ds005256-mriqc/sub-0003_ses-02_task-narratives_acq-mb8_run-02_bold.html
Felix Hoffstaedter 8e7e457e38 [DATALAD RUNCMD] Compute MRIQC for sub-0003
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^^^ Do not change lines above ^^^
2025-09-18 19:06:40 +02:00

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<title>sub-0003_ses-02_task-narratives_acq-mb8_run-02_bold :: MRIQC's BOLD fMRI report</title>
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<li class="nav-item"><a class="nav-link" href="#Basic echo-wise reports">Basic echo-wise reports</a></li>
<li class="nav-item"><a class="nav-link" href="#Extended echo-wise reports">Extended echo-wise reports</a></li>
<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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<div id="Basic echo-wise reports" class="mt-5">
<h1 class="sub-report-title pt-5 ps-4">Basic echo-wise reports</h1>
<div id="acquisition-mb8_datatype-figures_desc-stdev_run-02_session-02_subject-0003_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
<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">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-stdev_bold.svg" style="width: 100%" />
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<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-stdev_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-stdev_bold.svg</a></small>
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<div id="acquisition-mb8_datatype-figures_desc-background_run-02_session-02_subject-0003_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
<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">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-background_bold.svg" style="width: 100%" />
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<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-background_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-background_bold.svg</a></small>
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<div id="acquisition-mb8_datatype-figures_desc-zoomed_run-02_session-02_subject-0003_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
<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">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-zoomed_bold.svg" style="width: 100%" />
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<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-zoomed_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-zoomed_bold.svg</a></small>
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<h3 class="run-title mt-3">Carpetplot and nuisance signals</h3><p class="elem-caption">The so-called &laquo;carpetplot&raquo; may assist in assessing head-motion derived artifacts and respiation effects.</p> <div class="reportlet">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-carpet_bold.svg" style="width: 100%" />
</div>
<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-carpet_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-carpet_bold.svg</a></small>
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<div id="Extended echo-wise reports" class="mt-5">
<h1 class="sub-report-title pt-5 ps-4">Extended echo-wise reports</h1>
<div id="acquisition-mb8_datatype-figures_desc-mean_run-02_session-02_subject-0003_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
<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">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-mean_bold.svg" style="width: 100%" />
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<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-mean_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-mean_bold.svg</a></small>
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<div id="Extended reports shared across echos" class="mt-5">
<h1 class="sub-report-title pt-5 ps-4">Extended reports shared across echos</h1>
<div id="acquisition-mb8_datatype-figures_desc-brainmask_run-02_session-02_subject-0003_suffix-bold_task-narratives" class="ps-4 pe-4 mb-2">
<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">
<img class="svg-reportlet" src="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-brainmask_bold.svg" style="width: 100%" />
</div>
<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-brainmask_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-brainmask_bold.svg</a></small>
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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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<small>Get figure file: <a href="./sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-norm_bold.svg" target="_blank">sub-0003/figures/sub-0003_ses-02_task-narratives_acq-mb8_run-02_desc-norm_bold.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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<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-0003/ses-02/func/sub-0003_ses-02_task-narratives_acq-mb8_run-02_bold.nii.gz</td></tr>
<tr><td>Versions</td><td>MRIQC</td><td>24.1.0.dev0+gd5b13cb5.d20240826</td></tr>
<tr><td>Versions</td><td>NiPype</td><td>1.8.6</td></tr>
<tr><td>Versions</td><td>TemplateFlow</td><td>24.2.0</td></tr>
<tr><td colspan=2>md5sum</td><td>bcd6361c088fa72ea220f563e19c41c2</td></tr>
</table>
</div>
</div>
</div>
<div class="accordion-item">
<h2 class="accordion-header" id="about-metadata-1">
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Dataset Information
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</h2>
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<div class="accordion-body metadata-table">
<table id="about-metadata-table-1" class="table table-sm table-striped">
<tr><td colspan=2>AcquisitionMatrixPE</td><td>82</td></tr>
<tr><td colspan=2>AcquisitionNumber</td><td>1</td></tr>
<tr><td colspan=2>AcquisitionTime</td><td>12:21:52.702500</td></tr>
<tr><td colspan=2>BandwidthPerPixelPhaseEncode</td><td>24.888</td></tr>
<tr><td colspan=2>BaseResolution</td><td>82</td></tr>
<tr><td colspan=2>BodyPartExamined</td><td>BRAIN</td></tr>
<tr><td colspan=2>ConsistencyInfo</td><td>N4_VE11C_LATEST_20160120</td></tr>
<tr><td colspan=2>ConversionSoftware</td><td>dcm2niix</td></tr>
<tr><td colspan=2>ConversionSoftwareVersion</td><td>v1.0.20201102</td></tr>
<tr><td colspan=2>DerivedVendorReportedEchoSpacing</td><td>0.00049</td></tr>
<tr><td colspan=2>DeviceSerialNumber</td><td>66112</td></tr>
<tr><td colspan=2>DwellTime</td><td>2e-06</td></tr>
<tr><td colspan=2>EchoTime</td><td>0.0272</td></tr>
<tr><td colspan=2>EchoTrainLength</td><td>82</td></tr>
<tr><td colspan=2>EffectiveEchoSpacing</td><td>0.00049</td></tr>
<tr><td colspan=2>FlipAngle</td><td>44</td></tr>
<tr><td colspan=2>ImageComments</td><td>Unaliased MB8/PE3</td></tr>
<tr><td colspan=2>ImageOrientationPatientDICOM</td><td>[0.9998, 0.0186801, 0.00716731, -0.0195463, 0.988417, 0.150497]</td></tr>
<tr><td colspan=2>ImageType</td><td>['ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC']</td></tr>
<tr><td colspan=2>ImagingFrequency</td><td>123.252</td></tr>
<tr><td colspan=2>InPlanePhaseEncodingDirectionDICOM</td><td>COL</td></tr>
<tr><td colspan=2>InstitutionAddress</td><td>Maynard 3,Hanover,NH,US,03755</td></tr>
<tr><td colspan=2>InstitutionName</td><td>Dartmouth College - PBS</td></tr>
<tr><td colspan=2>InstitutionalDepartmentName</td><td>Department</td></tr>
<tr><td colspan=2>MRAcquisitionType</td><td>2D</td></tr>
<tr><td colspan=2>MagneticFieldStrength</td><td>3</td></tr>
<tr><td colspan=2>Manufacturer</td><td>Siemens</td></tr>
<tr><td colspan=2>ManufacturersModelName</td><td>Prisma</td></tr>
<tr><td colspan=2>Modality</td><td>MR</td></tr>
<tr><td colspan=2>MultibandAccelerationFactor</td><td>8</td></tr>
<tr><td colspan=2>PartialFourier</td><td>1</td></tr>
<tr><td colspan=2>PatientPosition</td><td>HFS</td></tr>
<tr><td colspan=2>PercentPhaseFOV</td><td>100</td></tr>
<tr><td colspan=2>PercentSampling</td><td>100</td></tr>
<tr><td colspan=2>PhaseEncodingDirection</td><td>j-</td></tr>
<tr><td colspan=2>PhaseEncodingSteps</td><td>82</td></tr>
<tr><td colspan=2>PhaseResolution</td><td>1</td></tr>
<tr><td colspan=2>PixelBandwidth</td><td>3050</td></tr>
<tr><td colspan=2>ProcedureStepDescription</td><td>Wager_Wager^1076_spacetop</td></tr>
<tr><td colspan=2>ProtocolName</td><td>func_run-02_task-narratives_acq-ap-mb8</td></tr>
<tr><td colspan=2>PulseSequenceDetails</td><td>%CustomerSeq%\cmrr_mbep2d_bold</td></tr>
<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>0.114268</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-02_task-narratives_acq-ap-mb8</td></tr>
<tr><td colspan=2>SeriesNumber</td><td>10</td></tr>
<tr><td colspan=2>ShimSetting</td><td>[4153, -7750, -7256, 545, -20, -11, 56, 78]</td></tr>
<tr><td colspan=2>SliceThickness</td><td>2.7</td></tr>
<tr><td colspan=2>SliceTiming</td><td>[0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19, 0, 0.2525, 0.065, 0.315, 0.1275, 0.3775, 0.19]</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>250.1</td></tr>
<tr><td colspan=2>WipMemBlock</td><td>b55809b0-92a8-4df6-af21-ca6865b9ccc6||Sequence: R016 ve11c/master r/e634e98; Dec 19 2017 11:00:25 by eja</td></tr>
<tr><td>dcmmeta</td><td>affine</td><td>[[-2.682389736175537, -0.05244136601686478, 0.011537091806530952, 114.67627716064453], [-0.050117410719394684, 2.651851177215576, 0.4066378176212311, -95.9087905883789], [0.01922936737537384, -0.40377146005630493, 2.6691782474517822, -37.86857986450195], [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, 1098]</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>
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</table>
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Extracted Image quality metrics (IQMs)
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<table id="about-metadata-table-2" class="table table-sm table-striped">
<tr><td colspan=3>aor</td><td>0.0007578388278388278</td></tr>
<tr><td colspan=3>aqi</td><td>0.021252103846153846</td></tr>
<tr><td colspan=3>dummy_trs</td><td>6</td></tr>
<tr><td>dvars</td><td colspan=2>nstd</td><td>37.636419294518795</td></tr>
<tr><td>dvars</td><td colspan=2>std</td><td>1.1932012233822191</td></tr>
<tr><td>dvars</td><td colspan=2>vstd</td><td>0.9945218305866194</td></tr>
<tr><td colspan=3>efc</td><td>0.4871</td></tr>
<tr><td colspan=3>fber</td><td>6701.063</td></tr>
<tr><td>fd</td><td colspan=2>mean</td><td>0.10597121747433244</td></tr>
<tr><td>fd</td><td colspan=2>num</td><td>68</td></tr>
<tr><td>fd</td><td colspan=2>perc</td><td>6.227106227106227</td></tr>
<tr><td>fwhm</td><td colspan=2>avg</td><td>2.3977217231620784</td></tr>
<tr><td>fwhm</td><td colspan=2>x</td><td>2.303327763266205</td></tr>
<tr><td>fwhm</td><td colspan=2>y</td><td>2.562574484358009</td></tr>
<tr><td>fwhm</td><td colspan=2>z</td><td>2.327262921862021</td></tr>
<tr><td colspan=3>gcor</td><td>0.00656441</td></tr>
<tr><td>gsr</td><td colspan=2>x</td><td>0.004630107432603836</td></tr>
<tr><td>gsr</td><td colspan=2>y</td><td>0.04126482456922531</td></tr>
<tr><td>size</td><td colspan=2>t</td><td>1092</td></tr>
<tr><td>size</td><td colspan=2>x</td><td>82</td></tr>
<tr><td>size</td><td colspan=2>y</td><td>82</td></tr>
<tr><td>size</td><td colspan=2>z</td><td>56</td></tr>
<tr><td colspan=3>snr</td><td>3.981912135094701</td></tr>
<tr><td>spacing</td><td colspan=2>tr</td><td>0.46000000834465027</td></tr>
<tr><td>spacing</td><td colspan=2>x</td><td>2.682926893234253</td></tr>
<tr><td>spacing</td><td colspan=2>y</td><td>2.682926893234253</td></tr>
<tr><td>spacing</td><td colspan=2>z</td><td>2.700000047683716</td></tr>
<tr><td>summary</td><td>bg</td><td>k</td><td>16.9032</td></tr>
<tr><td>summary</td><td>bg</td><td>mad</td><td>35.4331</td></tr>
<tr><td>summary</td><td>bg</td><td>mean</td><td>180.0249</td></tr>
<tr><td>summary</td><td>bg</td><td>median</td><td>42.0</td></tr>
<tr><td>summary</td><td>bg</td><td>n</td><td>296689.0</td></tr>
<tr><td>summary</td><td>bg</td><td>p05</td><td>14.0</td></tr>
<tr><td>summary</td><td>bg</td><td>p95</td><td>965.0</td></tr>
<tr><td>summary</td><td>bg</td><td>stdv</td><td>360.9055</td></tr>
<tr><td>summary</td><td>fg</td><td>k</td><td>2.74</td></tr>
<tr><td>summary</td><td>fg</td><td>mad</td><td>489.5943</td></tr>
<tr><td>summary</td><td>fg</td><td>mean</td><td>3253.7638</td></tr>
<tr><td>summary</td><td>fg</td><td>median</td><td>3421.0</td></tr>
<tr><td>summary</td><td>fg</td><td>n</td><td>79855.0</td></tr>
<tr><td>summary</td><td>fg</td><td>p05</td><td>1167.0</td></tr>
<tr><td>summary</td><td>fg</td><td>p95</td><td>4256.0</td></tr>
<tr><td>summary</td><td>fg</td><td>stdv</td><td>859.1296</td></tr>
<tr><td colspan=3>tsnr</td><td>40.812889146618545</td></tr>
</table>
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});
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>