td>Siemens</td></tr>
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<tr><td colspan=2>ManufacturersModelName</td><td>Prisma</td></tr>
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<tr><td colspan=2>Modality</td><td>MR</td></tr>
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<tr><td colspan=2>MultibandAccelerationFactor</td><td>8</td></tr>
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<tr><td colspan=2>PartialFourier</td><td>1</td></tr>
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<tr><td colspan=2>PatientPosition</td><td>HFS</td></tr>
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<tr><td colspan=2>PercentPhaseFOV</td><td>100</td></tr>
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<tr><td colspan=2>PercentSampling</td><td>100</td></tr>
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<tr><td colspan=2>PhaseEncodingDirection</td><td>j-</td></tr>
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<tr><td colspan=2>PhaseEncodingSteps</td><td>82</td></tr>
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<tr><td colspan=2>PhaseResolution</td><td>1</td></tr>
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<tr><td colspan=2>PixelBandwidth</td><td>3050</td></tr>
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<tr><td colspan=2>ProcedureStepDescription</td><td>Wager_Wager^1076_spacetop</td></tr>
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<tr><td colspan=2>ProtocolName</td><td>func_run-01_task-narratives_acq-ap-mb8</td></tr>
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<tr><td colspan=2>PulseSequenceDetails</td><td>%CustomerSeq%\cmrr_mbep2d_bold</td></tr>
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<tr><td colspan=2>ReceiveCoilActiveElements</td><td>HEA;HEP</td></tr>
|
|
<tr><td colspan=2>ReceiveCoilName</td><td>Head_32</td></tr>
|
|
<tr><td colspan=2>ReconMatrixPE</td><td>82</td></tr>
|
|
<tr><td colspan=2>RepetitionTime</td><td>0.46</td></tr>
|
|
<tr><td colspan=2>SAR</td><td>0.098047</td></tr>
|
|
<tr><td colspan=2>ScanOptions</td><td>FS</td></tr>
|
|
<tr><td colspan=2>ScanningSequence</td><td>EP</td></tr>
|
|
<tr><td colspan=2>SequenceName</td><td>epfid2d1_82</td></tr>
|
|
<tr><td colspan=2>SequenceVariant</td><td>SK\SS</td></tr>
|
|
<tr><td colspan=2>SeriesDescription</td><td>func_run-01_task-narratives_acq-ap-mb8</td></tr>
|
|
<tr><td colspan=2>SeriesNumber</td><td>10</td></tr>
|
|
<tr><td colspan=2>ShimSetting</td><td>[4222, -7760, -7253, 117, -143, -142, -138, 61]</td></tr>
|
|
<tr><td colspan=2>SliceThickness</td><td>2.7</td></tr>
|
|
<tr><td colspan=2>SliceTiming</td><td>[0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875, 0, 0.25, 0.0625, 0.315, 0.125, 0.3775, 0.1875]</td></tr>
|
|
<tr><td colspan=2>SoftwareVersions</td><td>syngo MR E11</td></tr>
|
|
<tr><td colspan=2>SpacingBetweenSlices</td><td>2.7</td></tr>
|
|
<tr><td colspan=2>StationName</td><td>AWP66112</td></tr>
|
|
<tr><td colspan=2>TaskName</td><td>narratives</td></tr>
|
|
<tr><td colspan=2>TotalReadoutTime</td><td>0.03969</td></tr>
|
|
<tr><td colspan=2>TxRefAmp</td><td>294.696</td></tr>
|
|
<tr><td colspan=2>WipMemBlock</td><td>68bd2eab-f699-4f70-a8f5-5b23eee9c569||Sequence: R016 ve11e/master r/434b28f1; Aug 7 2019 18:53:46 by eja</td></tr>
|
|
<tr><td>dcmmeta</td><td>affine</td><td>[[-2.6823794841766357, -0.04635284096002579, -0.028252320364117622, 112.27888488769531], [-0.04365839809179306, 2.671813726425171, -0.24153044819831848, -85.49154663085938], [-0.03210391104221344, 0.2394973635673523, 2.6890265941619873, -108.26502990722656], [0.0, 0.0, 0.0, 1.0]]</td></tr>
|
|
<tr><td>dcmmeta</td><td>reorient_transform</td><td>[[0.0, -1.0, 0.0, 81.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]</td></tr>
|
|
<tr><td>dcmmeta</td><td>shape</td><td>[82, 82, 56, 967]</td></tr>
|
|
<tr><td>dcmmeta</td><td>slice_dim</td><td>2</td></tr>
|
|
<tr><td>dcmmeta</td><td>version</td><td>0.6</td></tr>
|
|
<tr><td colspan=2>time</td><td>{'samples': {'AcquisitionNumber': [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 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8901.0, 8928.0, 8955.0, 8913.0, 8934.0, 8986.0, 8915.0, 8916.0, 8962.0, 8898.0, 8914.0, 8958.0, 8888.0, 8901.0, 8946.0, 8872.0, 8906.0, 8948.0, 8910.0, 8946.0, 8976.0, 8929.0, 8941.0, 8906.0, 8894.0, 8937.0, 8912.0, 8916.0, 8904.0, 8935.0, 8962.0, 8916.0, 8951.0, 8933.0, 8937.0, 8967.0, 8936.0, 8939.0, 8945.0, 8934.0, 8917.0, 8936.0, 8956.0, 8968.0, 8942.0, 8968.0, 8944.0, 8958.0, 8952.0, 8940.0, 8971.0, 8924.0, 8943.0, 8993.0, 8952.0, 8935.0, 8965.0, 8906.0, 8934.0, 8957.0, 8896.0, 8914.0, 8961.0, 8896.0, 8930.0, 8959.0, 8919.0, 8932.0, 8929.0, 8930.0, 8958.0, 8928.0, 8918.0, 8983.0, 8940.0, 8941.0, 8938.0, 8955.0, 8970.0, 8897.0, 8943.0, 8989.0, 8960.0, 8975.0, 8946.0, 8957.0, 8996.0, 8989.0, 8938.0, 8954.0, 8919.0, 8908.0, 8912.0, 8914.0, 8924.0, 8945.0, 8904.0, 8947.0, 8982.0, 8908.0, 8910.0, 8916.0, 8906.0, 8918.0, 8931.0, 8911.0, 8974.0, 8975.0, 8911.0, 8938.0, 8908.0, 8911.0, 8938.0, 8888.0, 8888.0, 8936.0, 8904.0, 8916.0, 8948.0, 8930.0, 8920.0, 8965.0, 8922.0, 8941.0, 8964.0, 8884.0, 8914.0, 8949.0, 8912.0, 8915.0, 8962.0, 8939.0, 8943.0, 8953.0, 8943.0, 8972.0, 8922.0, 8940.0, 8990.0, 8938.0, 8966.0, 8922.0, 8969.0, 8982.0, 8957.0, 8972.0, 8930.0, 8977.0, 9019.0, 8935.0, 8919.0, 8958.0, 8893.0, 8925.0, 8954.0, 8913.0, 8930.0, 8953.0, 8924.0, 8927.0, 8958.0, 8916.0, 8946.0, 8972.0, 8929.0, 8947.0, 8911.0, 8914.0, 8939.0, 8908.0, 8910.0, 8955.0, 8897.0, 8931.0, 8963.0, 8939.0, 8941.0, 8932.0, 8937.0, 8965.0, 8944.0, 8930.0, 8963.0, 8921.0, 8943.0, 8969.0, 8938.0, 8942.0, 8969.0, 8905.0, 8923.0, 8968.0, 8941.0, 8959.0, 8987.0, 8956.0, 8971.0, 8979.0, 8921.0, 8951.0, 8923.0, 8957.0, 8971.0, 8941.0, 8978.0, 8989.0, 8939.0, 8958.0, 8915.0, 8930.0, 8961.0, 8917.0, 8957.0, 8923.0, 8951.0, 8949.0, 8940.0, 8984.0, 8925.0, 8938.0, 9005.0, 8920.0, 8936.0, 8936.0, 8960.0, 8984.0, 8926.0, 8973.0, 8957.0, 8945.0, 8986.0, 8942.0, 8975.0, 8990.0, 8920.0, 8937.0, 8994.0, 8930.0, 8911.0, 8941.0, 8888.0, 8907.0, 8936.0, 8900.0, 8907.0, 8940.0, 8906.0, 8895.0, 8941.0, 8884.0, 8919.0, 8945.0, 8903.0, 8923.0, 8963.0, 8903.0, 8918.0, 8957.0, 8918.0, 8932.0, 8944.0, 8921.0, 8952.0, 8977.0, 8914.0, 8919.0, 8947.0, 8936.0, 8958.0, 8967.0, 8937.0, 8923.0, 8945.0, 8917.0, 8938.0, 8906.0, 8942.0, 8970.0, 8963.0, 8952.0, 8943.0, 8944.0, 8992.0, 8936.0, 8966.0, 8977.0, 8951.0, 9013.0, 8935.0, 8980.0, 9010.0, 8968.0, 8999.0, 8952.0, 8983.0, 9016.0, 8940.0, 8940.0, 8985.0, 8950.0, 8952.0, 8948.0, 8939.0, 8982.0, 8907.0, 8935.0, 8988.0, 8942.0, 8913.0, 8959.0, 8923.0, 8917.0, 8961.0, 8923.0, 8910.0, 8954.0, 8910.0, 8918.0, 8961.0, 8936.0, 8941.0, 8982.0, 8938.0, 8951.0, 8976.0, 8918.0, 8954.0, 8894.0, 8942.0, 8973.0, 8912.0, 8937.0, 8966.0, 8892.0, 8954.0, 9003.0, 8948.0, 8990.0, 8960.0, 8980.0, 8948.0, 8963.0, 8992.0, 8943.0, 8917.0, 8963.0, 8925.0, 8914.0, 8978.0, 8903.0, 8920.0, 8962.0, 8899.0, 8914.0, 8952.0, 8882.0, 8902.0, 8959.0, 8948.0, 8940.0, 8965.0, 8935.0, 8923.0, 8962.0, 8946.0, 8955.0, 8950.0, 8939.0, 8968.0, 8931.0, 8921.0, 8966.0, 8930.0, 8921.0, 8967.0, 8923.0, 8940.0, 8968.0, 8937.0, 8951.0, 8964.0, 8933.0, 8967.0, 8925.0, 8941.0, 8969.0, 8907.0, 8942.0, 8982.0, 8888.0, 8916.0, 8964.0, 8949.0, 8956.0, 8949.0, 8939.0, 8968.0, 8914.0, 8934.0, 8964.0, 8922.0, 8941.0, 8984.0, 8939.0, 8941.0, 8966.0, 8922.0, 8957.0, 8967.0, 8945.0, 8989.0, 8926.0, 8942.0, 8985.0, 8952.0, 8970.0, 8927.0, 8958.0, 8969.0, 8942.0, 8987.0, 8940.0, 8958.0, 8984.0, 8936.0, 8985.0, 8945.0, 8921.0, 8925.0, 8931.0, 8961.0, 8936.0, 8942.0, 8938.0, 8941.0, 8986.0, 8955.0, 8976.0, 8972.0, 8945.0, 8992.0, 8963.0, 8939.0, 8981.0, 8939.0, 8956.0, 8988.0, 8950.0, 8987.0, 8957.0, 8959.0, 8981.0, 8939.0, 8973.0, 8932.0, 8966.0, 8965.0, 8966.0, 8972.0, 8910.0, 8944.0, 8987.0, 8949.0, 9001.0, 8986.0, 8970.0, 9016.0, 8967.0, 8994.0, 8931.0, 8960.0, 8988.0, 8939.0, 8974.0, 9016.0, 8941.0, 8939.0, 8986.0, 8914.0, 8932.0, 8958.0, 8881.0, 8914.0, 8975.0, 8913.0, 8918.0, 8968.0, 8923.0, 8941.0, 8965.0, 8903.0, 8933.0, 8962.0, 8889.0, 8938.0, 8966.0, 8956.0, 8960.0, 8970.0, 8948.0, 8993.0, 8911.0, 8943.0, 9003.0, 8944.0, 8977.0, 8988.0, 8956.0, 8975.0, 8986.0, 8921.0, 8970.0, 8948.0, 8938.0, 8962.0, 8923.0, 8955.0, 8980.0, 8936.0, 8972.0, 8965.0, 8938.0, 8969.0, 8929.0, 8950.0, 8962.0, 8933.0, 8967.0, 8900.0, 8944.0, 8985.0, 8960.0, 8977.0, 8986.0, 8922.0, 8951.0, 8963.0, 8915.0, 8909.0, 8938.0, 8922.0, 8966.0, 8945.0, 8917.0, 8961.0, 8931.0, 8925.0, 8966.0, 8953.0, 8942.0, 8967.0, 8954.0, 8970.0, 8982.0, 8937.0, 8949.0, 8954.0, 8975.0, 8997.0, 8949.0, 8946.0, 8985.0, 8926.0, 8955.0, 8968.0, 8947.0, 8992.0, 8981.0, 8983.0, 8970.0, 8945.0, 9005.0, 8977.0, 8964.0, 8958.0, 8965.0, 9011.0, 8953.0, 8999.0, 8993.0, 8950.0, 9007.0, 8966.0, 8997.0, 8960.0, 8960.0, 8997.0, 8955.0, 8941.0, 8996.0, 8956.0, 8942.0, 8989.0, 8945.0, 8937.0, 8981.0, 8928.0, 8914.0, 8964.0, 8930.0, 8921.0, 8967.0, 8946.0, 8919.0, 8963.0, 8929.0, 8922.0, 8981.0, 8922.0, 8942.0, 8984.0, 8924.0, 8938.0, 8966.0, 8940.0, 8971.0, 8943.0, 8962.0, 8954.0, 8946.0, 8972.0, 8930.0, 8963.0, 8972.0, 8962.0, 8992.0, 8933.0, 8973.0, 8926.0, 8957.0, 8952.0, 8942.0, 8987.0, 8921.0, 8945.0, 9009.0, 8951.0, 8921.0, 8983.0, 8932.0, 8935.0, 8960.0, 8940.0, 8910.0, 8952.0, 8938.0, 8916.0, 8962.0, 8922.0, 8940.0, 8968.0, 8939.0, 8940.0, 8959.0, 8918.0, 8932.0, 8937.0, 8941.0, 8976.0, 8963.0, 8978.0, 8975.0, 8950.0, 8994.0, 8942.0, 8944.0, 9006.0, 8963.0, 8976.0, 8946.0, 8948.0]}, 'slices': {}}</td></tr>
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</table>
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</div>
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</div>
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</div>
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<div class="accordion-item">
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<h2 class="accordion-header" id="about-metadata-2">
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<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-2-collapse" aria-controls="about-metadata-2-collapse">
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Extracted Image quality metrics (IQMs)
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</button>
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</h2>
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<div id="about-metadata-2-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-2-heading" data-bs-parent="#about-metadata-2">
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<div class="accordion-body metadata-table">
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<table id="about-metadata-table-2" class="table table-sm table-striped">
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<tr><td colspan=3>aor</td><td>0.00021452849740932645</td></tr>
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<tr><td colspan=3>aqi</td><td>0.02180850445595855</td></tr>
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<tr><td colspan=3>dummy_trs</td><td>2</td></tr>
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<tr><td>dvars</td><td colspan=2>nstd</td><td>44.15782719924268</td></tr>
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<tr><td>dvars</td><td colspan=2>std</td><td>1.2950857363589199</td></tr>
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<tr><td>dvars</td><td colspan=2>vstd</td><td>0.9961955736721992</td></tr>
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<tr><td colspan=3>efc</td><td>0.5143</td></tr>
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<tr><td colspan=3>fber</td><td>3892.2017</td></tr>
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<tr><td>fd</td><td colspan=2>mean</td><td>0.10157798579219308</td></tr>
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<tr><td>fd</td><td colspan=2>num</td><td>44</td></tr>
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<tr><td>fd</td><td colspan=2>perc</td><td>4.5595854922279795</td></tr>
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<tr><td>fwhm</td><td colspan=2>avg</td><td>2.2614830054256925</td></tr>
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<tr><td>fwhm</td><td colspan=2>x</td><td>2.1829815843172993</td></tr>
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<tr><td>fwhm</td><td colspan=2>y</td><td>2.4905933951650807</td></tr>
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<tr><td>fwhm</td><td colspan=2>z</td><td>2.1108740367946974</td></tr>
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<tr><td colspan=3>gcor</td><td>0.0116439</td></tr>
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<tr><td>gsr</td><td colspan=2>x</td><td>-0.004948325455188751</td></tr>
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<tr><td>gsr</td><td colspan=2>y</td><td>0.03350474685430527</td></tr>
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<tr><td>size</td><td colspan=2>t</td><td>965</td></tr>
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<tr><td>size</td><td colspan=2>x</td><td>82</td></tr>
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<tr><td>size</td><td colspan=2>y</td><td>82</td></tr>
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<tr><td>size</td><td colspan=2>z</td><td>56</td></tr>
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<tr><td colspan=3>snr</td><td>4.361902815667244</td></tr>
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<tr><td>spacing</td><td colspan=2>tr</td><td>0.46000000834465027</td></tr>
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<tr><td>spacing</td><td colspan=2>x</td><td>2.682926893234253</td></tr>
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<tr><td>spacing</td><td colspan=2>y</td><td>2.682926893234253</td></tr>
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<tr><td>spacing</td><td colspan=2>z</td><td>2.700000047683716</td></tr>
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<tr><td>summary</td><td>bg</td><td>k</td><td>20.5814</td></tr>
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<tr><td>summary</td><td>bg</td><td>mad</td><td>51.0092</td></tr>
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<tr><td>summary</td><td>bg</td><td>mean</td><td>211.9889</td></tr>
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<tr><td>summary</td><td>bg</td><td>median</td><td>53.0</td></tr>
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<tr><td>summary</td><td>bg</td><td>n</td><td>292786.0</td></tr>
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<tr><td>summary</td><td>bg</td><td>p05</td><td>15.0</td></tr>
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<tr><td>summary</td><td>bg</td><td>p95</td><td>1048.0</td></tr>
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<tr><td>summary</td><td>bg</td><td>stdv</td><td>389.0973</td></tr>
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<tr><td>summary</td><td>fg</td><td>k</td><td>3.5141</td></tr>
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<tr><td>summary</td><td>fg</td><td>mad</td><td>460.4264</td></tr>
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<tr><td>summary</td><td>fg</td><td>mean</td><td>3205.9167</td></tr>
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<tr><td>summary</td><td>fg</td><td>median</td><td>3333.0</td></tr>
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<tr><td>summary</td><td>fg</td><td>n</td><td>83758.0</td></tr>
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<tr><td>summary</td><td>fg</td><td>p05</td><td>1412.0</td></tr>
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<tr><td>summary</td><td>fg</td><td>p95</td><td>4101.0</td></tr>
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<tr><td>summary</td><td>fg</td><td>stdv</td><td>764.1115</td></tr>
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<tr><td colspan=3>tsnr</td><td>43.04853090411052</td></tr>
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</table>
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</div>
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</div>
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</div>
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</div>
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</div>
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</div>
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<div id="qcrating-menu" class="card position-fixed d-none" style="width: 30%; top: 100px; left: 65%; max-height: 85%; overflow-y: auto;">
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<div class="card-header m-0">
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Rating widget
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<button type="button" class="btn-close position-absolute top-0 end-0" aria-label="Close" id="close-qcrating-menu" onclick="toggle_rating()" style="margin: 10px 10px 0 0"></button>
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</div>
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<div class="card-body">
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<div class="accordion">
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<div class="accordion-item">
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<h2 class="accordion-header" id="qcslider-head">
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|
<button class="accordion-button" type="button" data-bs-toggle="collapse" data-bs-target="#qcslider-collapse" aria-expanded="true" aria-controls="qcslider-collapse">Overall Quality Rating</button>
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</h2>
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<div id="qcslider-collapse" class="accordion-collapse collapse show" aria-labelledby="qcslider-head">
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<div class="accordion-body">
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<input type="range" min="1.0" max="4.0" step="0.05" value="2.5" id="qcslider" class="slider">
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<ul class="list-group list-group-horizontal slider-labels" style="width: 100%">
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<li class="list-group-item list-group-item-danger small" style="font-size: 0.7em; width: 25%; text-align:center">Exclude</li>
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<li class="list-group-item list-group-item-warning small" style="font-size: 0.7em; width: 25%; text-align:center">Poor</li>
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<li class="list-group-item list-group-item-primary small" style="font-size: 0.7em; width: 25%; text-align:center">Acceptable</li>
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<li class="list-group-item list-group-item-success small" style="font-size: 0.7em; width: 25%; text-align:center">Excellent</li>
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</ul>
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</div>
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</div>
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</div>
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<div class="accordion-item">
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<h2 class="accordion-header" id="qcartifacts-head">
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<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#qcartifacts-collapse" aria-expanded="false" aria-controls="qcartifacts-collapse">
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Record specific artifacts
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</button>
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</h2>
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<div id="qcartifacts-collapse" class="accordion-collapse collapse" aria-labelledby="qcartifacts-head">
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<div class="accordion-body">
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<fieldset id="qcartifacts-group" class="form-group">
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<div class="form-check form-switch small">
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<input class="form-check-input" type="checkbox" name="head-motion" id="qcartifacts-item-0" />
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<label class="form-check-label" for="qcartifacts-item-0">Head motion artifacts</label>
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</div>
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<div class="form-check form-switch small">
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<input class="form-check-input" type="checkbox" name="eye-spillover" id="qcartifacts-item-1" />
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<label class="form-check-label" for="qcartifacts-item-1">Eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
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</div>
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<div class="form-check form-switch small">
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<input class="form-check-input" type="checkbox" name="noneye-spillover" id="qcartifacts-item-2" />
|
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<label class="form-check-label" for="qcartifacts-item-2">Non-eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
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</div>
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<div class="form-check form-switch small">
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<input class="form-check-input" type="checkbox" name="coil-failure" id="qcartifacts-item-3" />
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<label class="form-check-label" for="qcartifacts-item-3">Coil failure</label>
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</div>
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<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="noise-global" id="qcartifacts-item-4" />
|
|
<label class="form-check-label" for="qcartifacts-item-4">Global noise</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="noise-local" id="qcartifacts-item-5" />
|
|
<label class="form-check-label" for="qcartifacts-item-5">Local noise</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="em-perturbation" id="qcartifacts-item-6" />
|
|
<label class="form-check-label" for="qcartifacts-item-6"><abbr title="electromagnetic">EM</abbr> interference/perturbation</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="wrap-around" id="qcartifacts-item-7" />
|
|
<label class="form-check-label" for="qcartifacts-item-7">Problematic <abbr title="field-of-view">FoV</abbr> prescription / wrap-around</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="ghost-aliasing" id="qcartifacts-item-8" />
|
|
<label class="form-check-label" for="qcartifacts-item-8">Aliasing ghosts</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="ghost-other" id="qcartifacts-item-9" />
|
|
<label class="form-check-label" for="qcartifacts-item-9">Other ghosts (for example, <abbr title="radiofrequency">RF</abbr> spoiling)</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="inu" id="qcartifacts-item-10" />
|
|
<label class="form-check-label" for="qcartifacts-item-10">Intensity non-uniformity (B<sub>1</sub> bias)</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="field-variation" id="qcartifacts-item-11" />
|
|
<label class="form-check-label" for="qcartifacts-item-11">Temporal B<sub>1</sub> field non-uniformity variation</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="processing" id="qcartifacts-item-12" />
|
|
<label class="form-check-label" for="qcartifacts-item-12">Processing such as denoising, defacing or resamplings happened</label>
|
|
</div>
|
|
<div class="form-check form-switch small">
|
|
<input class="form-check-input" type="checkbox" name="uncategorized" id="qcartifacts-item-13" />
|
|
<label class="form-check-label" for="qcartifacts-item-13">Other uncategorized artifact(s)</label>
|
|
</div>
|
|
</fieldset>
|
|
</div> <!-- accordion-body -->
|
|
</div> <!-- accordion-collapse -->
|
|
</div> <!-- accordion-item -->
|
|
<div class="accordion-item">
|
|
<h2 class="accordion-header" id="qcextra-head">
|
|
<button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#qcextra-collapse" aria-expanded="false" aria-controls="qcextra-collapse">
|
|
Extra details
|
|
</button>
|
|
</h2>
|
|
<div id="qcextra-collapse" class="accordion-collapse collapse" aria-labelledby="qcextra-head">
|
|
<div class="accordion-body">
|
|
<div class="input-group">
|
|
<span class="input-group-text">Comments</span>
|
|
<textarea class="form-control" aria-label="Comments" id="qcextra-comments"></textarea>
|
|
</div>
|
|
|
|
<p style="margin-top: 20px; font-weight: bold">Rater confidence</p>
|
|
<input type="range" min="0.0" max="4.0" step="0.05" value="3.5" id="qcextra-confidence" class="slider" style="margin-left: 22%;width: 56%;">
|
|
<ul class="list-group list-group-horizontal slider-labels" style="width: 100%">
|
|
<li class="list-group-item list-group-item-warning small" style="width: 50%; text-align:center">Doubtful</li>
|
|
<li class="list-group-item list-group-item-success bg-success text-white small" style="width: 50%; text-align:center">Confident</li>
|
|
</ul>
|
|
</div> <!-- accordion-body -->
|
|
</div> <!-- accordion-collapse -->
|
|
</div> <!-- accordion-item -->
|
|
</div>
|
|
<div style="margin-top: 10px">
|
|
<a class="btn btn-primary disabled" id="btn-download" href="">Download</a>
|
|
<button class="btn btn-primary" id="btn-post" value="8sSYVI0XjFqacEMZ8wF4" disabled>Share publicly</button>
|
|
</div>
|
|
<script type="text/javascript">
|
|
var MINIMUM_RATING_TIME = 10
|
|
$('#qcslider').on('input', function() {
|
|
|
|
if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
|
|
$('#btn-download').removeClass('disabled');
|
|
$('#btn-download').removeAttr('aria-disabled');
|
|
$('#btn-post').removeAttr('disabled');
|
|
};
|
|
|
|
$('#qcslider-collapse .list-group-item').removeClass(function(index, classname) {
|
|
return (classname.match(/(^|\s)bg-\S+/g) || []).join(' ');
|
|
});
|
|
$('#qcslider-collapse .list-group-item').removeClass(function(index, classname) {
|
|
return (classname.match(/(^|\s)text-\S+/g) || []).join(' ');
|
|
});
|
|
|
|
if ( $(this).val() < 1.5 ) {
|
|
$('#qcslider-collapse .list-group-item-danger').addClass('bg-danger text-white');
|
|
} else if ( $(this).val() > 3.5 ) {
|
|
$('#qcslider-collapse .list-group-item-success').addClass('bg-success text-white');
|
|
} else if ( $(this).val() < 2.5 ) {
|
|
$('#qcslider-collapse .list-group-item-warning').addClass('bg-warning text-dark');
|
|
} else {
|
|
$('#qcslider-collapse .list-group-item-primary').addClass('bg-primary text-white');
|
|
};
|
|
|
|
var payload = read_form();
|
|
});
|
|
|
|
$('#qcextra-confidence').on('input', function() {
|
|
if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
|
|
$('#btn-download').removeClass('disabled');
|
|
$('#btn-download').removeAttr('aria-disabled');
|
|
$('#btn-post').removeAttr('disabled');
|
|
};
|
|
|
|
$('#qcextra-collapse .list-group-item').removeClass(function(index, classname) {
|
|
return (classname.match(/(^|\s)bg-\S+/g) || []).join(' ');
|
|
});
|
|
$('#qcextra-collapse .list-group-item').removeClass(function(index, classname) {
|
|
return (classname.match(/(^|\s)text-\S+/g) || []).join(' ');
|
|
});
|
|
|
|
if ( $(this).val() < 2.0 ) {
|
|
$('#qcextra-collapse .list-group-item-warning').addClass('bg-warning text-dark');
|
|
} else {
|
|
$('#qcextra-collapse .list-group-item-success').addClass('bg-success text-white');
|
|
};
|
|
|
|
var payload = read_form();
|
|
});
|
|
|
|
|
|
$('#qcextra-comments').bind('input propertychange', function() {
|
|
if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
|
|
$('#btn-download').removeClass('disabled');
|
|
$('#btn-download').removeAttr('aria-disabled');
|
|
$('#btn-post').removeAttr('disabled');
|
|
};
|
|
});
|
|
|
|
$( '#btn-post' ).click( function() {
|
|
var payload = read_form();
|
|
var md5sum = "unspecified";
|
|
var params = {
|
|
'rating': payload['rating'],
|
|
'md5sum': md5sum,
|
|
'name': "",
|
|
'comment': JSON.stringify(payload['artifacts'])
|
|
};
|
|
|
|
// disable development releases
|
|
var authorization = $(this).val();
|
|
var ratingReq = new XMLHttpRequest();
|
|
ratingReq.open("POST", "https://mriqc.nimh.nih.gov:443/api/v1/rating");
|
|
ratingReq.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
|
|
ratingReq.setRequestHeader("Authorization", authorization);
|
|
ratingReq.onload = function () {
|
|
status = ratingReq.status;
|
|
$('#btn-post').removeClass('btn-primary');
|
|
$('#btn-post').attr('disabled', true);
|
|
$('#btn-post').attr('aria-disabled', true);
|
|
$('#btn-post').prop('disabled');
|
|
$('#btn-post').addClass('disabled');
|
|
$('#btn-post').removeClass('active');
|
|
if (status === "201") {
|
|
$('#btn-post').addClass('btn-success');
|
|
$('#btn-post').html('Posted!');
|
|
} else {
|
|
$('#btn-post').addClass('btn-danger');
|
|
$('#btn-post').html('Failed');
|
|
};
|
|
};
|
|
ratingReq.send(JSON.stringify(params));
|
|
});
|
|
|
|
$( 'body' ).on( 'click', '#qcartifacts-group input', function(e) {
|
|
if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
|
|
$('#btn-download').removeClass('disabled');
|
|
$('#btn-download').removeAttr('aria-disabled');
|
|
$('#btn-post').removeAttr('disabled');
|
|
};
|
|
|
|
var payload = read_form();
|
|
});
|
|
|
|
$( 'body' ).on( 'click', '#qcrating-toggler', function(e) {
|
|
toggle_rating();
|
|
});
|
|
</script>
|
|
</div>
|
|
|
|
<script type="text/javascript">
|
|
function toggle(id) {
|
|
var element = document.getElementById(id);
|
|
if(element.style.display == 'block')
|
|
element.style.display = 'none';
|
|
else
|
|
element.style.display = 'block';
|
|
}
|
|
</script>
|
|
</body>
|
|
</html> |