{"id":5733,"date":"2023-09-04T03:22:17","date_gmt":"2023-09-04T03:22:17","guid":{"rendered":"https:\/\/cm.vastapps.dev\/tcia-collection\/rhuh-gbm\/"},"modified":"2023-09-13T12:05:22","modified_gmt":"2023-09-13T12:05:22","slug":"rhuh-gbm","status":"publish","type":"tcia_collection","link":"https:\/\/cm.vastapps.dev\/tcia-collection\/rhuh-gbm\/","title":{"rendered":"RHUH-GBM"},"featured_media":8521,"template":"","citation-tax":[],"cancer_types":["Astrocytoma"],"citations":[4723,4724,2925],"collection_doi":"10.7937\/4545-c905","collection_download_info":"Some data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\">help@cancerimagingarchive.net<\/a> before accessing the data.\n\nClick the Versions tab for more info about data releases.","collection_downloads":[5331,5332,5333],"full_export":"<div class=\"sectionColumnWrapper\"><div class=\"sectionMacro\"><div class=\"sectionMacroRow\"><div class=\"columnMacro\" style=\"width:70%;min-width:70%;max-width:70%;\"><h1 style=\"margin-top: 30.0px;color: rgb(23,43,77);\" id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Summary\">Summary<\/h1>This data collection consists of multiparametric MRI scans of 40 adult patients with histopathologically confirmed WHO grade 4 astrocytoma, who underwent surgery at the R\u00edo Hortega University Hospital in Valladolid, Spain, between January 2018 and December 2022. The dataset encompasses 600 MRI series, covering three time points: preoperative, early post-operative (less than 72 hours after surgery), and the follow-up scan, at which recurrence is diagnosed. Patients included in the sample underwent gross total resection (GTR) or near total resection (NTR), defined as having no residual tumor enhancement and an extent of resection of more than 95% of the initial enhancing volume, respectively. The modified Response Assessment in Neuro-Oncology criteria (RANO) were used to define tumor progression.<\/p><p>The dataset contains T1-weighted (T1w), T2-weighted (T2w), Fluid Attenuated Inversion Recovery (FLAIR), T1w contrast-enhanced (T1ce) sequences, and diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps. It also includes clinical and demographic data, IDH status, treatment information, and volumetric assessment of the extent of the resection. Moreover, the dataset comprises expert-validated segmentations of tumor subregions (e.g., enhancing tumor, necrosis, peritumoral region), generated through computer-aided methods from preoperative, postoperative, and follow-up scans.<\/p><p>This dataset is unique in its inclusion of patients who underwent extensive resection of &gt; 95% of the enhancing tumor. It also stands out from other publicly available datasets by providing early postoperative studies and segmentations, filling the gap in preoperative-focused datasets. By making these data publicly available, the scientific community can analyze recurrence patterns in patients who underwent total or near-total resection and develop new registration and segmentation algorithms focused on post-surgical and follow-up studies.<\/div><div class=\"columnMacro\" style=\"width:30%;min-width:30%;max-width:30%;\"><p><span class=\"confluence-embedded-file-wrapper\"><img class=\"confluence-embedded-image\" draggable=\"false\" src=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/embedded-page\/Public\/The%20R%C3%ADo%20Hortega%20University%20Hospital%20Glioblastoma%20dataset:%20a%20comprehensive%20collection%20of%20preoperative,%20early%20postoperative%20and%20recurrence%20MRI%20scans%20(RHUH-GBM)\/tcia-rhuh-gbm.jpg?api=v2\"><\/span><\/p><\/div><\/div><\/div><\/div><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Acknowledgements\"><span>Acknowledgements<\/span><\/h3><ul><li><p>This work was partially funded by a grant awarded by the &quot;<strong>Instituto Carlos III, Proyectos I-D-i, Acci\u00f3n Estrat\u00e9gica en Salud 2022<\/strong>&quot; under the project titled &quot;<em>Prediction of tumor recurrence in glioblastomas using magnetic resonance imaging, machine learning, and transcriptomic analysis: A supratotal resection guided by artificial intelligence<\/em>,&quot; reference PI22\/01680.<br\/><br\/><\/p><\/li><\/ul><div class=\"tab-style-builtin\"><div class=\"localtabs-macro\"><div class=\"aui-tabs horizontal-tabs\" role=\"application\" data-aui-responsive=\"true\"><ul class=\"tabs-menu\"><li class=\"menu-item bv-localtab  active-tab \"><a href=\"#1457552349ba0f6d7166845d88ea4d96f32f0c097\"><strong>Data Access<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575523498a69c5e18ad4bc6830e870bde7ad1e6\"><strong>Detailed Description<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#145755234fe28d6f997f64317a780ac52342f7cd0\"><strong>Citations &amp; Data Usage Policy<\/strong><\/a> <\/li><li class=\"menu-item bv-localtab \"><a href=\"#14575523474ca2fa474884476a4946bc25b29b0ed\"><strong>Versions<\/strong><\/a> <\/li><\/ul><div class=\"tabs-pane  active-pane \" id=\"1457552349ba0f6d7166845d88ea4d96f32f0c097\" active=\"true\" name=\"Data Access\" ><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-DataAccess\">Data Access<\/h3><p>\nSome data in this collection contains images that could potentially be used to reconstruct a human face.  To safeguard the privacy of participants, users must sign and submit a <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted License Agreement<\/a> to <a href=\"mailto:help@cancerimagingarchive.net\" class=\"external-link\" rel=\"nofollow\">help@cancerimagingarchive.net<\/a> before accessing the data.<\/p><div class=\"table-wrap\"><table class=\"wrapped relative-table confluenceTable\" style=\"width: 84.0354%;\"><colgroup><col style=\"width: 47.9418%;\"\/><col style=\"width: 30.2821%;\"\/><col style=\"width: 21.7209%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Images\u00a0 (DICOM, 16 GB)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/145755234\/RHUH-GBM_v1_20230606.tcia\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?MinNumberOfStudiesCriteria=1&amp;CollectionCriteria=RHUH-GBM\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><br\/><\/p><p><span style=\"color: rgb(33,37,41);text-decoration: none;\">(Download requires <\/span><a href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" style=\"text-decoration: none;text-align: left;\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/><\/p><p>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><span style=\"color: rgb(33,37,41);\">Brain-extracted Images, Segmentations (NIfTI, 2.9 GB) <\/span><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/370?passcode=0fa12ea901d90e410b13ee46f9bc3c315fa66aa4\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><span style=\"color: rgb(33,37,41);\">(Download and apply the\u00a0<\/span><a href=\"https:\/\/www.ibm.com\/aspera\/connect\/\" style=\"text-decoration: none;text-align: left;\" class=\"external-link\" rel=\"nofollow\">IBM-Aspera-Connect plugin\u00a0<\/a><span style=\"color: rgb(33,37,41);\">to your browser to retrieve this faspex package)\u00a0<\/span><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Clinical data (CSV)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/145755234\/clinical_data_TCIA_RHUH-GBM.csv?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><p>Click the Versions tab for more info about data releases.<\/p><h3 style=\"text-align: left;\" id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-AdditionalResourcesforthisDataset\">Additional Resources for this Dataset<\/h3><p>The following external resources have been made available by the data submitters.\u00a0 These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.<\/p><ul><li>The source code used for image preprocessing in this collection can be found at <a href=\"https:\/\/github.com\/smcch\/RHUH-GBM-dataset-MRI-preprocessing\" class=\"external-link\" rel=\"nofollow\">https:\/\/github.com\/smcch\/RHUH-GBM-dataset-MRI-preprocessing<\/a><\/li><\/ul><\/div><div class=\"tabs-pane \" id=\"14575523498a69c5e18ad4bc6830e870bde7ad1e6\" name=\"Detailed Description\" ><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-DetailedDescription\">Detailed Description<\/h3><div class=\"table-wrap\"><table class=\"wrapped confluenceTable\"><colgroup><col\/><col\/><\/colgroup><tbody><tr><th class=\"confluenceTh\"><p>Image Statistics<\/p><\/th><th style=\"text-align: center;\" class=\"confluenceTh\">Radiology Image Statistics<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Modalities<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>MR<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Patients<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>40<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Studies<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>120<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Series<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>600<\/p><\/td><\/tr><tr><td class=\"confluenceTd\"><p>Number of Images<\/p><\/td><td style=\"text-align: center;\" class=\"confluenceTd\"><p>37,425 (DICOM) + 720 (NIfTI)<\/p><\/td><\/tr><tr><td class=\"confluenceTd\">Images Size (GB)<\/td><td style=\"text-align: center;\" class=\"confluenceTd\">16 GB (DICOM) + 2.9 GB (NIfTI)<\/td><\/tr><\/tbody><\/table><\/div><p><br\/><\/p><h4 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Theinclusioncriteriawere:\">The inclusion criteria were:<\/h4><p>Primary newly diagnosed WHO grade 4 astrocytoma adult patients (age over 18 years) who underwent surgery. Gross total resections (GTR) and Near Total Resection (NTR) were defined as no residual tumor enhancement and an extent of resection of more than 95% of the initial enhancing volume, respectively. Patients were treated with systemic temozolomide according to the Stupp protocol. Tumor progression was defined according to the modified Response assessment in neuro-oncology criteria (RANO). All the patients in our collection had primary glioblastomas. They were all newly diagnosed, with the exception of two patients who had undergone previous surgery and chemo\/radiotherapy.<\/p><h4 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Theexclusioncriteriawere:\">The exclusion criteria were:<\/h4><p>Other histopathological diagnoses, patients in which it was impossible to establish the diagnosis of progression vs. pseudo-progression, missing MRI sequences, and poor-quality MRI scans due to the presence of artifacts.<\/p><h4 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Thedatasetincludesclinicalandpathologicalinformation:\"><span style=\"color: rgb(33,37,41);\">The dataset includes clinical and pathological information: <\/span><\/h4><p><span style=\"color: rgb(33,37,41);\">Age, Sex, preoperative and postoperative Karnofsky performance score, Overall survival, Progression-free survival, percentage of the extent of resection of enhancing tumor, systemic therapy received, details of RT received (dose, technique, number of fractions, isodose), IDH status, ATRX mutation, and Ki-67 index, size of enhancing tumor recurrence.<\/span><\/p><p><span style=\"color: rgb(33,37,41);\"><strong>Note:\u00a0<\/strong> in the Clinical data file, In this dataset, some patients were still alive at the end of the data collection period, and their survival times are not yet known. These patients are considered right-censored = yes. In survival analysis, 'right censoring' occurs when the event of interest has not occurred for some study participants by the end of the study period or by the time the data was collected. This means that the survival time of censored participants is not fully observed or known.\u00a0<\/span><\/p><p><span style=\"color: rgb(33,37,41);\">The dataset includes the segmentations of the enhancing tumor, necrosis, and peritumoral region from the pre-postoperative and follow-up studies that experts have manually corrected. The dataset represents a sample of unique characteristics by including patients with an extent of resection of &gt; 95 % of the enhancing tumor.<span>\u00a0<\/span><\/span><\/p><p><br\/><\/p><h4 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-MRIacquisitionprotocol:\"><span style=\"color: rgb(33,37,41);\">MRI acquisition protocol: <\/span><\/h4><p><span style=\"color: rgb(33,37,41);\">The dataset includes T1-weighted (T1w), T2-weighted (T2w), FLAIR (Fluid attenuated inversion recovery), T1w contrast-enhanced (T1ce) sequences, and diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps from 3 scanners at 2 centers. Please see the manuscript, Supplementary Table 1: MRI acquisition parameters, for detail.<\/span><\/p><p><br\/><\/p><h4 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-MRIscansunderwentpreprocessingusingaspecificpipeline.\">MRI scans underwent preprocessing using a specific pipeline.<\/h4><ul><li>This process involved converting DICOM to NiFTI using the dicom2niix tool (<a href=\"https:\/\/github.com\/rordenlab\/dcm2niix\/releases\/tag\/v1.0.20220720\" class=\"external-link\" rel=\"nofollow\">https:\/\/github.com\/rordenlab\/dcm2niix\/releases\/tag\/v1.0.20220720<\/a>),<\/li><li>registering T1ce scans for each subject to the SRI24 anatomical atlas space using FLIRT (FMRIB\u2019s Linear Image Registration Tool) (<a href=\"https:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki\/FSL\" class=\"external-link\" rel=\"nofollow\">https:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki\/FSL<\/a>),<\/li><li>coregistering T1w, T2w, FLAIR scans, and ADC maps to the transformed T1ce scan,<\/li><li>extracting the brain from all co-registered scans with Synthstrip (<a href=\"https:\/\/surfer.nmr.mgh.harvard.edu\/docs\/synthstrip\/\" class=\"external-link\" rel=\"nofollow\">https:\/\/surfer.nmr.mgh.harvard.edu\/docs\/synthstrip\/<\/a>), and<\/li><li>normalizing intensity using the normalization tools included in the Cancer Imaging Phenomics Toolkit (CaPTk) (<a href=\"https:\/\/www.nitrc.org\/projects\/captk\/\" class=\"external-link\" rel=\"nofollow\">https:\/\/www.nitrc.org\/projects\/captk\/<\/a>).\u00a0<\/li><li>Computer-assisted segmentations were created using Deep-Medic (<a href=\"https:\/\/github.com\/deepmedic\/deepmedic\" class=\"external-link\" rel=\"nofollow\">https:\/\/github.com\/deepmedic\/deepmedic<\/a>) from the preprocessed images at each time point, resulting in three labels: 1) <strong>necrosis<\/strong>, 2) <strong>peritumoral signal alteration<\/strong> (including edema and non-enhancing tumor), and 3) <strong>enhancing tumor<\/strong>. Two expert neurosurgeons reviewed and manually corrected all segmentations.<\/li><\/ul><p><br\/><\/p><p><br\/><\/p><\/div><div class=\"tabs-pane \" id=\"145755234fe28d6f997f64317a780ac52342f7cd0\" name=\"Citations BITVOODOO_ANDamp; Data Usage Policy\" ><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-Citations&amp;DataUsagePolicy\">Citations &amp; Data Usage Policy<\/h3><p>\n<p>\nUsers must abide by the <a href=\"https:\/\/wiki.cancerimagingarchive.net\/x\/c4hF\" class=\"external-link\" rel=\"nofollow\">TCIA Data Usage Policy and Restrictions<\/a>. Attribution should include references to the following citations:\n<\/p><\/p><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Data Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span>Cepeda, <\/span><span style=\"letter-spacing: 0.0px;\">S.,\u00a0<\/span><span>Garc\u00eda-Garc\u00eda, <\/span><span style=\"letter-spacing: 0.0px;\">S.,\u00a0<\/span><span>Arrese, <\/span><span style=\"letter-spacing: 0.0px;\">I.,\u00a0<\/span><span>Herrero, <\/span><span style=\"letter-spacing: 0.0px;\">F.,\u00a0<\/span><span>Escudero, <\/span><span style=\"letter-spacing: 0.0px;\">T.,\u00a0<\/span><span>Zamora, <\/span><span style=\"letter-spacing: 0.0px;\">T.,\u00a0 &amp; <\/span><span>Sarabia,\u00a0<\/span><span style=\"letter-spacing: 0.0px;\">R. (2023) <strong>The R\u00edo Hortega University Hospital Glioblastoma dataset: a comprehensive collection of preoperative, early postoperative and recurrence MRI scans (RHUH-GBM)<\/strong> [Dataset]. The Cancer Imaging Archive. <span class=\"nolink\"><a href=\"https:\/\/doi.org\/10.7937\/4545-c905\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.7937\/4545-c905<\/a>\u00a0 \u00a0 \u00a0<br\/><\/span><\/span><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">Publication Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p>Cepeda, S., Garcia-Garcia, S., Arrese, I., Herrero, F., Escudero, T., Zamora, T., &amp; Sarabia, R. (2023). <strong>The Rio Hortega University Hospital Glioblastoma dataset: a comprehensive collection of preoperative, early postoperative and recurrence MRI scans (RHUH-GBM) (Version 2)<\/strong>. arXiv. <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2305.00005\" class=\"external-link\" rel=\"nofollow\">https:\/\/doi.org\/10.48550\/arXiv.2305.00005<\/a><\/p><\/div><\/div><div class=\"confluence-information-macro confluence-information-macro-information\"><p class=\"title\">TCIA Citation<\/p><span class=\"aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon\"><\/span><div class=\"confluence-information-macro-body\"><p><span style=\"color: rgb(0,0,0);text-decoration: none;\">Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., &amp; Prior, F. (2013). <strong>The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository<\/strong>. In Journal of Digital Imaging (Vol. 26, Issue 6, pp. 1045\u20131057). Springer Science and Business Media LLC.<\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"> <\/span><span style=\"color: rgb(102,102,102);text-decoration: none;\"><a title=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" href=\"https:\/\/doi.org\/10.1007\/s10278-013-9622-7\" class=\"external-link\" rel=\"nofollow\"><span>https:\/\/doi.org\/10.1007\/s10278-013-9622-7<\/span><\/a><\/span><\/p><\/div><\/div><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-OtherPublicationsUsingThisData\">Other Publications Using This Data<\/h3><p><span>TCIA maintains\u00a0<\/span><a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\" class=\"external-link\" rel=\"nofollow\">a list of publications<\/a><span> which leverage TCIA data. <\/span> If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\" class=\"external-link\" rel=\"nofollow\">contact TCIA's Helpdesk<\/a>.<\/p><\/div><div class=\"tabs-pane \" id=\"14575523474ca2fa474884476a4946bc25b29b0ed\" name=\"Versions\" ><h3 id=\"TheR\u00edoHortegaUniversityHospitalGlioblastomadataset:acomprehensivecollectionofpreoperative,earlypostoperativeandrecurrenceMRIscans(RHUHGBM)-VersionX(Current):Updated2023\/06\/09\">Version X (Current): Updated 2023\/06\/09<\/h3><div class=\"table-wrap\"><table class=\"relative-table wrapped confluenceTable\" style=\"width: 84.0354%;\"><colgroup><col style=\"width: 47.9418%;\"\/><col style=\"width: 30.2821%;\"\/><col style=\"width: 21.7209%;\"\/><\/colgroup><tbody><tr><th class=\"confluenceTh\">Data Type<\/th><th class=\"confluenceTh\">Download all or Query\/Filter<\/th><th class=\"confluenceTh\">License<\/th><\/tr><tr><td class=\"confluenceTd\"><p>Images\u00a0 (DICOM, 16 GB)<\/p><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/145755234\/RHUH-GBM_v1_20230606.tcia\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/nbia.cancerimagingarchive.net\/nbia-search\/?MinNumberOfStudiesCriteria=1&amp;CollectionCriteria=RHUH-GBM\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-search-color\"><i class=\"fa fa-search\" \/> Search<\/button><\/a>\u00a0\n<\/span><br\/><\/p><p><span style=\"color: rgb(33,37,41);text-decoration: none;\">(Download requires <\/span><a style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/wiki.cancerimagingarchive.net\/display\/NBIA\/Downloading+TCIA+Images\" rel=\"nofollow\">NBIA Data Retriever<\/a>)<\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p><br\/><\/p><p>\n<a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/4556915\/TCIA%20Restricted%20License%2020220519.pdf?version=1&amp;modificationDate=1652964581655&amp;api=v2\" class=\"external-link\" rel=\"nofollow\">TCIA Restricted<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\"><span style=\"color: rgb(33,37,41);\">Brain-extracted Images, Segmentations (NIfTI, 2.9 GB) <\/span><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/faspex.cancerimagingarchive.net\/aspera\/faspex\/external_deliveries\/370?passcode=0fa12ea901d90e410b13ee46f9bc3c315fa66aa4\" class=\"external-link\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><span style=\"color: rgb(33,37,41);\">(Download and apply the\u00a0<\/span><a rel=\"nofollow\" class=\"external-link\" style=\"text-decoration: none;text-align: left;\" href=\"https:\/\/www.ibm.com\/aspera\/connect\/\">IBM-Aspera-Connect plugin\u00a0<\/a><span style=\"color: rgb(33,37,41);\">to your browser to retrieve this faspex package)\u00a0<\/span><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><tr><td class=\"confluenceTd\">Clinical data (CSV)<\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n\n<span class=\"confluence-embedded-file-wrapper confluence-embedded-manual-size\">\n   <a href=\"https:\/\/wiki.cancerimagingarchive.net\/download\/attachments\/145755234\/clinical_data_TCIA_RHUH-GBM.csv?api=v2\" rel=\"nofollow\"><button class=\"tcia-btn tcia-download-color\"><i class=\"fa fa-cloud-download\" \/> Download<\/button><\/a>\u00a0\n<\/span><\/p><\/div><\/td><td class=\"confluenceTd\"><div class=\"content-wrapper\"><p>\n<a href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\" class=\"external-link\" rel=\"nofollow\">CC BY 4.0<\/a><\/p><\/div><\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><\/div><p><br\/><\/p><p><br\/><\/p>","versions":false,"additional_resources":"The following external resources have been made available by the data submitters.\u00a0 These are not hosted or supported by TCIA, but may be useful to researchers utilizing this collection.\n<ul><li>The source code used for image preprocessing in this collection can be found at <a href=\"https:\/\/github.com\/smcch\/RHUH-GBM-dataset-MRI-preprocessing\">https:\/\/github.com\/smcch\/RHUH-GBM-dataset-MRI-preprocessing<\/a><\/li><\/ul>","cancer_locations":["Head"],"collection_page_accessibility":"Public","publications_related":"","version_change_log":"","version_change_log_archived":"","analysis_results":"","collection_status":"Complete","publications_using":"TCIA maintains\u00a0<a href=\"https:\/\/www.cancerimagingarchive.net\/publications\/\">a list of publications<\/a> which leverage TCIA data.  If you have a manuscript you'd like to add please <a href=\"http:\/\/www.cancerimagingarchive.net\/support\/\">contact TCIA's Helpdesk<\/a>.","species":["Human"],"collection_title":"The R\u00edo Hortega University Hospital Glioblastoma dataset: a comprehensive collection of preoperative, early postoperative and recurrence MRI scans","detailed_description":"<br\/>\n<h4>The inclusion criteria were:<\/h4>\nPrimary newly diagnosed WHO grade 4 astrocytoma adult patients (age over 18 years) who underwent surgery. Gross total resections (GTR) and Near Total Resection (NTR) were defined as no residual tumor enhancement and an extent of resection of more than 95% of the initial enhancing volume, respectively. Patients were treated with systemic temozolomide according to the Stupp protocol. Tumor progression was defined according to the modified Response assessment in neuro-oncology criteria (RANO). All the patients in our collection had primary glioblastomas. They were all newly diagnosed, with the exception of two patients who had undergone previous surgery and chemo\/radiotherapy.\n<h4>The exclusion criteria were:<\/h4>\nOther histopathological diagnoses, patients in which it was impossible to establish the diagnosis of progression vs. pseudo-progression, missing MRI sequences, and poor-quality MRI scans due to the presence of artifacts.\n<h4>The dataset includes clinical and pathological information: <\/h4>\nAge, Sex, preoperative and postoperative Karnofsky performance score, Overall survival, Progression-free survival, percentage of the extent of resection of enhancing tumor, systemic therapy received, details of RT received (dose, technique, number of fractions, isodose), IDH status, ATRX mutation, and Ki-67 index, size of enhancing tumor recurrence.\n<strong>Note:\u00a0<\/strong> in the Clinical data file, In this dataset, some patients were still alive at the end of the data collection period, and their survival times are not yet known. These patients are considered right-censored = yes. In survival analysis, 'right censoring' occurs when the event of interest has not occurred for some study participants by the end of the study period or by the time the data was collected. This means that the survival time of censored participants is not fully observed or known.\u00a0\nThe dataset includes the segmentations of the enhancing tumor, necrosis, and peritumoral region from the pre-postoperative and follow-up studies that experts have manually corrected. The dataset represents a sample of unique characteristics by including patients with an extent of resection of &gt; 95 % of the enhancing tumor.\u00a0\n<br\/>\n<h4>MRI acquisition protocol: <\/h4>\nThe dataset includes T1-weighted (T1w), T2-weighted (T2w), FLAIR (Fluid attenuated inversion recovery), T1w contrast-enhanced (T1ce) sequences, and diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps from 3 scanners at 2 centers. Please see the manuscript, Supplementary Table 1: MRI acquisition parameters, for detail.\n<br\/>\n<h4>MRI scans underwent preprocessing using a specific pipeline.<\/h4>\n<ul><li>This process involved converting DICOM to NiFTI using the dicom2niix tool (<a href=\"https:\/\/github.com\/rordenlab\/dcm2niix\/releases\/tag\/v1.0.20220720\">https:\/\/github.com\/rordenlab\/dcm2niix\/releases\/tag\/v1.0.20220720<\/a>),<\/li><li>registering T1ce scans for each subject to the SRI24 anatomical atlas space using FLIRT (FMRIB\u2019s Linear Image Registration Tool) (<a href=\"https:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki\/FSL\">https:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki\/FSL<\/a>),<\/li><li>coregistering T1w, T2w, FLAIR scans, and ADC maps to the transformed T1ce scan,<\/li><li>extracting the brain from all co-registered scans with Synthstrip (<a href=\"https:\/\/surfer.nmr.mgh.harvard.edu\/docs\/synthstrip\/\">https:\/\/surfer.nmr.mgh.harvard.edu\/docs\/synthstrip\/<\/a>), and<\/li><li>normalizing intensity using the normalization tools included in the Cancer Imaging Phenomics Toolkit (CaPTk) (<a href=\"https:\/\/www.nitrc.org\/projects\/captk\/\">https:\/\/www.nitrc.org\/projects\/captk\/<\/a>).\u00a0<\/li><li>Computer-assisted segmentations were created using Deep-Medic (<a href=\"https:\/\/github.com\/deepmedic\/deepmedic\">https:\/\/github.com\/deepmedic\/deepmedic<\/a>) from the preprocessed images at each time point, resulting in three labels: 1) <strong>necrosis<\/strong>, 2) <strong>peritumoral signal alteration<\/strong> (including edema and non-enhancing tumor), and 3) <strong>enhancing tumor<\/strong>. Two expert neurosurgeons reviewed and manually corrected all segmentations.<\/li><\/ul>\n<br\/>\n<br\/>","related_analysis_results":false,"subjects":"40","collection_short_title":"RHUH-GBM","data_types":["MR"],"date_updated":"2023-09-13","collection_browse_title":"","supporting_data":["Clinical","Image Analyses"],"collection_featured_image":{"ID":"8521","post_author":"6","post_date":"2023-09-13 04:13:54","post_date_gmt":"2023-09-13 04:13:54","post_content":"","post_title":"tcia-rhuh-gbm","post_excerpt":"","post_status":"inherit","comment_status":"open","ping_status":"closed","post_password":"","post_name":"tcia-rhuh-gbm","to_ping":"","pinged":"","post_modified":"2023-09-13 12:05:22","post_modified_gmt":"2023-09-13 12:05:22","post_content_filtered":"","post_parent":"5733","guid":"https:\/\/cm.vastapps.dev\/wp-content\/uploads\/tcia-rhuh-gbm.jpg","menu_order":"0","post_type":"attachment","post_mime_type":"image\/jpeg","comment_count":"0","pod_item_id":"8521"},"collection_summary":"<h3>Summary<\/h3>This data collection consists of multiparametric MRI scans of 40 adult patients with histopathologically confirmed WHO grade 4 astrocytoma, who underwent surgery at the R\u00edo Hortega University Hospital in Valladolid, Spain, between January 2018 and December 2022. The dataset encompasses 600 MRI series, covering three time points: preoperative, early post-operative (less than 72 hours after surgery), and the follow-up scan, at which recurrence is diagnosed. Patients included in the sample underwent gross total resection (GTR) or near total resection (NTR), defined as having no residual tumor enhancement and an extent of resection of more than 95% of the initial enhancing volume, respectively. The modified Response Assessment in Neuro-Oncology criteria (RANO) were used to define tumor progression.<p>The dataset contains T1-weighted (T1w), T2-weighted (T2w), Fluid Attenuated Inversion Recovery (FLAIR), T1w contrast-enhanced (T1ce) sequences, and diffusion-weighted imaging-derived apparent diffusion coefficient (ADC) maps. It also includes clinical and demographic data, IDH status, treatment information, and volumetric assessment of the extent of the resection. Moreover, the dataset comprises expert-validated segmentations of tumor subregions (e.g., enhancing tumor, necrosis, peritumoral region), generated through computer-aided methods from preoperative, postoperative, and follow-up scans.<\/p><p>This dataset is unique in its inclusion of patients who underwent extensive resection of &gt; 95% of the enhancing tumor. It also stands out from other publicly available datasets by providing early postoperative studies and segmentations, filling the gap in preoperative-focused datasets. By making these data publicly available, the scientific community can analyze recurrence patterns in patients who underwent total or near-total resection and develop new registration and segmentation algorithms focused on post-surgical and follow-up studies.<\/p><div><p><\/p><\/div>","collection_acknowledgements":"<ul><li><p>This work was partially funded by a grant awarded by the \"<strong>Instituto Carlos III, Proyectos I-D-i, Acci\u00f3n Estrat\u00e9gica en Salud 2022<\/strong>\" under the project titled \"<em>Prediction of tumor recurrence in glioblastomas using magnetic resonance imaging, machine learning, and transcriptomic analysis: A supratotal resection guided by artificial intelligence<\/em>,\" reference PI22\/01680.<br\/><br\/><\/p><\/li><\/ul>","collection_funding":"","hide_from_browse_table":[],"_links":{"self":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections\/5733"}],"collection":[{"href":"https:\/\/cm.vastapps.dev\/api\/v1\/collections"}],"about":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/types\/tcia_collection"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media\/8521"}],"wp:attachment":[{"href":"https:\/\/cm.vastapps.dev\/api\/wp\/v2\/media?parent=5733"}],"wp:term":[{"taxonomy":"tcia_citation_tax","embeddable":true,"href":"https:\/\/cm.vastapps.dev\/api\/v1\/citation-tax?post=5733"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}