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- <div id="Basic visual report" class="mt-5">
- <h1 class="sub-report-title pt-5 ps-4">Basic visual report</h1>
- <div id="datatype-figures_desc-zoomed_subject-10377_suffix-T1w" class="ps-4 pe-4 mb-2">
- <h3 class="run-title mt-3">Zoomed-in mosaic view of 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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- </div>
- <small>Get figure file: <a href="./sub-10377/figures/sub-10377_desc-zoomed_T1w.svg" target="_blank">sub-10377/figures/sub-10377_desc-zoomed_T1w.svg</a></small>
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- <div id="datatype-figures_desc-background_subject-10377_suffix-T1w" class="ps-4 pe-4 mb-2">
- <h3 class="run-title mt-3">View of the background of the anatomical image</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">
- <img class="svg-reportlet" src="./sub-10377/figures/sub-10377_desc-background_T1w.svg" style="width: 100%" />
- </div>
- <small>Get figure file: <a href="./sub-10377/figures/sub-10377_desc-background_T1w.svg" target="_blank">sub-10377/figures/sub-10377_desc-background_T1w.svg</a></small>
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- <div id="About" class="mt-5">
- <h1 class="sub-report-title pt-5 ps-4">About</h1>
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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 id="meta-about-metadata" class="ps-4 pe-4 mb-2">
- <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
- reconstructing the provenance of the corresponding derivatives.
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- <div class="accordion-body metadata-table">
- <table id="about-metadata-table-0" class="table table-sm table-striped">
- <tr><td colspan=2>Execution environment</td><td>singularity</td></tr>
- <tr><td colspan=2>Input filename</td><td><BIDS root>/sub-10377/anat/sub-10377_T1w.nii.gz</td></tr>
- <tr><td>Versions</td><td>MRIQC</td><td>23.1.0</td></tr>
- <tr><td>Versions</td><td>NiPype</td><td>1.8.6</td></tr>
- <tr><td>Versions</td><td>TemplateFlow</td><td>0.8.1</td></tr>
- <tr><td colspan=2>md5sum</td><td>b631b0b9950229269e08b749957ceb3d</td></tr>
- <tr><td>warnings</td><td>large_rot_frame</td><td>True</td></tr>
- <tr><td>warnings</td><td>small_air_mask</td><td>False</td></tr>
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- </div>
- </div>
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- <h2 class="accordion-header" id="about-metadata-1">
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- Dataset Information
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- <tr><td>AccelNumReferenceLines</td><td>32</td></tr>
- <tr><td>AccelerationFactorPE</td><td>2</td></tr>
- <tr><td>AcquisitionMatrix</td><td>0/256/256/0</td></tr>
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- <tr><td>EchoTime</td><td>0.0035</td></tr>
- <tr><td>EchoTrainLength</td><td>1</td></tr>
- <tr><td>FlipAngle</td><td>7</td></tr>
- <tr><td>ImageType</td><td>ORIGINAL/PRIMARY/M/ND/NORM</td></tr>
- <tr><td>ImagingFrequency</td><td>123250095</td></tr>
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- <tr><td>NumberOfAverages</td><td>1</td></tr>
- <tr><td>NumberOfPhaseEncodingSteps</td><td>255</td></tr>
- <tr><td>PatientPosition</td><td>HFS</td></tr>
- <tr><td>PercentPhaseFieldOfView</td><td>100</td></tr>
- <tr><td>PercentSampling</td><td>100</td></tr>
- <tr><td>PhaseEncodingDirection</td><td>i-</td></tr>
- <tr><td>PixelBandwidth</td><td>200</td></tr>
- <tr><td>ProtocolName</td><td>MPRAGE - BWM</td></tr>
- <tr><td>ReceiveCoilName</td><td>HeadMatrix</td></tr>
- <tr><td>RepetitionTime</td><td>2.53</td></tr>
- <tr><td>ScanOptions</td><td>IR</td></tr>
- <tr><td>ScanningSequence</td><td>GR/IR</td></tr>
- <tr><td>SequenceName</td><td>*tfl3d1_ns</td></tr>
- <tr><td>SequenceVariant</td><td>SP/MP</td></tr>
- <tr><td>SoftwareVersions</td><td>syngo MR B15</td></tr>
- <tr><td>TotalScanTimeSec</td><td>363</td></tr>
- <tr><td>TransmitCoilName</td><td>Body</td></tr>
- <tr><td>VariableFlipAngleFlag</td><td>N</td></tr>
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- Extracted Image quality metrics (IQMs)
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- <tr><td colspan=3>cjv</td><td>0.9301269751374728</td></tr>
- <tr><td colspan=3>cnr</td><td>0.9187957956119976</td></tr>
- <tr><td colspan=3>efc</td><td>0.6619267432121638</td></tr>
- <tr><td colspan=3>fber</td><td>3492.744696437838</td></tr>
- <tr><td>fwhm</td><td colspan=2>avg</td><td>3.108005567765568</td></tr>
- <tr><td>fwhm</td><td colspan=2>x</td><td>2.99128</td></tr>
- <tr><td>fwhm</td><td colspan=2>y</td><td>3.303961318681319</td></tr>
- <tr><td>fwhm</td><td colspan=2>z</td><td>3.0287753846153844</td></tr>
- <tr><td>icvs</td><td colspan=2>csf</td><td>0.2593425086734089</td></tr>
- <tr><td>icvs</td><td colspan=2>gm</td><td>0.365076682283451</td></tr>
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- <tr><td>inu</td><td colspan=2>med</td><td>0.742638349533081</td></tr>
- <tr><td>inu</td><td colspan=2>range</td><td>0.34297496676445016</td></tr>
- <tr><td>qi</td><td colspan=2>1</td><td>0.0</td></tr>
- <tr><td>qi</td><td colspan=2>2</td><td>0.0009400746926458012</td></tr>
- <tr><td>rpve</td><td colspan=2>csf</td><td>3.62460112972019</td></tr>
- <tr><td>rpve</td><td colspan=2>gm</td><td>3.463726801527138</td></tr>
- <tr><td>rpve</td><td colspan=2>wm</td><td>3.5489832964136045</td></tr>
- <tr><td>size</td><td colspan=2>x</td><td>176</td></tr>
- <tr><td>size</td><td colspan=2>y</td><td>256</td></tr>
- <tr><td>size</td><td colspan=2>z</td><td>256</td></tr>
- <tr><td>snr</td><td colspan=2>csf</td><td>1.6449811477287057</td></tr>
- <tr><td>snr</td><td colspan=2>gm</td><td>4.220214299372831</td></tr>
- <tr><td>snr</td><td colspan=2>total</td><td>4.6628198522087265</td></tr>
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- <tr><td>snrd</td><td colspan=2>gm</td><td>56.07934447029552</td></tr>
- <tr><td>snrd</td><td colspan=2>total</td><td>51.636949520530294</td></tr>
- <tr><td>snrd</td><td colspan=2>wm</td><td>71.98712479438849</td></tr>
- <tr><td>spacing</td><td colspan=2>x</td><td>1.0</td></tr>
- <tr><td>spacing</td><td colspan=2>y</td><td>0.7109375</td></tr>
- <tr><td>spacing</td><td colspan=2>z</td><td>0.7109375</td></tr>
- <tr><td>summary</td><td>bg</td><td>k</td><td>121.31463586472502</td></tr>
- <tr><td>summary</td><td>bg</td><td>mad</td><td>9.020182195565457</td></tr>
- <tr><td>summary</td><td>bg</td><td>mean</td><td>28.899694565348373</td></tr>
- <tr><td>summary</td><td>bg</td><td>median</td><td>6.084020435810089</td></tr>
- <tr><td>summary</td><td>bg</td><td>n</td><td>3175833.0</td></tr>
- <tr><td>summary</td><td>bg</td><td>p05</td><td>0.0</td></tr>
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- <tr><td>summary</td><td>bg</td><td>stdv</td><td>92.00647980969565</td></tr>
- <tr><td>summary</td><td>csf</td><td>k</td><td>-0.9022984616318968</td></tr>
- <tr><td>summary</td><td>csf</td><td>mad</td><td>193.66331173879036</td></tr>
- <tr><td>summary</td><td>csf</td><td>mean</td><td>391.264848934784</td></tr>
- <tr><td>summary</td><td>csf</td><td>median</td><td>369.6042414754629</td></tr>
- <tr><td>summary</td><td>csf</td><td>n</td><td>804094.0419075459</td></tr>
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- <tr><td>summary</td><td>csf</td><td>p95</td><td>772.488074734807</td></tr>
- <tr><td>summary</td><td>csf</td><td>stdv</td><td>224.68586473420524</td></tr>
- <tr><td>summary</td><td>gm</td><td>k</td><td>2.699322829150619</td></tr>
- <tr><td>summary</td><td>gm</td><td>mad</td><td>102.28886609771229</td></tr>
- <tr><td>summary</td><td>gm</td><td>mean</td><td>782.0424512233907</td></tr>
- <tr><td>summary</td><td>gm</td><td>median</td><td>772.1230335086584</td></tr>
- <tr><td>summary</td><td>gm</td><td>n</td><td>1131923.9046660622</td></tr>
- <tr><td>summary</td><td>gm</td><td>p05</td><td>492.04515274614096</td></tr>
- <tr><td>summary</td><td>gm</td><td>p95</td><td>1092.9030109867454</td></tr>
- <tr><td>summary</td><td>gm</td><td>stdv</td><td>182.95817171100975</td></tr>
- <tr><td>summary</td><td>wm</td><td>k</td><td>-0.006887552415072218</td></tr>
- <tr><td>summary</td><td>wm</td><td>mad</td><td>101.43194878913357</td></tr>
- <tr><td>summary</td><td>wm</td><td>mean</td><td>985.0825852952963</td></tr>
- <tr><td>summary</td><td>wm</td><td>median</td><td>991.1477691978216</td></tr>
- <tr><td>summary</td><td>wm</td><td>n</td><td>1164492.054739539</td></tr>
- <tr><td>summary</td><td>wm</td><td>p05</td><td>774.2524406611919</td></tr>
- <tr><td>summary</td><td>wm</td><td>p95</td><td>1173.6683822721243</td></tr>
- <tr><td>summary</td><td>wm</td><td>stdv</td><td>122.01343330259769</td></tr>
- <tr><td>tpm</td><td>overlap</td><td>csf</td><td>0.21354141881158895</td></tr>
- <tr><td>tpm</td><td>overlap</td><td>gm</td><td>0.518062614413164</td></tr>
- <tr><td>tpm</td><td>overlap</td><td>wm</td><td>0.5425863583905439</td></tr>
- <tr><td colspan=3>wm2max</td><td>0.5554965227549148</td></tr>
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- <div id="qcartifacts-collapse" class="accordion-collapse collapse" aria-labelledby="qcartifacts-head">
- <div class="accordion-body">
- <fieldset id="qcartifacts-group" class="form-group">
- <div class="form-check form-switch small">
- <input class="form-check-input" type="checkbox" name="head-motion" id="qcartifacts-item-0" />
- <label class="form-check-label" for="qcartifacts-item-0">Head motion artifacts</label>
- </div>
- <div class="form-check form-switch small">
- <input class="form-check-input" type="checkbox" name="eye-spillover" id="qcartifacts-item-1" />
- <label class="form-check-label" for="qcartifacts-item-1">Eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
- </div>
- <div class="form-check form-switch small">
- <input class="form-check-input" type="checkbox" name="noneye-spillover" id="qcartifacts-item-2" />
- <label class="form-check-label" for="qcartifacts-item-2">Non-eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
- </div>
- <div class="form-check form-switch small">
- <input class="form-check-input" type="checkbox" name="coil-failure" id="qcartifacts-item-3" />
- <label class="form-check-label" for="qcartifacts-item-3">Coil failure</label>
- </div>
- <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>
- </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://localhost:8000/");
- 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>
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