TheAxonLab
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defacing-and-qc-ixi-reports


			
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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-0716_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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<small>Get figure file: <a href="./sub-0716/figures/sub-0716_desc-zoomed_T1w.svg" target="_blank">sub-0716/figures/sub-0716_desc-zoomed_T1w.svg</a></small>

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<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">
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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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<tr><td colspan=2>Execution environment</td><td>singularity</td></tr>
<tr><td colspan=2>Input filename</td><td><BIDS root>/sub-0716/anat/sub-0716_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>6a325605ad3a47fe6f936a9123ca6e7f</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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<tr><td>InstitutionName</td><td>HH</td></tr>
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      <table id="about-metadata-table-2" class="table table-sm table-striped">
<tr><td colspan=3>cjv</td><td>0.8033288208165773</td></tr>
<tr><td colspan=3>cnr</td><td>1.2143740140616064</td></tr>
<tr><td colspan=3>efc</td><td>0.6179095342474307</td></tr>
<tr><td colspan=3>fber</td><td>26913.801394146984</td></tr>
<tr><td>fwhm</td><td colspan=2>avg</td><td>4.827111396120471</td></tr>
<tr><td>fwhm</td><td colspan=2>x</td><td>4.126742188361413</td></tr>
<tr><td>fwhm</td><td colspan=2>y</td><td>5.5464106666666675</td></tr>
<tr><td>fwhm</td><td colspan=2>z</td><td>4.808181333333334</td></tr>
<tr><td>icvs</td><td colspan=2>csf</td><td>0.2603869135747137</td></tr>
<tr><td>icvs</td><td colspan=2>gm</td><td>0.36456395634168015</td></tr>
<tr><td>icvs</td><td colspan=2>wm</td><td>0.37504913008360613</td></tr>
<tr><td>inu</td><td colspan=2>med</td><td>0.3656998574733734</td></tr>
<tr><td>inu</td><td colspan=2>range</td><td>0.15298795700073242</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>0.0010004637982122015</td></tr>
<tr><td>rpve</td><td colspan=2>csf</td><td>5.9405386286316215</td></tr>
<tr><td>rpve</td><td colspan=2>gm</td><td>5.818591989090386</td></tr>
<tr><td>rpve</td><td colspan=2>wm</td><td>5.8941642155668355</td></tr>
<tr><td>size</td><td colspan=2>x</td><td>150</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>2.582508779453608</td></tr>
<tr><td>snr</td><td colspan=2>gm</td><td>7.22872919347312</td></tr>
<tr><td>snr</td><td colspan=2>total</td><td>8.788707738301262</td></tr>
<tr><td>snr</td><td colspan=2>wm</td><td>16.554885241977058</td></tr>
<tr><td>snrd</td><td colspan=2>csf</td><td>28.149180669405624</td></tr>
<tr><td>snrd</td><td colspan=2>gm</td><td>44.80179002581143</td></tr>
<tr><td>snrd</td><td colspan=2>total</td><td>42.09067161594705</td></tr>
<tr><td>snrd</td><td colspan=2>wm</td><td>53.32104415262411</td></tr>
<tr><td>spacing</td><td colspan=2>x</td><td>1.1999974250793457</td></tr>
<tr><td>spacing</td><td colspan=2>y</td><td>0.9375</td></tr>
<tr><td>spacing</td><td colspan=2>z</td><td>0.9375</td></tr>
<tr><td>summary</td><td>bg</td><td>k</td><td>388.234386847417</td></tr>
<tr><td>summary</td><td>bg</td><td>mad</td><td>0.0</td></tr>
<tr><td>summary</td><td>bg</td><td>mean</td><td>4.1044810267179175</td></tr>
<tr><td>summary</td><td>bg</td><td>median</td><td>0.0</td></tr>
<tr><td>summary</td><td>bg</td><td>n</td><td>2585550.0</td></tr>
<tr><td>summary</td><td>bg</td><td>p05</td><td>0.0</td></tr>
<tr><td>summary</td><td>bg</td><td>p95</td><td>24.568758621811867</td></tr>
<tr><td>summary</td><td>bg</td><td>stdv</td><td>11.988536565227113</td></tr>
<tr><td>summary</td><td>csf</td><td>k</td><td>-0.05211912456727319</td></tr>
<tr><td>summary</td><td>csf</td><td>mad</td><td>152.9370291761511</td></tr>
<tr><td>summary</td><td>csf</td><td>mean</td><td>518.6049186364779</td></tr>
<tr><td>summary</td><td>csf</td><td>median</td><td>515.1102606058121</td></tr>
<tr><td>summary</td><td>csf</td><td>n</td><td>424542.89623467764</td></tr>
<tr><td>summary</td><td>csf</td><td>p05</td><td>180.29349515587091</td></tr>
<tr><td>summary</td><td>csf</td><td>p95</td><td>842.5711103007197</td></tr>
<tr><td>summary</td><td>csf</td><td>stdv</td><td>199.46094977066306</td></tr>
<tr><td>summary</td><td>gm</td><td>k</td><td>0.45449352342906035</td></tr>
<tr><td>summary</td><td>gm</td><td>mad</td><td>73.94198177900911</td></tr>
<tr><td>summary</td><td>gm</td><td>mean</td><td>821.7130305092553</td></tr>
<tr><td>summary</td><td>gm</td><td>median</td><td>819.8413306176662</td></tr>
<tr><td>summary</td><td>gm</td><td>n</td><td>594396.3763895527</td></tr>
<tr><td>summary</td><td>gm</td><td>p05</td><td>633.7611817345023</td></tr>
<tr><td>summary</td><td>gm</td><td>p95</td><td>1012.0023698583245</td></tr>
<tr><td>summary</td><td>gm</td><td>stdv</td><td>113.41421417691028</td></tr>
<tr><td>summary</td><td>wm</td><td>k</td><td>-0.22297051556739245</td></tr>
<tr><td>summary</td><td>wm</td><td>mad</td><td>51.294068972557454</td></tr>
<tr><td>summary</td><td>wm</td><td>mean</td><td>970.7928576144105</td></tr>
<tr><td>summary</td><td>wm</td><td>median</td><td>975.7377051860094</td></tr>
<tr><td>summary</td><td>wm</td><td>n</td><td>611491.7287127938</td></tr>
<tr><td>summary</td><td>wm</td><td>p05</td><td>864.1239434629679</td></tr>
<tr><td>summary</td><td>wm</td><td>p95</td><td>1059.251868724823</td></tr>
<tr><td>summary</td><td>wm</td><td>stdv</td><td>58.93951501866289</td></tr>
<tr><td>tpm</td><td>overlap</td><td>csf</td><td>0.2130789309658062</td></tr>
<tr><td>tpm</td><td>overlap</td><td>gm</td><td>0.5129239028259539</td></tr>
<tr><td>tpm</td><td>overlap</td><td>wm</td><td>0.540882204805801</td></tr>
<tr><td colspan=3>wm2max</td><td>0.6930337861372344</td></tr>
</table>

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            </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>