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sub-001_ses-pilot021_acq-undistorted_T2w.html

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    107. 

  107.     <ul class="navbar-nav me-auto mb-2 mb-lg-0">
    108. 

  108.         <li class="nav-item"><a class="nav-link" href="#Basic visual report">Basic visual report</a></li>
    109. 

  109.         <li class="nav-item"><a class="nav-link" href="#Extended visual report">Extended visual report</a></li>
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  115.                 <li><a class="dropdown-item" href="#errors">Errors</a></li>
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    130. 

  130.     <h1 class="text-danger"> The navigation menu uses Javascript. Without it this report might not work as expected </h1>
    131. 

  131. </noscript>
    132. 

  132. 

  133.     <div id="Basic visual report" class="mt-5">
    134. 

  134.     <h1 class="sub-report-title pt-5 ps-4">Basic visual report</h1>
    135. 

  135.         <div id="acquisition-undistorted_datatype-figures_desc-background_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    136. 

  136. <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">
    137. 

  137. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-background_T2w.svg" style="width: 100%" />
    138. 

  138. </div>
    139. 

  139. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-background_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-background_T2w.svg</a></small>
    140. 

  140. 

  141.         </div>
    142. 

  142.         <div id="acquisition-undistorted_datatype-figures_desc-zoomed_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    143. 

  143. <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">
    144. 

  144. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-zoomed_T2w.svg" style="width: 100%" />
    145. 

  145. </div>
    146. 

  146. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-zoomed_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-zoomed_T2w.svg</a></small>
    147. 

  147. 

  148.         </div>
    149. 

  149.     </div>
    150. 

  150.     <div id="Extended visual report" class="mt-5">
    151. 

  151.     <h1 class="sub-report-title pt-5 ps-4">Extended visual report</h1>
    152. 

  152.         <div id="acquisition-undistorted_datatype-figures_desc-airmask_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    153. 

  153. <h3 class="run-title mt-3">&laquo;Hat&raquo;-mask</h3><p class="elem-caption">The <em>hat</em>-mask calculated internally by MRIQC. Some metrics will use this mask, for instance, to find out artifacts and estimate the spread of gaussian noise added to the signal. This mask leaves out the air around the face to avoid measuring noise sourcing from the eyeballs and their movement.</p>                    <div class="reportlet">
    154. 

  154. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-airmask_T2w.svg" style="width: 100%" />
    155. 

  155. </div>
    156. 

  156. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-airmask_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-airmask_T2w.svg</a></small>
    157. 

  157. 

  158.         </div>
    159. 

  159.         <div id="acquisition-undistorted_datatype-figures_desc-noisefit_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    160. 

  160. <h3 class="run-title mt-3">Distribution of the noise within the <em>hat</em> mask</h3><p class="elem-caption">The noise fit internally estimated by MRIQC to calculate the QI<sub>1</sub> index proposed by <a href="https://doi.org/10.1002/mrm.21992" target="_blank">Mortamet et al. (2009)</a>.</p>                    <div class="reportlet">
    161. 

  161. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-noisefit_T2w.svg" style="width: 100%; max-width: 450px" />
    162. 

  162. </div>
    163. 

  163. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-noisefit_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-noisefit_T2w.svg</a></small>
    164. 

  164. 

  165.         </div>
    166. 

  166.         <div id="acquisition-undistorted_datatype-figures_desc-artifacts_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    167. 

  167. <h3 class="run-title mt-3">Artifactual intensities on the background</h3><p class="elem-caption">Mask of artifactual intensities identified within the <em>hat</em>-mask.</p>                    <div class="reportlet">
    168. 

  168. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-artifacts_T2w.svg" style="width: 100%" />
    169. 

  169. </div>
    170. 

  170. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-artifacts_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-artifacts_T2w.svg</a></small>
    171. 

  171. 

  172.         </div>
    173. 

  173.         <div id="acquisition-undistorted_datatype-figures_desc-brainmask_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    174. 

  174. <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">
    175. 

  175. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-brainmask_T2w.svg" style="width: 100%" />
    176. 

  176. </div>
    177. 

  177. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-brainmask_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-brainmask_T2w.svg</a></small>
    178. 

  178. 

  179.         </div>
    180. 

  180.         <div id="acquisition-undistorted_datatype-figures_desc-head_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    181. 

  181. <h3 class="run-title mt-3">Head mask</h3><p class="elem-caption">A mask of the head calculated internally by MRIQC.</p>                    <div class="reportlet">
    182. 

  182. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-head_T2w.svg" style="width: 100%" />
    183. 

  183. </div>
    184. 

  184. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-head_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-head_T2w.svg</a></small>
    185. 

  185. 

  186.         </div>
    187. 

  187.         <div id="acquisition-undistorted_datatype-figures_desc-segmentation_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    188. 

  188. <h3 class="run-title mt-3">Brain tissue segmentation</h3><p class="elem-caption">Brain tissue segmentation, as internally extracted by MRIQC. Defects on this segmentation, as well as noisy tissue labels could indicate problematic aspects of the image quality-wise.</p>                    <div class="reportlet">
    189. 

  189. <img class="svg-reportlet" src="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-segmentation_T2w.svg" style="width: 100%" />
    190. 

  190. </div>
    191. 

  191. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-segmentation_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-segmentation_T2w.svg</a></small>
    192. 

  192. 

  193.         </div>
    194. 

  194.         <div id="acquisition-undistorted_datatype-figures_desc-norm_session-pilot021_subject-001_suffix-T2w" class="ps-4 pe-4 mb-2">
    195. 

  195. <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">
    196. 

  196. <object class="svg-reportlet" type="image/svg+xml" data="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-norm_T2w.svg" style="">
    197. 

  197. Problem loading figure sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-norm_T2w.svg. If the link below works, please try reloading the report in your browser.</object>
    198. 

  198. </div>
    199. 

  199. <small>Get figure file: <a href="./sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-norm_T2w.svg" target="_blank">sub-001/figures/sub-001_ses-pilot021_acq-undistorted_desc-norm_T2w.svg</a></small>
    200. 

  200. 

  201.         </div>
    202. 

  202.     </div>
    203. 

  203.     <div id="About" class="mt-5">
    204. 

  204.     <h1 class="sub-report-title pt-5 ps-4">About</h1>
    205. 

  205.         <div id="errors" class="ps-4 pe-4 mb-2">
    206. 

  206. <h2 class="sub-report-group mt-4">Errors</h2>                    <p class="alert alert-success" role="alert">No errors to report!</p>
    207. 

  207.         </div>
    208. 

  208.         <div id="meta-about-metadata" class="ps-4 pe-4 mb-2">
    209. 

  209. <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
    210. 

  210. reconstructing the provenance of the corresponding derivatives.
    211. 

  211. </p>                    <div class="accordion accordion-flush" id="about-metadata">
    212. 

  212. 

  213. 

  214.   <div class="accordion-item">
    215. 

  215.     <h2 class="accordion-header" id="about-metadata-0">
    216. 

  216.       <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-0-collapse" aria-controls="about-metadata-0-collapse">
    217. 

  217.         Provenance Information
    218. 

  218.       </button>
    219. 

  219.     </h2>
    220. 

  220.     <div id="about-metadata-0-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-0-heading" data-bs-parent="#about-metadata-0">
    221. 

  221.       <div class="accordion-body metadata-table">
    222. 

  222.       <table id="about-metadata-table-0" class="table table-sm table-striped">
    223. 

  223. <tr><td colspan=2>Execution environment</td><td>singularity</td></tr>
    224. 

  224. <tr><td colspan=2>Input filename</td><td><BIDS root>/sub-001/ses-pilot021/anat/sub-001_ses-pilot021_acq-undistorted_T2w.nii.gz</td></tr>
    225. 

  225. <tr><td>Versions</td><td>MRIQC</td><td>24.1.0.dev0+g3fe90466.d20240417</td></tr>
    226. 

  226. <tr><td>Versions</td><td>NiPype</td><td>1.8.6</td></tr>
    227. 

  227. <tr><td>Versions</td><td>TemplateFlow</td><td>24.2.0</td></tr>
    228. 

  228. <tr><td colspan=2>md5sum</td><td>14cd8ba7c12be2d435da20afa80d3044</td></tr>
    229. 

  229. <tr><td>warnings</td><td>large_rot_frame</td><td>True</td></tr>
    230. 

  230. <tr><td>warnings</td><td>small_air_mask</td><td>False</td></tr>
    231. 

  231. </table>
    232. 

  232. 

  233.       </div>
    234. 

  234.     </div>
    235. 

  235.   </div>
    236. 

  236. 

  237. 

  238.   <div class="accordion-item">
    239. 

  239.     <h2 class="accordion-header" id="about-metadata-1">
    240. 

  240.       <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-1-collapse" aria-controls="about-metadata-1-collapse">
    241. 

  241.         Dataset Information
    242. 

  242.       </button>
    243. 

  243.     </h2>
    244. 

  244.     <div id="about-metadata-1-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-1-heading" data-bs-parent="#about-metadata-1">
    245. 

  245.       <div class="accordion-body metadata-table">
    246. 

  246.       <table id="about-metadata-table-1" class="table table-sm table-striped">
    247. 

  247. <tr><td colspan=2>AcquisitionMatrixPE</td><td>320</td></tr>
    248. 

  248. <tr><td colspan=2>AcquisitionNumber</td><td>1</td></tr>
    249. 

  249. <tr><td colspan=2>AcquisitionTime</td><td>18:46:8.040000</td></tr>
    250. 

  250. <tr><td colspan=2>BaseResolution</td><td>320</td></tr>
    251. 

  251. <tr><td colspan=2>BodyPartExamined</td><td>BRAIN</td></tr>
    252. 

  252. <tr><td colspan=2>CoilCombinationMethod</td><td>Adaptive Combine</td></tr>
    253. 

  253. <tr><td colspan=2>CoilString</td><td>HeadNeck_64</td></tr>
    254. 

  254. <tr><td colspan=2>ConversionSoftware</td><td>dcm2niix</td></tr>
    255. 

  255. <tr><td colspan=2>ConversionSoftwareVersion</td><td>v1.0.20220720</td></tr>
    256. 

  256. <tr><td colspan=2>DeviceSerialNumber</td><td>67014</td></tr>
    257. 

  257. <tr><td colspan=2>DwellTime</td><td>2.2e-06</td></tr>
    258. 

  258. <tr><td colspan=2>EchoTime</td><td>0.413</td></tr>
    259. 

  259. <tr><td colspan=2>EchoTrainLength</td><td>248</td></tr>
    260. 

  260. <tr><td colspan=2>FlipAngle</td><td>120</td></tr>
    261. 

  261. <tr><td colspan=2>HeudiconvVersion</td><td>1.0.0</td></tr>
    262. 

  262. <tr><td colspan=2>ImageOrientationPatientDICOM</td><td>[-0.0136075, 0.993968, 0.108823, 0.0619847, 0.109462, -0.992056]</td></tr>
    263. 

  263. <tr><td colspan=2>ImageType</td><td>['ORIGINAL', 'PRIMARY', 'M', 'NORM', 'DIS3D', 'MFSPLIT']</td></tr>
    264. 

  264. <tr><td colspan=2>ImageTypeText</td><td>['ORIGINAL', 'PRIMARY', 'M', 'NONE']</td></tr>
    265. 

  265. <tr><td colspan=2>ImagingFrequency</td><td>123.248</td></tr>
    266. 

  266. <tr><td colspan=2>InPlanePhaseEncodingDirectionDICOM</td><td>ROW</td></tr>
    267. 

  267. <tr><td colspan=2>InstitutionAddress</td><td>Rue du Bugnon 21,Lausanne,District,CH,1011</td></tr>
    268. 

  268. <tr><td colspan=2>InstitutionName</td><td>CHUV</td></tr>
    269. 

  269. <tr><td colspan=2>MRAcquisitionType</td><td>3D</td></tr>
    270. 

  270. <tr><td colspan=2>MagneticFieldStrength</td><td>3</td></tr>
    271. 

  271. <tr><td colspan=2>Manufacturer</td><td>Siemens</td></tr>
    272. 

  272. <tr><td colspan=2>ManufacturersModelName</td><td>MAGNETOM Prisma Fit</td></tr>
    273. 

  273. <tr><td colspan=2>MatrixCoilMode</td><td>GRAPPA</td></tr>
    274. 

  274. <tr><td colspan=2>Modality</td><td>MR</td></tr>
    275. 

  275. <tr><td colspan=2>NonlinearGradientCorrection</td><td>True</td></tr>
    276. 

  276. <tr><td colspan=2>ParallelReductionFactorInPlane</td><td>3</td></tr>
    277. 

  277. <tr><td colspan=2>PartialFourier</td><td>1</td></tr>
    278. 

  278. <tr><td colspan=2>PatientPosition</td><td>HFS</td></tr>
    279. 

  279. <tr><td colspan=2>PercentPhaseFOV</td><td>100</td></tr>
    280. 

  280. <tr><td colspan=2>PercentSampling</td><td>100</td></tr>
    281. 

  281. <tr><td colspan=2>PhaseEncodingDirection</td><td>i</td></tr>
    282. 

  282. <tr><td colspan=2>PhaseEncodingSteps</td><td>320</td></tr>
    283. 

  283. <tr><td colspan=2>PhaseResolution</td><td>1</td></tr>
    284. 

  284. <tr><td colspan=2>PixelBandwidth</td><td>710</td></tr>
    285. 

  285. <tr><td colspan=2>ProcedureStepDescription</td><td>RESEARCH Oscar</td></tr>
    286. 

  286. <tr><td colspan=2>ProtocolName</td><td>anat-T2w__space</td></tr>
    287. 

  287. <tr><td colspan=2>PulseSequenceDetails</td><td>%SiemensSeq%\space</td></tr>
    288. 

  288. <tr><td colspan=2>ReceiveCoilActiveElements</td><td>HC1-7;NC1,2</td></tr>
    289. 

  289. <tr><td colspan=2>ReceiveCoilName</td><td>HeadNeck_64</td></tr>
    290. 

  290. <tr><td colspan=2>ReconMatrixPE</td><td>320</td></tr>
    291. 

  291. <tr><td colspan=2>RefLinesPE</td><td>24</td></tr>
    292. 

  292. <tr><td colspan=2>RepetitionTime</td><td>3.2</td></tr>
    293. 

  293. <tr><td colspan=2>SAR</td><td>0.133069</td></tr>
    294. 

  294. <tr><td colspan=2>ScanOptions</td><td>PFP\PER</td></tr>
    295. 

  295. <tr><td colspan=2>ScanningSequence</td><td>SE</td></tr>
    296. 

  296. <tr><td colspan=2>SequenceName</td><td>*spcR_282ns</td></tr>
    297. 

  297. <tr><td colspan=2>SequenceVariant</td><td>SP\SK</td></tr>
    298. 

  298. <tr><td colspan=2>SeriesDescription</td><td>anat-T2w__space</td></tr>
    299. 

  299. <tr><td colspan=2>SeriesNumber</td><td>42</td></tr>
    300. 

  300. <tr><td colspan=2>ShimSetting</td><td>[8227, -5660, -6265, 329, -51, -148, 54, 19]</td></tr>
    301. 

  301. <tr><td colspan=2>SliceThickness</td><td>0.8</td></tr>
    302. 

  302. <tr><td colspan=2>SoftwareVersions</td><td>syngo MR XA30</td></tr>
    303. 

  303. <tr><td colspan=2>StationName</td><td>LRG10884</td></tr>
    304. 

  304. <tr><td colspan=2>TxRefAmp</td><td>247.681</td></tr>
    305. 

  305. <tr><td>dcmmeta</td><td>affine</td><td>[[0.7990000247955322, -0.010885999538004398, 0.049587760120630264, -99.09886169433594], [0.006000000052154064, 0.7951744198799133, 0.08756960183382034, -110.36433410644531], [-0.05050000175833702, -0.0870584025979042, 0.7936447858810425, -118.18616485595703], [0.0, 0.0, 0.0, 1.0]]</td></tr>
    306. 

  306. <tr><td>dcmmeta</td><td>reorient_transform</td><td>[[0.0, 0.0, -1.0, 319.0], [0.0, -1.0, 0.0, 319.0], [-1.0, 0.0, 0.0, 239.0], [0.0, 0.0, 0.0, 1.0]]</td></tr>
    307. 

  307. <tr><td>dcmmeta</td><td>shape</td><td>[240, 320, 320]</td></tr>
    308. 

  308. <tr><td>dcmmeta</td><td>slice_dim</td><td>0</td></tr>
    309. 

  309. <tr><td>dcmmeta</td><td>version</td><td>0.6</td></tr>
    310. 

  310. </table>
    311. 

  311. 

  312.       </div>
    313. 

  313.     </div>
    314. 

  314.   </div>
    315. 

  315. 

  316. 

  317.   <div class="accordion-item">
    318. 

  318.     <h2 class="accordion-header" id="about-metadata-2">
    319. 

  319.       <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#about-metadata-2-collapse" aria-controls="about-metadata-2-collapse">
    320. 

  320.         Extracted Image quality metrics (IQMs)
    321. 

  321.       </button>
    322. 

  322.     </h2>
    323. 

  323.     <div id="about-metadata-2-collapse" class="accordion-collapse collapse" aria-labelledby="about-metadata-2-heading" data-bs-parent="#about-metadata-2">
    324. 

  324.       <div class="accordion-body metadata-table">
    325. 

  325.       <table id="about-metadata-table-2" class="table table-sm table-striped">
    326. 

  326. <tr><td colspan=3>cjv</td><td>1.594667111111111</td></tr>
    327. 

  327. <tr><td colspan=3>cnr</td><td>0.6068209250464595</td></tr>
    328. 

  328. <tr><td colspan=3>efc</td><td>0.4956</td></tr>
    329. 

  329. <tr><td colspan=3>fber</td><td>3939.5237</td></tr>
    330. 

  330. <tr><td>fwhm</td><td colspan=2>avg</td><td>2.5918010708271573</td></tr>
    331. 

  331. <tr><td>fwhm</td><td colspan=2>x</td><td>2.4947157911698468</td></tr>
    332. 

  332. <tr><td>fwhm</td><td colspan=2>y</td><td>2.810549958119542</td></tr>
    333. 

  333. <tr><td>fwhm</td><td colspan=2>z</td><td>2.4701374631920836</td></tr>
    334. 

  334. <tr><td>icvs</td><td colspan=2>csf</td><td>0.2714610395886847</td></tr>
    335. 

  335. <tr><td>icvs</td><td colspan=2>gm</td><td>0.34445733834702347</td></tr>
    336. 

  336. <tr><td>icvs</td><td colspan=2>wm</td><td>0.38408162206429186</td></tr>
    337. 

  337. <tr><td>inu</td><td colspan=2>med</td><td>0.9958595037460327</td></tr>
    338. 

  338. <tr><td>inu</td><td colspan=2>range</td><td>0.3817537069320679</td></tr>
    339. 

  339. <tr><td>qi</td><td colspan=2>1</td><td>0.0</td></tr>
    340. 

  340. <tr><td>qi</td><td colspan=2>2</td><td>0.0031327445301400788</td></tr>
    341. 

  341. <tr><td>rpve</td><td colspan=2>csf</td><td>8.336814740157111</td></tr>
    342. 

  342. <tr><td>rpve</td><td colspan=2>gm</td><td>8.183123383992127</td></tr>
    343. 

  343. <tr><td>rpve</td><td colspan=2>wm</td><td>8.220821506978208</td></tr>
    344. 

  344. <tr><td>size</td><td colspan=2>x</td><td>240</td></tr>
    345. 

  345. <tr><td>size</td><td colspan=2>y</td><td>320</td></tr>
    346. 

  346. <tr><td>size</td><td colspan=2>z</td><td>320</td></tr>
    347. 

  347. <tr><td>snr</td><td colspan=2>csf</td><td>1.5135475881343396</td></tr>
    348. 

  348. <tr><td>snr</td><td colspan=2>gm</td><td>4.148188814561813</td></tr>
    349. 

  349. <tr><td>snr</td><td colspan=2>total</td><td>3.994455510091664</td></tr>
    350. 

  350. <tr><td>snr</td><td colspan=2>wm</td><td>6.321630127578841</td></tr>
    351. 

  351. <tr><td>snrd</td><td colspan=2>csf</td><td>40.38528441733923</td></tr>
    352. 

  352. <tr><td>snrd</td><td colspan=2>gm</td><td>32.2029578351532</td></tr>
    353. 

  353. <tr><td>snrd</td><td colspan=2>total</td><td>33.13603016470073</td></tr>
    354. 

  354. <tr><td>snrd</td><td colspan=2>wm</td><td>26.819848241609755</td></tr>
    355. 

  355. <tr><td>spacing</td><td colspan=2>x</td><td>0.8006202578544617</td></tr>
    356. 

  356. <tr><td>spacing</td><td colspan=2>y</td><td>0.800000011920929</td></tr>
    357. 

  357. <tr><td>spacing</td><td colspan=2>z</td><td>0.800000011920929</td></tr>
    358. 

  358. <tr><td>summary</td><td>bg</td><td>k</td><td>1102.7377</td></tr>
    359. 

  359. <tr><td>summary</td><td>bg</td><td>mad</td><td>0.0</td></tr>
    360. 

  360. <tr><td>summary</td><td>bg</td><td>mean</td><td>4.7616</td></tr>
    361. 

  361. <tr><td>summary</td><td>bg</td><td>median</td><td>0.0</td></tr>
    362. 

  362. <tr><td>summary</td><td>bg</td><td>n</td><td>6920778.0</td></tr>
    363. 

  363. <tr><td>summary</td><td>bg</td><td>p05</td><td>0.0</td></tr>
    364. 

  364. <tr><td>summary</td><td>bg</td><td>p95</td><td>19.0</td></tr>
    365. 

  365. <tr><td>summary</td><td>bg</td><td>stdv</td><td>27.383</td></tr>
    366. 

  366. <tr><td>summary</td><td>csf</td><td>k</td><td>-1.2671</td></tr>
    367. 

  367. <tr><td>summary</td><td>csf</td><td>mad</td><td>1774.259</td></tr>
    368. 

  368. <tr><td>summary</td><td>csf</td><td>mean</td><td>1734.9323</td></tr>
    369. 

  369. <tr><td>summary</td><td>csf</td><td>median</td><td>1688.0</td></tr>
    370. 

  370. <tr><td>summary</td><td>csf</td><td>n</td><td>790105.5442572581</td></tr>
    371. 

  371. <tr><td>summary</td><td>csf</td><td>p05</td><td>29.0</td></tr>
    372. 

  372. <tr><td>summary</td><td>csf</td><td>p95</td><td>3574.0</td></tr>
    373. 

  373. <tr><td>summary</td><td>csf</td><td>stdv</td><td>1115.2599</td></tr>
    374. 

  374. <tr><td>summary</td><td>gm</td><td>k</td><td>36.598</td></tr>
    375. 

  375. <tr><td>summary</td><td>gm</td><td>mad</td><td>221.3647</td></tr>
    376. 

  376. <tr><td>summary</td><td>gm</td><td>mean</td><td>1348.4467</td></tr>
    377. 

  377. <tr><td>summary</td><td>gm</td><td>median</td><td>1346.0</td></tr>
    378. 

  378. <tr><td>summary</td><td>gm</td><td>n</td><td>1002566.162718791</td></tr>
    379. 

  379. <tr><td>summary</td><td>gm</td><td>p05</td><td>871.0</td></tr>
    380. 

  380. <tr><td>summary</td><td>gm</td><td>p95</td><td>1874.0</td></tr>
    381. 

  381. <tr><td>summary</td><td>gm</td><td>stdv</td><td>324.4788</td></tr>
    382. 

  382. <tr><td>summary</td><td>wm</td><td>k</td><td>115.7165</td></tr>
    383. 

  383. <tr><td>summary</td><td>wm</td><td>mad</td><td>137.4354</td></tr>
    384. 

  384. <tr><td>summary</td><td>wm</td><td>mean</td><td>1132.181</td></tr>
    385. 

  385. <tr><td>summary</td><td>wm</td><td>median</td><td>1121.0</td></tr>
    386. 

  386. <tr><td>summary</td><td>wm</td><td>n</td><td>1117895.2953990202</td></tr>
    387. 

  387. <tr><td>summary</td><td>wm</td><td>p05</td><td>887.0</td></tr>
    388. 

  388. <tr><td>summary</td><td>wm</td><td>p95</td><td>1403.0</td></tr>
    389. 

  389. <tr><td>summary</td><td>wm</td><td>stdv</td><td>177.3276</td></tr>
    390. 

  390. <tr><td>tpm</td><td>overlap</td><td>csf</td><td>0.21646969897080412</td></tr>
    391. 

  391. <tr><td>tpm</td><td>overlap</td><td>gm</td><td>0.497522063613448</td></tr>
    392. 

  392. <tr><td>tpm</td><td>overlap</td><td>wm</td><td>0.5200833581467031</td></tr>
    393. 

  393. <tr><td colspan=3>wm2max</td><td>0.283624698411974</td></tr>
    394. 

  394. </table>
    395. 

  395. 

  396.       </div>
    397. 

  397.     </div>
    398. 

  398.   </div>
    399. 

  399. 

  400. </div>
    401. 

  401.         </div>
    402. 

  402.     </div>
    403. 

  403. 

  404. <div id="qcrating-menu" class="card position-fixed d-none" style="width: 30%; top: 100px; left: 65%;">
    405. 

  405. <div class="card-header m-0">
    406. 

  406.     Rating widget
    407. 

  407.     <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>
    408. 

  408. </div>
    409. 

  409. <div class="card-body">
    410. 

  410. <div class="accordion">
    411. 

  411.   <div class="accordion-item">
    412. 

  412.     <h2 class="accordion-header" id="qcslider-head">
    413. 

  413.       <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>
    414. 

  414.     </h2>
    415. 

  415.     <div id="qcslider-collapse" class="accordion-collapse collapse show" aria-labelledby="qcslider-head">
    416. 

  416.       <div class="accordion-body">
    417. 

  417.         <input type="range" min="1.0" max="4.0" step="0.05" value="2.5" id="qcslider" class="slider">
    418. 

  418.         <ul class="list-group list-group-horizontal slider-labels" style="width: 100%">
    419. 

  419.             <li class="list-group-item list-group-item-danger small" style="font-size: 0.7em; width: 25%; text-align:center">Exclude</li>
    420. 

  420.             <li class="list-group-item list-group-item-warning small" style="font-size: 0.7em; width: 25%; text-align:center">Poor</li>
    421. 

  421.             <li class="list-group-item list-group-item-primary small" style="font-size: 0.7em; width: 25%; text-align:center">Acceptable</li>
    422. 

  422.             <li class="list-group-item list-group-item-success small" style="font-size: 0.7em; width: 25%; text-align:center">Excellent</li>
    423. 

  423.         </ul>
    424. 

  424.       </div>
    425. 

  425.     </div>
    426. 

  426.   </div>
    427. 

  427. 

  428.   <div class="accordion-item">
    429. 

  429.     <h2 class="accordion-header" id="qcartifacts-head">
    430. 

  430.       <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#qcartifacts-collapse" aria-expanded="false" aria-controls="qcartifacts-collapse">
    431. 

  431.         Record specific artifacts
    432. 

  432.       </button>
    433. 

  433.     </h2>
    434. 

  434.     <div id="qcartifacts-collapse" class="accordion-collapse collapse" aria-labelledby="qcartifacts-head">
    435. 

  435.       <div class="accordion-body">
    436. 

  436.         <fieldset id="qcartifacts-group" class="form-group">
    437. 

  437.             <div class="form-check form-switch small">
    438. 

  438.                 <input class="form-check-input" type="checkbox" name="head-motion" id="qcartifacts-item-0" />
    439. 

  439.                 <label class="form-check-label" for="qcartifacts-item-0">Head motion artifacts</label>
    440. 

  440.             </div>
    441. 

  441.             <div class="form-check form-switch small">
    442. 

  442.                 <input class="form-check-input" type="checkbox" name="eye-spillover" id="qcartifacts-item-1" />
    443. 

  443.                 <label class="form-check-label" for="qcartifacts-item-1">Eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
    444. 

  444.             </div>
    445. 

  445.             <div class="form-check form-switch small">
    446. 

  446.                 <input class="form-check-input" type="checkbox" name="noneye-spillover" id="qcartifacts-item-2" />
    447. 

  447.                 <label class="form-check-label" for="qcartifacts-item-2">Non-eye spillover through <abbr title="phase-encoding">PE</abbr> axis</label>
    448. 

  448.             </div>
    449. 

  449.             <div class="form-check form-switch small">
    450. 

  450.                 <input class="form-check-input" type="checkbox" name="coil-failure" id="qcartifacts-item-3" />
    451. 

  451.                 <label class="form-check-label" for="qcartifacts-item-3">Coil failure</label>
    452. 

  452.             </div>
    453. 

  453.             <div class="form-check form-switch small">
    454. 

  454.                 <input class="form-check-input" type="checkbox" name="noise-global" id="qcartifacts-item-4" />
    455. 

  455.                 <label class="form-check-label" for="qcartifacts-item-4">Global noise</label>
    456. 

  456.             </div>
    457. 

  457.             <div class="form-check form-switch small">
    458. 

  458.                 <input class="form-check-input" type="checkbox" name="noise-local" id="qcartifacts-item-5" />
    459. 

  459.                 <label class="form-check-label" for="qcartifacts-item-5">Local noise</label>
    460. 

  460.             </div>
    461. 

  461.             <div class="form-check form-switch small">
    462. 

  462.                 <input class="form-check-input" type="checkbox" name="em-perturbation" id="qcartifacts-item-6" />
    463. 

  463.                 <label class="form-check-label" for="qcartifacts-item-6"><abbr title="electromagnetic">EM</abbr> interference/perturbation</label>
    464. 

  464.             </div>
    465. 

  465.             <div class="form-check form-switch small">
    466. 

  466.                 <input class="form-check-input" type="checkbox" name="wrap-around" id="qcartifacts-item-7" />
    467. 

  467.                 <label class="form-check-label" for="qcartifacts-item-7">Problematic <abbr title="field-of-view">FoV</abbr> prescription / wrap-around</label>
    468. 

  468.             </div>
    469. 

  469.             <div class="form-check form-switch small">
    470. 

  470.                 <input class="form-check-input" type="checkbox" name="ghost-aliasing" id="qcartifacts-item-8" />
    471. 

  471.                 <label class="form-check-label" for="qcartifacts-item-8">Aliasing ghosts</label>
    472. 

  472.             </div>
    473. 

  473.             <div class="form-check form-switch small">
    474. 

  474.                 <input class="form-check-input" type="checkbox" name="ghost-other" id="qcartifacts-item-9" />
    475. 

  475.                 <label class="form-check-label" for="qcartifacts-item-9">Other ghosts (for example, <abbr title="radiofrequency">RF</abbr> spoiling)</label>
    476. 

  476.             </div>
    477. 

  477.             <div class="form-check form-switch small">
    478. 

  478.                 <input class="form-check-input" type="checkbox" name="inu" id="qcartifacts-item-10" />
    479. 

  479.                 <label class="form-check-label" for="qcartifacts-item-10">Intensity non-uniformity (B<sub>1</sub> bias)</label>
    480. 

  480.             </div>
    481. 

  481.             <div class="form-check form-switch small">
    482. 

  482.                 <input class="form-check-input" type="checkbox" name="field-variation" id="qcartifacts-item-11" />
    483. 

  483.                 <label class="form-check-label" for="qcartifacts-item-11">Temporal B<sub>1</sub> field non-uniformity variation</label>
    484. 

  484.             </div>
    485. 

  485.             <div class="form-check form-switch small">
    486. 

  486.                 <input class="form-check-input" type="checkbox" name="processing" id="qcartifacts-item-12" />
    487. 

  487.                 <label class="form-check-label" for="qcartifacts-item-12">Processing such as denoising, defacing or resamplings happened</label>
    488. 

  488.             </div>
    489. 

  489.             <div class="form-check form-switch small">
    490. 

  490.                 <input class="form-check-input" type="checkbox" name="uncategorized" id="qcartifacts-item-13" />
    491. 

  491.                 <label class="form-check-label" for="qcartifacts-item-13">Other uncategorized artifact(s)</label>
    492. 

  492.             </div>
    493. 

  493.         </fieldset>
    494. 

  494.       </div> <!-- accordion-body -->
    495. 

  495.     </div> <!-- accordion-collapse -->
    496. 

  496.   </div> <!-- accordion-item -->
    497. 

  497.   <div class="accordion-item">
    498. 

  498.     <h2 class="accordion-header" id="qcextra-head">
    499. 

  499.       <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#qcextra-collapse" aria-expanded="false" aria-controls="qcextra-collapse">
    500. 

  500.         Extra details
    501. 

  501.       </button>
    502. 

  502.     </h2>
    503. 

  503.     <div id="qcextra-collapse" class="accordion-collapse collapse" aria-labelledby="qcextra-head">
    504. 

  504.       <div class="accordion-body">
    505. 

  505.         <div class="input-group">
    506. 

  506.           <span class="input-group-text">Comments</span>
    507. 

  507.           <textarea class="form-control" aria-label="Comments" id="qcextra-comments"></textarea>
    508. 

  508.         </div>
    509. 

  509. 

  510.         <p style="margin-top: 20px; font-weight: bold">Rater confidence</p>
    511. 

  511.         <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%;">
    512. 

  512.         <ul class="list-group list-group-horizontal slider-labels" style="width: 100%">
    513. 

  513.             <li class="list-group-item list-group-item-warning small" style="width: 50%; text-align:center">Doubtful</li>
    514. 

  514.             <li class="list-group-item list-group-item-success bg-success text-white small" style="width: 50%; text-align:center">Confident</li>
    515. 

  515.         </ul>
    516. 

  516.        </div> <!-- accordion-body -->
    517. 

  517.     </div> <!-- accordion-collapse -->
    518. 

  518.   </div> <!-- accordion-item -->
    519. 

  519. </div>
    520. 

  520. <div style="margin-top: 10px">
    521. 

  521. <a class="btn btn-primary disabled" id="btn-download" href="">Download</a>
    522. 

  522. </div>
    523. 

  523. <script type="text/javascript">
    524. 

  524. var MINIMUM_RATING_TIME = 10
    525. 

  525. $('#qcslider').on('input', function() {
    526. 

  526. 

  527.     if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
    528. 

  528.         $('#btn-download').removeClass('disabled');
    529. 

  529.         $('#btn-download').removeAttr('aria-disabled');
    530. 

  530.         $('#btn-post').removeAttr('disabled');
    531. 

  531.     };
    532. 

  532. 

  533.     $('#qcslider-collapse .list-group-item').removeClass(function(index, classname) {
    534. 

  534.         return (classname.match(/(^|\s)bg-\S+/g) || []).join(' ');
    535. 

  535.     });
    536. 

  536.     $('#qcslider-collapse .list-group-item').removeClass(function(index, classname) {
    537. 

  537.         return (classname.match(/(^|\s)text-\S+/g) || []).join(' ');
    538. 

  538.     });
    539. 

  539. 

  540.     if ( $(this).val() < 1.5 ) {
    541. 

  541.         $('#qcslider-collapse .list-group-item-danger').addClass('bg-danger text-white');
    542. 

  542.     } else if ( $(this).val() > 3.5 ) {
    543. 

  543.         $('#qcslider-collapse .list-group-item-success').addClass('bg-success text-white');
    544. 

  544.     } else if ( $(this).val() < 2.5 ) {
    545. 

  545.         $('#qcslider-collapse .list-group-item-warning').addClass('bg-warning text-dark');
    546. 

  546.     } else {
    547. 

  547.         $('#qcslider-collapse .list-group-item-primary').addClass('bg-primary text-white');
    548. 

  548.     };
    549. 

  549. 

  550.     var payload = read_form();
    551. 

  551. });
    552. 

  552. 

  553. $('#qcextra-confidence').on('input', function() {
    554. 

  554.     if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
    555. 

  555.         $('#btn-download').removeClass('disabled');
    556. 

  556.         $('#btn-download').removeAttr('aria-disabled');
    557. 

  557.         $('#btn-post').removeAttr('disabled');
    558. 

  558.     };
    559. 

  559. 

  560.     $('#qcextra-collapse .list-group-item').removeClass(function(index, classname) {
    561. 

  561.         return (classname.match(/(^|\s)bg-\S+/g) || []).join(' ');
    562. 

  562.     });
    563. 

  563.     $('#qcextra-collapse .list-group-item').removeClass(function(index, classname) {
    564. 

  564.         return (classname.match(/(^|\s)text-\S+/g) || []).join(' ');
    565. 

  565.     });
    566. 

  566. 

  567.     if ( $(this).val() < 2.0 ) {
    568. 

  568.         $('#qcextra-collapse .list-group-item-warning').addClass('bg-warning text-dark');
    569. 

  569.     } else {
    570. 

  570.         $('#qcextra-collapse .list-group-item-success').addClass('bg-success text-white');
    571. 

  571.     };
    572. 

  572. 

  573.     var payload = read_form();
    574. 

  574. });
    575. 

  575. 

  576. 

  577. $('#qcextra-comments').bind('input propertychange', function() {
    578. 

  578.     if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
    579. 

  579.         $('#btn-download').removeClass('disabled');
    580. 

  580.         $('#btn-download').removeAttr('aria-disabled');
    581. 

  581.         $('#btn-post').removeAttr('disabled');
    582. 

  582.     };
    583. 

  583. });
    584. 

  584. 

  585. $( '#btn-post' ).click( function() {
    586. 

  586.     var payload = read_form();
    587. 

  587.     var md5sum = "unspecified";
    588. 

  588.     var params = {
    589. 

  589.         'rating': payload['rating'],
    590. 

  590.         'md5sum': md5sum,
    591. 

  591.         'name': "",
    592. 

  592.         'comment': JSON.stringify(payload['artifacts'])
    593. 

  593.     };
    594. 

  594. 

  595.     // disable development releases
    596. 

  596.     var authorization = $(this).val();
    597. 

  597.     var ratingReq = new XMLHttpRequest();
    598. 

  598.     ratingReq.open("POST", "https://mriqc.nimh.nih.gov:443/api/v1/rating");
    599. 

  599.     ratingReq.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
    600. 

  600.     ratingReq.setRequestHeader("Authorization", authorization);
    601. 

  601.     ratingReq.onload = function () {
    602. 

  602.         status = ratingReq.status;
    603. 

  603.         $('#btn-post').removeClass('btn-primary');
    604. 

  604.         $('#btn-post').attr('disabled', true);
    605. 

  605.         $('#btn-post').attr('aria-disabled', true);
    606. 

  606.         $('#btn-post').prop('disabled');
    607. 

  607.         $('#btn-post').addClass('disabled');
    608. 

  608.         $('#btn-post').removeClass('active');
    609. 

  609.         if (status === "201") {
    610. 

  610.             $('#btn-post').addClass('btn-success');
    611. 

  611.             $('#btn-post').html('Posted!');
    612. 

  612.         } else {
    613. 

  613.             $('#btn-post').addClass('btn-danger');
    614. 

  614.             $('#btn-post').html('Failed');
    615. 

  615.         };
    616. 

  616.     };
    617. 

  617.     ratingReq.send(JSON.stringify(params));
    618. 

  618. });
    619. 

  619. 

  620. $( 'body' ).on( 'click', '#qcartifacts-group input', function(e) {
    621. 

  621.     if ( (Date.now() - timestamp) / 1000 > MINIMUM_RATING_TIME) {
    622. 

  622.         $('#btn-download').removeClass('disabled');
    623. 

  623.         $('#btn-download').removeAttr('aria-disabled');
    624. 

  624.         $('#btn-post').removeAttr('disabled');
    625. 

  625.     };
    626. 

  626.     
    627. 

  627.     var payload = read_form();
    628. 

  628. });
    629. 

  629. 

  630. $( 'body' ).on( 'click', '#qcrating-toggler', function(e) {
    631. 

  631.     toggle_rating();
    632. 

  632. });
    633. 

  633. </script>
    634. 

  634. </div>
    635. 

  635. 

  636. <script type="text/javascript">
    637. 

  637. function toggle(id) {
    638. 

  638.     var element = document.getElementById(id);
    639. 

  639.     if(element.style.display == 'block')
    640. 

  640.         element.style.display = 'none';
    641. 

  641.     else
    642. 

  642.         element.style.display = 'block';
    643. 

  643. }
    644. 

  644. </script>
    645. 

  645. </body>
    646. 

  646. </html>
    647.